bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbed soliton excitations of Rao-dust Alfvén waves in magnetized dusty plasmas
Authors: Kavitha L. , Lavanya C. , Senthil Kumar V. , Gopi D. , Pasqua A.
Published: April 2016

We investigate the propagation dynamics of the perturbed soliton excitations in a three component fully ionized dusty magnetoplasma consisting of electrons, ions, and heavy charged dust particulates. We derive the governing equation of motion for the two dimensional Rao-dust magnetohydrodynamic (R-D-MHD) wave by employing the inertialess electron equation of motion, inertial ion equation of motion, the continuity equations in a plasma with immobile charged dust grains, together with the Maxwell's equations, by assuming quasi neutrality and neglecting the displacement current in Ampere's law. Furthermore, we assume the massive dust particles are practically immobile since we are interested in timescales much shorter than the dusty plasma period, thereby neglecting any damping of the modes due to the grain charge fluctuations. We invoke the reductive perturbation method to represent the governing dynamics by a perturbed cubic nonlinear Schrödinger (pCNLS) equation. We solve the pCNLS, along the lines of Kodama-Ablowitz multiple scale nonlinear perturbation technique and explored the R-D-MHD waves as solitary wave excitations in a magnetized dusty plasma. Since Alfvén waves play an important role in energy transport in driving field-aligned currents, particle acceleration and heating, solar flares, and the solar wind, this representation of R-D-MHD waves as soliton excitations may have extensive applications to study the lower part of the earth's ionosphere.
Current profile redistribution driven by neutral beam injection in a reversed-field pinch
Authors: Parke E. , Anderson J. K. , Brower D. L. , Den Hartog D. J. , Ding W. X. , Johnson C. A. , Lin L.
Published: April 2016

Neutral beam injection in reversed-field pinch (RFP) plasmas on the Madison Symmetric Torus [Dexter et al., Fusion Sci. Technol. 19, 131 (1991)] drives current redistribution with increased on-axis current density but negligible net current drive. Internal fluctuations correlated with tearing modes are observed on multiple diagnostics; the behavior of tearing mode correlated structures is consistent with flattening of the safety factor profile. The first application of a parametrized model for island flattening to temperature fluctuations in an RFP allows inferrence of rational surface locations for multiple tearing modes. The m = 1, n = 6 mode is observed to shift inward by 1.1 ± 0.6 cm with neutral beam injection. Tearing mode rational surface measurements provide a strong constraint for equilibrium reconstruction, with an estimated reduction of q0 by 5% and an increase in on-axis current density of 8% ± 5%. The inferred on-axis current drive is consistent with estimates of fast ion density using TRANSP [Goldston et al., J. Comput. Phys. 43, 61 (1981)].
Linear and weakly nonlinear global instability of a fluid flow through a collapsible channel
Authors: Amaouche Mustapha , Di Labbio Giuseppe
Published: April 2016

Interactions between an internal flow and wall deformation occur in many biological systems. Such interactions can involve a complex and rich dynamical behavior and a number of peculiarities which depend on the flow parameter range. The aim of this paper is to present a variant (obtained via a weighted residual approach) of the averaged one-dimensional model derived by Stewart et al. [“Local and global instabilities of flow in a flexible-walled channel,” Eur. J. Mech. B/Fluids 28, 541–557 (2009)]. The asymptotic expansions for small Reynolds numbers of these two models, compared to the exact solution obtained from the lubrication approach, reveal some quantitative difference, even at higher Reynolds numbers. Qualitatively, the two models give similar results at least at a linear level. It is shown that for relatively low membrane tension (T), there are distinct regions in the (T, R) parameter space where steady bifurcating flows may occur. These flows can also be observed at vanishingly small Reynolds numbers combined with relatively high membrane tension. At sufficiently high T and R, the bifurcating flow is rather time periodic. A weakly nonlinear analysis is then performed in both cases leading to the derivation of evolution equations for the amplitudes of the bifurcating flows. The amplitude equations show that the saddle node bifurcation has a transcritical character while the Hopf bifurcation is either subcritical or supercritical, depending both on the mode number and membrane tension.
Restraining non-specific adsorption of protein using Parylene C-caulked polydimethylsiloxane
Authors: Liu Yaoping , Zhang Lingqian , Wu Wengang , Zhao Meiping , Wang Wei
Published: April 2016

Non-specific adsorption (NSA) of proteins on surface is a critical issue in polydimethylsiloxane (PDMS)-based microfluidics, which may either considerably decrease the efficiency of a continuous flow reaction or cause a large background noise in a heterogeneous sensing. This work introduced a new method to restrain NSA of protein by caulking PDMS with Parylene C, i.e., forming a Parylene C-caulked PDMS (pcPDMS) surface. The caulking depth of Parylene C inside PDMS matrix was characterized by laser scanning confocal microscopy based on a detectable autofluorescence intensity difference between Parylene C and PDMS after being annealed at 270 °C for 2 h in nitrogen. NSA of bovine serum albumin (BSA) on the inner surfaces of PDMS and pcPDMS microchannels was experimentally compared. The results indicated that the adsorbed BSA on the pcPDMS surface were 35.2% of that on the pristine PDMS surface after the BSA solution flowing through the microchannels at a flow rate of 2000 nL/min, a typical scenario of the continuous flow reaction. In a case mimicking the heterogeneous sensing, after a 60 min washing of phosphate buffered saline flow on a pre-saturated BSA adsorbed surface, the residual BSA on the pcPDMS surface was only 4.5% of that on the pristine PDMS surface. Adsorption/desorption coefficients of BSA on the PDMS and the pcPDMS surfaces were extracted from the experimental results based on the first-order Langmuir model, which indicated that the pcPDMS has a lower adsorption coefficient (Ka) and a higher desorption coefficient (Kd), compared to those of the pristine PDMS. A preliminary experiment also indicated that Taq polymerase kept 93.0% activity after flowing through a pcPDMS microchannel, while only 28.9% activity was left after passing a pristine PDMS microchannel under the same operation condition.
In-situ gallium-doping for forming p+ germanium-tin and application in germanium-tin p-i-n photodetector
Authors: Wang Wei , Vajandar Saumitra , Lim Sin Leng , Dong Yuan , D'Costa Vijay Richard , Osipowicz Thomas , Tok Eng Soon , Yeo Yee-Chia
Published: April 2016

The in-situ Ga doping technique was used to form heavily p-type doped germanium-tin (Ge1−xSnx) layers by molecular beam epitaxy, avoiding issues such as Sn precipitation and surface segregation at high annealing temperatures that are associated with the alternative implant and anneal approach. In this way, an electrically active Ga concentration of up to ∼3.2 × 1020 cm−3 can be realized for Ge1−xSnx. The impacts of varying the Ga concentration on the crystalline quality and the mobility of p-type Ge1−xSnx were investigated. High crystalline quality Ge0.915Sn0.085 can be realized with an active Ga concentration of up to ∼1.2 × 1020 cm−3. More than 98% of the Sn atoms are located on substitutional lattice sites, although the substitutionality of Sn in p-type Ge1−xSnx decreases with an increasing Ga concentration. When the Ga concentration introduced is higher than 3.2 × 1020 cm−3, excess Ga atoms cannot be substitutionally incorporated, and segregation of Ga and Sn towards the surface during growth is observed. The in-situ Ga-doped Ge0.915Sn0.085 epitaxy was integrated in a Ge0.915Sn0.085-on-Si p-i-n (PIN) photodiode fabrication process, and well-behaved Ge0.915Sn0.085/Si PIN junction characteristics were obtained. A large forward-bias current to reverse bias current ratio of 6 × 104 and a low reverse current (dark current) of 0.24 μA were achieved at Vbias = −1 V.
Integrated fusion simulation with self-consistent core-pedestal coupling
Authors: Meneghini O. , Snyder P. B. , Smith S. P. , Candy J. , Staebler G. M. , Belli E. A. , Lao L. L. , Park J. M. , Green D. L. , Elwasif W. , Grierson B. A. , Holland C.
Published: April 2016

Accurate prediction of fusion performance in present and future tokamaks requires taking into account the strong interplay between core transport, pedestal structure, current profile, and plasma equilibrium. An integrated modeling workflow capable of calculating the steady-state self-consistent solution to this strongly coupled problem has been developed. The workflow leverages state-of-the-art components for collisional and turbulent core transport, equilibrium and pedestal stability. Testing against a DIII-D discharge shows that the workflow is capable of robustly predicting the kinetic profiles (electron and ion temperature and electron density) from the axis to the separatrix in a good agreement with the experiments. An example application is presented, showing self-consistent optimization for the fusion performance of the 15 MA D-T ITER baseline scenario as functions of the pedestal density and ion effective charge Zeff.
Band alignment of HfO2/AlN heterojunction investigated by X-ray photoelectron spectroscopy
Authors: Ye Gang , Wang Hong , Ji Rong
Published: April 2016

The band alignment between AlN and Atomic-Layer-Deposited (ALD) HfO2 was determined by X-ray photoelectron spectroscopy (XPS). The shift of Al 2p core-levels to lower binding energies with the decrease of take-off angles θ indicated upward band bending occurred at the AlN surface. Based on the angle-resolved XPS measurements combined with numerical calculations, valence band discontinuity ΔEV of 0.4 ± 0.2 eV at HfO2/AlN interface was determined by taking AlN surface band bending into account. By taking the band gap of HfO2 and AlN as 5.8 eV and 6.2 eV, respectively, a type-II band line-up was found between HfO2 and AlN.
Replacing synthetic N with clovers or alfalfa in bermudagrass pastures. 2. Herbage nutritive value for growing beef steers
Authors: Beck P. , Hess T. , Hubbell D. , Gadberry M. S. , Jennings J. , Sims M.
Published: April 2016

The objective of this study was to evaluate the effects of including alfalfa (ALF, Medicago sativa L.) or a combination of white (Trifolium repens L.) and red (Trifolium pretense L.) clovers (CLVR) inter-seeded into bermudagrass (Cynodon dactylon L. Pers.) on herbage nutritive value compared with monocultures of bermudagrass fertilised with 0 (0N), 56 (56N), or 112 (112N) kg nitrogen (N)/ha over four grazing seasons. At the end of the fourth year (during the winter), legume plants in ALF and CLVR were killed and the carryover N benefit on bermudagrass nutritive value was evaluated during the fifth year. Pre-grazing herbage of all pastures exceeded the dietary recommendations for growing steers to maintain 0.9 kg/day average daily liveweight gain for crude protein and total digestible nutrients, 118 and 617 g kg/DM, respectively. Post-grazing herbage in ALF was below 600 g/kg total digestible nutrients at all times during the grazing season, post-grazing total digestible nutrients of CLVR was below 600 g/kg during the late summer and autumn. Post-grazing herbage of monoculture bermudagrass pastures fell below 600 g/kg in the middle of summer regardless of N fertilisation. Carryover N benefits of legumes were similar to 112N in the early summer, but were not different than 0N and 56N during the late summer and autumn. Replacing applications of synthetic N in bermudagrass swards with inter-seeding of either clovers or alfalfa produce herbage with equivalent nutritive value to heavily N fertilised monocultures of bermudagrass during the early summer, and similar to moderately N fertilised in the late summer and autumn. The inclusion of legumes in bermudagrass swards can reduce the reliance on synthetic N fertilisation with little overall effect on herbage nutritive quality possibly decreasing environmental impacts of grazing production systems.
Mechanical nociceptive threshold testing in Bos indicus bull calves
Authors: Musk Gabrielle C. , Laurence Michael , Collins Teresa , Tuke Jonathan , Hyndman Timothy H.
Published: April 2016

The aim of this prospective, controlled, randomised trial was to develop a technique for mechanical nociceptive threshold testing (NTT) to assess pain in Bos indicus bull calves undergoing surgical castration. Analgesia was provided by 0.5 mg/kg subcutaneous (SC) meloxicam (M) and/or 2 mg/kg of intra-testicular and SC (at the surgery sites) lidocaine (L). Forty-eight Brahman bull calves at 6–8 months of age were divided into six study groups, each with eight animals: no surgery control; surgical castration (C) without analgesia; C and Mpre-op; C and Mpost-op; C, L and Mpost-op; C and L. Mechanical NTT was performed the day before surgery (Day –1) and on Days 1, 2, 6, 10 and 13 after surgery. A handheld manual pneumatic device with a 1-mm (diameter) blunt pin was used to deliver a mechanical stimulus to a maximum of 27 Newtons either side of the most dorsal aspect of the sacrum. The most frequent responses to the mechanical stimulus were lifting or kicking of the leg on the same side as the stimulus (31%) and stepping away from the stimulus (24.9%). Data were analysed with a mixed effect linear model with the nociceptive threshold (NT) as the response variable and day and analgesic treatment as predictors (P < 0.05 was considered significant). For all groups, there was a trend towards decreasing NT over the study period but there were no significant differences between groups. Step down model selection with day, batch and treatment terms revealed a significant effect of day (P < 0.001) and batch (P = 0.007). Mechanical NTT for assessment of pain in Bos indicus bull calves requires further refinement to determine if this is a useful method of pain assessment.
Impact of phytogenic feed additives on growth performance, nutrient digestion and methanogenesis in growing buffaloes
Authors: Samal L. , Chaudhary L. C. , Agarwal N. , Kamra D. N.
Published: April 2016

Twenty growing buffalo calves were fed on a basal diet consisting of wheat straw and concentrate mixture in a randomised block design, to study the effect of feeding phytogenic feed additives on growth performance, nutrient utilisation and methanogenesis. The four groups were viz. control (no additive), Mix-1 (ajwain oil and lemon grass oil in 1 : 1 ratio @ 0.05% of dry matter intake), Mix-2 (garlic and soapnut in 2 : 1 ratio @ 2% of DMI) and Mix-3 (garlic, soapnut, harad and ajwain in 2 : 1 : 1 : 1 ratio @ 1% of DMI). The experimental feeding was continued for a period of 8 months. A metabolism trial was conducted after 130 days of feeding. Methane emission from animals was measured by open-circuit indirect respiration calorimeter. The feed conversion efficiency was higher by 9.5% in Mix-1, 7% in Mix-2 and 10.2% in Mix-3 group than in control. The digestibility of nutrients was similar except crude protein, which was improved (P < 0.05) in treatment groups. All buffalo calves were in positive nitrogen balance. Comparative faecal nitrogen decreased and urinary nitrogen increased in all the supplemented groups compared with in the control group. Methane emission (in terms of L/kg dry matter intake and L/kg digestible dry matter intake) was reduced by 13.3% and 17.8% in Mix-1, 10.9% and 13.5% in Mix-2 and 5.1% and 9.8% in Mix-3 groups as compared with control. When expressed in L/kg organic matter intake and L/kg digestible organic matter intake, methane production was reduced by 13.3% and 16.7% in Mix-1, 10.9% and 12.9% in Mix-2 and 5.1% and 8.4% in Mix-3 groups compared with the control group. These feed additives inhibited methane emission without adversely affecting feed utilisation by the animals. The faecal energy, urinary energy and methane energy losses were not affected (P > 0.05) due to feeding of these additives. Further, long-term feeding experiments should be conducted on a large number of animals to validate these effects before they can be recommended for use at a field level.
Cultural experiences of student and new‐graduate dietitians in the Gomeroi gaaynggal ArtsHealth program: a quality assurance project
Authors: Rae Kym , Bohringer Emma , Ashman Amy , Brown Leanne , Collins Clare
Published: April 2016

Issue addressed

Undergraduate dietetic students are required to demonstrate cultural awareness and culturally respectful communication to meet national competencies, but exposure to practical experiences may be limited. The Gomeroi gaaynggal ArtsHealth Centre was established in 2009 after community consultation with the Indigenous community in Tamworth, New South Wales. The Centre provides a safe and welcoming space where women can create art while discussing health issues with visiting health professionals and students. The present study aimed to evaluate the cultural experiences of student and new‐graduate dietitians visiting an Aboriginal ArtsHealth centre through a quality assurance project.

Methods

Six student and new‐graduate dietitians were invited to provide feedback on their experiences for this report. A generic inductive approach was used for qualitative data analysis.

Results

Key qualitative themes of ‘building rapport’ and ‘developing cultural understanding’ were identified. Four of the participants interviewed felt they gained a deeper understanding of the context around health disparity for Indigenous Australians through their experiences. Key ways to build rapport with community members were identified.

Conclusions

Results suggest that first‐hand experiences working in an Aboriginal ArtsHealth centre are effective in building cultural competency skills for student and new‐graduate dietitians. These experiences could be better supported through improved preparation for the cultural setting, and ongoing monitoring of participant experiences is recommended.

So what?

The authors encourage undergraduate dietetic programs and students to seek out opportunities for further development of cultural awareness through increased practical experiences working with Indigenous communities.
Reorientation of health services: enablers and barriers faced by organisations when increasing health promotion capacity
Authors: McFarlane K. , Judd J. , Devine S. , Watt K.
Published: April 2016

Issue addressed

Primary healthcare settings are important providers of health promotion approaches. However, organisational challenges can affect their capacity to deliver these approaches. This review identified the common enablers and barriers health organisations faced and it aimed to explore the experiences health organisations, in particular Aboriginal organisations, had when increasing their health promotion capacity.

Methods

A systematic search of peer‐reviewed literature was conducted. Articles published between 1990–2014 that focused on a health care‐settings approach and discussed factors that facilitated or hindered an organisation's ability to increase health promotion capacity were included.

Results

Twenty‐five articles met the inclusion criteria. Qualitative (n = 18) and quantitative (n = 7) study designs were included. Only one article described the experiences of an Aboriginal health organisation. Enablers included: management support, skilled staff, provision of external support to the organisation, committed staffing and financial resources, leadership and the availability of external partners to work with. Barriers included: lack of management support, lack of dedicated health promotion staff, staff lacking skills or confidence, competing priorities and a lack of time and resources allocated to health promotion activities.

Conclusions

While the literature highlighted the importance of health promotion work, barriers can limit the delivery of health promotion approaches within primary healthcare organisations. A gap in the literature exists about how Aboriginal health organisations face these challenges.

So what?

Primary healthcare organisations wanting to increase their health promotion capacity can pre‐empt the common barriers and strengthen identified enablers through the shared learnings outlined in this review.
Forest fuels and potential fire behaviour 12 years after variable-retention harvest in lodgepole pine
Authors: Crotteau Justin S. , Keyes Christopher R. , Sutherland Elaine K. , Wright David K. , Egan Joel M.
Published: April 2016

Variable-retention harvesting in lodgepole pine offers an alternative to conventional, even-aged management. This harvesting technique promotes structural complexity and age-class diversity in residual stands and promotes resilience to disturbance. We examined fuel loads and potential fire behaviour 12 years after two modes of variable-retention harvesting (dispersed and aggregated retention patterns) crossed by post-harvest prescribed fire (burned or unburned) in central Montana. Results characterise 12-year post-treatment fuel loads. We found greater fuel load reduction in treated than untreated stands, namely in the 10- and 100-h classes (P = 0.002 and 0.049 respectively). Reductions in 1-h (P < 0.001), 10-h (P = 0.008) and 1000-h (P = 0.014) classes were greater in magnitude for unburned than burned treatments. Fire behaviour modelling incorporated the regenerating seedling cohort into the surface fuel complex. Our analysis indicates greater surface fireline intensity in treated than untreated stands (P < 0.001), and in unburned over burned stands (P = 0.001) in dry, windy weather. Although potential fire behaviour in treated stands is predicted to be more erratic, within-stand structural variability reduces probability of crown fire spread. Overall, results illustrate trade-offs between potential fire attributes that should be acknowledged with variable-retention harvesting.
Agents of Latin
Authors: Qi Lintao
Published: April 2016

Latin has a history of being used in English translations of erotic literary works,
but the process of producing and incorporating the Latin into the English
target texts has so far remained largely unexplored. Based on the
publisher’s archival materials, this paper uncovers the roles of and
relationships between the English translator, Latin translator, publisher,
printer and copyeditor for the use of Latin in Clement Egerton’s 1939 English translation
The Golden Lotus of the classic Chinese novel Jin
Ping Mei. I argue that pre-publication censorship was influenced
by sophisticated hierarchical and horizontal networks of agents. The Latin
passages in The Golden Lotus, which have always been
attributed to Egerton, are revealed by the archives to be the work of an
unknown Latin scholar. The use of Latin in The Golden
Lotus is both reflective of the social context of the 1930s and
representative of the complexity of the agential network in
translation.
From EPIC to EPTIC — Exploring simplification in interpreting and translation from an intermodal
perspective
Authors: Bernardini Silvia , Ferraresi Adriano , Miličević Maja
Published: April 2016

This article introduces EPTIC (the European Parliament Translation and Interpreting Corpus), a new bidirectional
(English<>Italian) corpus of interpreted and translated EU Parliament proceedings. Built as an extension of the
English<>Italian subsection of EPIC (the European Parliament Interpreting Corpus), EPTIC is an intermodal
corpus featuring the pseudo-parallel outputs of interpreting and translation processes, aligned to each other and to the
corresponding source texts (speeches by MEPs and their written up versions). As a first attempt at unearthing the potential of
EPTIC, we investigate lexical simplification replicating the methodology proposed by Laviosa (1998a; 1998b), but extending it to encompass both a monolingual comparable
and an intermodal perspective. Our results indicate that the mediation process reduces complexity in both modes of language
production and both language directions, with interpreters simplifying the input more than translators, and evidence of
simplification being more lexical in English and more lexico-syntactic in Italian.
Trait Emotional intelligence and translation
Authors: Hubscher-Davidson Séverine
Published: April 2016

A study of 155 professional translators was carried out to examine the relationship between trait emotional intelligence (trait EI) and literary translation, job satisfaction and career success. Participants were surveyed and their answers were correlated with scores from an emotional intelligence measure, the TEIQue. The analysis revealed that literary and non-literary translators have different trait EI profiles. Some significant correlations were found between trait EI and the variables of job satisfaction, career success, and literary translation experience. This is the first study to examine the effect of EI on translator working practices. Findings illustrate that trait EI may be predictive of some aspects of translator behaviour and highlight the relevance of exploring the emotional intelligence of professional translators.
Immunostimulatory effect of spinach aqueous extract on mouse macrophage-like J774.1 cells and mouse primary peritoneal macrophages
Authors: Ishida Momoko , Ose Saya , Nishi Kosuke , Sugahara Takuya
Published: April 2016

We herein report the immunostimulatory effect of spinach aqueous extract (SAE) on mouse macrophage-like J774.1 cells and mouse primary peritoneal macrophages. SAE significantly enhanced the production of interleukin (IL)-6 and tumor necrosis factor-α by both J774.1 cells and peritoneal macrophages by enhancing the expression levels of these cytokine genes. In addition, the phagocytosis activity of J774.1 cells was facilitated by SAE. Immunoblot analysis revealed that SAE activates mitogen-activated protein kinase and nuclear factor-κB cascades. It was found that SAE activates macrophages through not only TLR4, but also other receptors. The production of IL-6 was significantly enhanced by peritoneal macrophages from SAE-administered BALB/c mice, suggesting that SAE has a potential to stimulate macrophage activity in vivo. Taken together, these data indicate that SAE would be a beneficial functional food with immunostimulatory effects on macrophages.
Competition between Rhythmic and Linguistic Meaning Revisited: The Effect of Task Demands
Authors: Getz Laura M. , Wohltjen Sophie , Kubovy Michael
Published: April 2016

This paper revisits the conclusion of our previous work regarding the dominance of meaning in the competition between rhythmic parsing and linguistic parsing. We played five-note rhythm patterns in which each sound is a spoken word of a five-word sentence. We asked listeners to indicate the starting point of the rhythm while disregarding which word would normally be heard as the first word of the sentence. In four studies, we varied task demands by introducing differences in rhythm complexity, rhythm ambiguity, rhythm pairing, and semantic coherence. We found that task complexity affects the dominance of meaning. We therefore amend our previous conclusion: when processing resources are taxed, listeners do not always primarily attend to meaning; instead, they primarily attend to the aspect of the pattern (rhythm or meaning) that is more salient.
An example of PET. Computation of the Hausdorff dimension of the aperiodic set
Authors: Bédaride Nicolas , Bertazzon Jean-François
Published: April 2016

We introduce a family of piecewise isometries. This family is similar to the ones studied by Hooper and Schwartz. We prove that a renormalization scheme exists inside this family and compute the Hausdorff dimension of the discontinuity set. The methods use some cocycles and a continued fraction algorithm.
Modular perverse sheaves on flag varieties III: Positivity conditions
Authors: Achar Pramod , Riche Simon
Published: April 2016

We further develop the general theory of the “mixed modular derived category” introduced by the authors in a previous paper in this series. We then use it to study positivity and

Q
Q

-Koszulity phenomena on flag varieties.
Diophantine approximation for products of linear maps — logarithmic improvements
Authors: Gorodnik Alexander , Vishe Pankaj
Published: April 2016

This paper is devoted to the study of a problem of Cassels in multiplicative Diophantine approximation which involves minimising values of a product of affine linear forms computed at integral points. It was previously known that values of this product become arbitrary close to zero, and we establish that, in fact, they approximate zero with an explicit rate. Our approach is based on investigating quantitative density of orbits of higher-rank abelian groups.
Frames generated by compact group actions
Authors: Iverson Joseph
Published: April 2016

Let

K
K

be a compact group, and let

ρ
\rho

be a representation of

K
K

on a Hilbert space

H

ρ

\mathcal {H}_\rho

. We classify invariant subspaces of

H

ρ

\mathcal {H}_\rho

in terms of range functions, and investigate frames of the form

{
ρ
(
ξ
)

f
i

}

ξ
∈
K
,
i
∈
I

\{\rho (\xi ) f_i\}_{\xi \in K, i \in I}

. This is done first in the setting of translation invariance, where

K
K

is contained in a larger group

G
G

and

ρ
\rho

is left translation on

H

ρ

=

L
2

(
G
)

\mathcal {H}_\rho = L^2(G)

. For this case, our analysis relies on a new, operator-valued version of the Zak transform. For more general representations, we develop a calculational system known as a bracket to analyze representation structures and frames with a single generator. Several applications are explored. Then we turn our attention to frames with multiple generators, giving a duality theorem that encapsulates much of the existing research on frames generated by finite groups, as well as classical duality of frames and Riesz sequences.
MEMO: multi-experiment mixture model analysis of censored data
Authors: Geissen Eva-Maria , Hasenauer Jan , Heinrich Stephanie , Hauf Silke , Theis Fabian J. , Radde Nicole E.
Published: April 2016

Motivation: The statistical analysis of single-cell data is a challenge in cell biological studies. Tailored statistical models and computational methods are required to resolve the subpopulation structure, i.e. to correctly identify and characterize subpopulations. These approaches also support the unraveling of sources of cell-to-cell variability. Finite mixture models have shown promise, but the available approaches are ill suited to the simultaneous consideration of data from multiple experimental conditions and to censored data. The prevalence and relevance of single-cell data and the lack of suitable computational analytics make automated methods, that are able to deal with the requirements posed by these data, necessary.

Results: We present MEMO, a flexible mixture modeling framework that enables the simultaneous, automated analysis of censored and uncensored data acquired under multiple experimental conditions. MEMO is based on maximum-likelihood inference and allows for testing competing hypotheses. MEMO can be applied to a variety of different single-cell data types. We demonstrate the advantages of MEMO by analyzing right and interval censored single-cell microscopy data. Our results show that an examination of censoring and the simultaneous consideration of different experimental conditions are necessary to reveal biologically meaningful subpopulation structures. MEMO allows for a stringent analysis of single-cell data and enables researchers to avoid misinterpretation of censored data. Therefore, MEMO is a valuable asset for all fields that infer the characteristics of populations by looking at single individuals such as cell biology and medicine.

Availability and Implementation: MEMO is implemented in MATLAB and freely available via github (https://github.com/MEMO-toolbox/MEMO).

Contacts: eva-maria.geissen@ist.uni-stuttgart.de or nicole.radde@ist.uni-stuttgart.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
TreeQTL: hierarchical error control for eQTL findings
Authors: Peterson C. B. , Bogomolov M. , Benjamini Y. , Sabatti C.
Published: April 2016

Summary: Commonly used multiplicity adjustments fail to control the error rate for reported findings in many expression quantitative trait loci (eQTL) studies. TreeQTL implements a hierarchical multiple testing procedure which allows control of appropriate error rates defined relative to a grouping of the eQTL hypotheses.

Availability and Implementation: The R package TreeQTL is available for download at http://bioinformatics.org/treeqtl.

Contact:  sabatti@stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
SCell: integrated analysis of single-cell RNA-seq data
Authors: Diaz Aaron , Liu Siyuan J. , Sandoval Carmen , Pollen Alex , Nowakowski Tom J. , Lim Daniel A. , Kriegstein Arnold
Published: April 2016

Summary: Analysis of the composition of heterogeneous tissue has been greatly enabled by recent developments in single-cell transcriptomics. We present SCell, an integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface. Scripts and protocols for the high-throughput pre-processing of large ensembles of single-cell, RNA-seq datasets are provided as an additional resource.

Availability and Implementation: Binary executables for Windows, MacOS and Linux are available at http://sourceforge.net/projects/scell, source code and pre-processing scripts are available from https://github.com/diazlab/SCell.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  aaron.diaz@ucsf.edu
gkmSVM: an R package for gapped-kmer SVM
Authors: Ghandi Mahmoud , Mohammad-Noori Morteza , Ghareghani Narges , Lee Dongwon , Garraway Levi , Beer Michael A.
Published: April 2016

Summary: We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorithm. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.

Availability and Implementation: gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), for Linux, Mac OS and Windows platforms. The C ++ implementation is available at www.beerlab.org/gkmsvm

Contact:  mghandi@gmail.com or mbeer@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
OREMPRO web server: orientation and assessment of atomistic and coarse-grained structures of membrane proteins
Authors: Postic Guillaume , Ghouzam Yassine , Gelly Jean-Christophe
Published: April 2016

Summary: The experimental determination of membrane protein orientation within the lipid bilayer is extremely challenging, such that computational methods are most often the only solution. Moreover, obtaining all-atom 3D structures of membrane proteins is also technically difficult, and many of the available data are either experimental low-resolution structures or theoretical models, whose structural quality needs to be evaluated. Here, to address these two crucial problems, we propose OREMPRO, a web server capable of both (i) positioning α-helical and β-sheet transmembrane domains in the lipid bilayer and (ii) assessing their structural quality. Most importantly, OREMPRO uses the sole alpha carbon coordinates, which makes it the only web server compatible with both high and low structural resolutions. Finally, OREMPRO is also interesting in its ability to process coarse-grained protein models, by using coordinates of backbone beads in place of alpha carbons.

Availability and Implementation: http://www.dsimb.inserm.fr/OREMPRO/

Contact: guillaume.postic@univ-paris-diderot.fr or jean-christophe.gelly@univ-paris-diderot.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
Plant innate immunity in rice: a defense against pathogen infection
Authors: Liu Wende , Wang Guo-Liang
Published: April 2016

A large number of pathogenic microorganisms cause rice diseases that lead to enormous yield losses worldwide. Such losses are important because rice is a staple food for more than half of the world's population. Over the past two decades, the extensive study of the molecular interactions between rice and the fungal pathogen Magnaporthe oryzae and between rice and the bacterial pathogen Xanthomonas oryzae pv. oryzae has made rice a model for investigating plant–microbe interactions of monocotyledons. Impressive progress has been recently achieved in understanding the molecular basis of rice pathogen-associated molecular pattern-immunity and effector-triggered immunity. Here, we briefly summarize these recent advances, emphasizing the diverse functions of the structurally conserved fungal effectors, the regulatory mechanisms of the immune receptor complexes, and the novel strategies for breeding disease resistance. We also discuss future research challenges.
Organic light-emitting diodes: theoretical understanding of highly efficient materials and development of computational methodology
Authors: Shuai Zhigang , Peng Qian
Published: April 2016

Theoretical understanding of organic light-emitting diodes started from the quest to the nature of the primary excitation in organic molecular and polymeric materials. We found the electron correlation strength, bond-length alternation as well as the conjugation extent have strong influences on the orderings of the lowest lying excited states through the first application of density matrix renormalization group theory to quantum chemistry. The electro-injected free carriers (with spin 1/2) can form both singlet and triplet bound states. We found that the singlet exciton formation ratio can exceed the conventional 25% spin statistics limit. We proposed a vibration correlation function formalism to evaluate the excited-state decay rates, which is shown to not only give reasonable estimations for the quantum efficiency but also a quantitative account for the aggregation-induced emission (AIE). It is suggested to unravel the AIE mechanism through resonance Raman spectroscopy.
A Novel Shiga Toxin 1a-Converting Bacteriophage of Shigella sonnei With Close Relationship to Shiga Toxin 2-Converting Pages of Escherichia coli
Authors: Carter Christoph C. , Fierer Joshua , Chiu Wei Wei , Looney David J. , Strain Matthew , Mehta Sanjay R.
Published: April 2016

In recent studies, strains of non-dysenteriae 1 Shigella (NDS) expressing Shiga toxin have been reported. In this study, we report a novel stx1a-converting bacteriophage of Shigella sonnei associated with travel to Mexico. Phylogenetic comparison between this and other stx-converting phages suggests that toxigenic NDS strains have arisen through separate horizontal transfer events from toxigenic Escherichia coli.
Galactic center mini-spiral by ALMA: Possible origin of the central cluster
Authors: Tsuboi Masato , Kitamura Yoshimi , Miyoshi Makoto , Uehara Kenta , Tsutsumi Takahiro , Miyazaki Atsushi
Published: April 2016

We present continuum images of the “Galactic center mini-spiral” in the 100, 250, and 340 GHz bands with analysis of the Cy.0 data acquired from the Atacama Large Millimeter/submillimeter Array (ALMA) archive. Good u-v coverage of the data and the “self-calibration” method give us the opportunity to obtain dynamic ranges of over 2 × 104 in the resultant maps of the 250 and 340 GHz bands. In particular, the image of the 340 GHz band has high dynamic ranges unprecedented in sub-millimeter waves. The angular resolutions attained are 1${^{\prime\prime}_{.}}$57 × 1${^{\prime\prime}_{.}}$33 in the 100 GHz band, 0${^{\prime\prime}_{.}}$63 × 0${^{\prime\prime}_{.}}$53 in the 250 GHz band, and 0${^{\prime\prime}_{.}}$44 × 0${^{\prime\prime}_{.}}$38 in the 340 GHz band, respectively. The continuum images clearly depict the “mini-spiral,” which is an ionized gas stream in the vicinity of Sgr A*. We found a tight correlation between the dust emission peaks and the OB/WR stars in the northern arm of the “mini-spiral.” The core mass function of the dust cores identified by the clumpfind algorithm would obey the flat power-law dN/dM ∝ M−1.5±0.4 on the high-mass side. These support the scenario that the star-forming cloud has fallen into the immediate vicinity of Sgr A* for the origin of the central cluster.
Is anterior cruciate ligament preservation surgery better than reconstructing both bundles?
Authors: Sonnery-Cottet Bertrand , Barbosa Nuno Camelo , Tuteja Sanesh Vijay
Published: April 2016

Rupture of the anterior cruciate ligament (ACL) is one of the most common ligamentous injuries of the knee, with an incidence of 35 out of 100,000. An ACL reconstruction is now a routine procedure. Generally, good outcomes are expected from the surgery, with return to preinjury level of sports activity in most patients. Debate, however, continues regarding the advantages of preserving the ACL remnant and augmenting it with a graft as opposed to debridement of the remnant in a standard ACL reconstruction. The purpose of this article is to consider the scientific basis of ACL preservation surgery (remnant preservation and selective bundle reconstruction) and to compare the outcomes between an ACL-preserving surgery and a double-bundle reconstruction. Both techniques provide anteroposterior laxity control and some degree of control on rotational laxity. Although superior Lysholm and subjective International Knee Documentation Committee (IKDC) scores have been documented with double-bundle reconstructions, remnant-preserving procedures have several advantages and seem to have a valuable contribution either on single-bundle, selective, and double-bundle reconstructions. Based on our experience, we recommend the remnant preserving technique. However, longer follow-up is necessary to ascertain which procedure could restore the normal knee kinematics, thus providing better clinical outcomes.
Eruptive Disseminated Porokeratosis in a Patient With Type 2 Diabetes Mellitus
Authors: Yalcin Basak , Uysal Pinar I. , Kadan Elcin , Bozdoğan Önder
Published: April 2016

Porokeratosis includes a group of heterogenous disorders that represents distinct clinical subtypes of the same genetic pattern. Although entire pathogenesis of porokeratosis still remains unknown, certain factors including ultraviolet radiation and immunosuppression are suggested to be some of the factors inducing this disorder. Eruptive disseminated porokeratosis is a recently described form of porokeratosis, which frequently occurs in the presence of immunosuppresion or malignancy. The authors report here a unique case with sudden onset eruptive disseminated porokeratosis associated with diabetes mellitus.
Spitz Nevus Intermingling With a Hemangioma
Authors: Fernandez-Flores Angel , Saeb-Lima Marcela
Published: April 2016

We report on a Spitz nevus intermingling with a hemangioma in the same biopsy from the right thigh of a 10-year-old boy. The hemangioma was made of dilated vessels in superficial areas but of narrow and angulated vessels in the deep and lateral zones. The Spitz nevus was typical, showing maturation, and no worrisome cytological features. The immunohistochemical study demonstrated expression by the vascular component of CD31, CD34, factor VIII-related antigen, and Wilms tumor 1, whereas the vessels did not express D2-40 human herpes virus 8 or glucose transporter-1. The melanocytic component expressed HMB-45 (weakly and mainly in the superficial zones), Melan-A and S-100 protein. A perivascular continuous layer of pericytes expressing smooth muscle actin was also evident.
“Secretory” Carcinoma of the Skin Mimicking Secretory Carcinoma of the Breast: Case Report and Literature Review
Authors: Huang Sixia , Liu Yan , Su Jing , Liu Jianying , Guo Xiaoning , Mei Fang , Zheng Jie , Liao Songlin
Published: April 2016

Secretory carcinoma is a unique kind of adenocarcinoma. It has distinct histological features and a special genetic change, that is, t (12; 15) (p13; q25) translocation which leads to the expression of the ETV6-NTRK3 fusion gene. Secretory carcinoma has been found to occur both in the breast and salivary gland. Here the authors present a case of 22-year-old woman with a unique cutaneous neoplasm located at the axilla. The tumor was characterized histologically with the formation of round to ovoid microcysts and papillary structure, which was similar to the secretory carcinoma of the breast and salivary gland. Furthermore, the gene sequence analysis of reverse-transcription polymerase chain reaction products demonstrated the expression of the ETV6-NTRK3 fusion gene. To the authors' knowledge, this is the first case of secretory carcinoma from the skin which has the same genetic change as those from the breast and salivary gland. Local excision was performed on this patient. She had been followed up for nearly 1 year. No recurrence or metastasis was found yet.
Tick Bite Alopecia: A Report and Review
Authors: Lynch Michael C. , Milchak Marissa A. , Parnes Herbert , Ioffreda Michael D.
Published: April 2016

Tick bites can cause a number of local inflammatory reactions, which are often difficult to differentiate from those induced by other arthropod bites or stings. These include erythematous nodular or pustular lesions, erosive plaques, annular lesions of erythema chronicum migrans, and both scarring and nonscarring inflammatory alopecia. We report a case of nonscarring alopecia in a 21-year-old male who reported a recent history of tick bite to the scalp. The biopsy demonstrated a dense pseudolymphomatous inflammatory infiltrate with numerous eosinophils associated with hair follicle miniaturization and an elevated catagen–telogen count. Signs of external rubbing, including lichen simplex chronicus and the “hamburger sign”, were also visualized and are indicative of the associated pruritus. To the authors' knowledge, this is the fifth report of nonscarring tick bite alopecia in the literature and the first in an adult patient. This text will review the classic clinical presentation, histologic findings, and proposed mechanism of tick bite alopecia.
Cutaneous Metastasis of a Mucoepidermoid Carcinoma of the Pancreas: First Reported Case
Authors: Pandey Prasamsa , Al-Rohil Rami N. , Goldstein Jennifer B. , Tetzlaff Michael T. , Barnes Tamara G. , Baldwin Sarah E. , Fogelman David , Abraham Susan C. , Piha-Paul Sarina A.
Published: April 2016

Background:

Mucoepidermoid pancreatic cancer is a rare entity with only 8 cases reported in the literature. On review of the literature, the authors found that cutaneous metastases in pancreatic cancer are rare and have not been associated with the mucoepidermoid subtype. The authors present the first reported case of cutaneous metastasis in a patient with mucoepidermoid carcinoma of the pancreas.

Case Presentation:

A 50-year old white male with a metastatic invasive poorly differentiated mucoepidermoid carcinoma of the pancreas was found to have a slow growing lesion in the skin over his left upper quadrant while undergoing active therapy. The lesion was biopsied and the pathology was consistent with pancreatic origin sharing similar morphologic features when compared with the primary pancreactectomy specimen.

Conclusions:

Mucoepidermoid pancreatic cancer is an exceedingly rare subtype of pancreatic cancer, with very little information regarding its diagnosis, treatment, and patterns of metastases. Here, the authors present the first reported case of cutaneous metastases of mucoepidermoid pancreatic cancer.