bluuebunny/crossref_metadata_2025 huggingface dataset:
The Fast-Acting Inhibitor of Tissue-Type Plasminogen Activator in Plasma Is also the Primary Plasma Inhibitor of Urokinase
Authors: Kruithof Egbert K.O , Tran-Thang Chiên , Bachmann Fedor
Published: July 2018

We have compared the ability of a plasminogen activator inhibitor (PA-inhibitor) in human plasma, to form complexes with radioiodinated tissue-type plasminogen activator (t-PA) and high molecular weight urokinase (HMr-UK). Addition of 125I-t-PA (final concentration 10 IU/ml) or of 125I-HMr-UK (2 IU/ml) to a plasma containing 33 U/ml of PA-inhibitor resulted in the rapid formation of a 110,000 Mr complex of 125I-t-PA or a 95,000 Mr complex of 125I-HMr-UK with PA-inhibitor. Upon prolonged incubation of the plasma with 125I-HMr-UK a secondary complex of a Mr of 88,000 was observed, which probably derives from limited degradation of the 95,000 complex. Preincubation of the plasma with unlabelled t-PA, HMr-UK or LMr-UK at higher concentrations prevented the subsequent formation of complexes between radiolabelled PAs and the PA-inhibitor. These results thus demonstrate that t-PA and UK form complexes with the same PA-inhibitor. The rate of complex formation of 125I-t-PA or of 125I-HMr-UK with the plasma PA-inhibitor was similar (second order rate constant of association with PA-inhibitor in the order of 107 M−1s−1).
A Sensitive Assay, Specific for Endothelial Cell Type Plasminogen Activator Inhibitor in Blood Plasma
Authors: Sprengers E D
Published: July 2018

A polyclonal antibody raised against plasminogen activator (PA-)inhibitor from endothelial cells fully precipitates the PA-inhibitor in endothelial cell conditioned medium but only a part of the PA-inhibitory activity in blood plasma. This indicates that the PA-inhibitory activity in blood plasma is not due to a single inhibitory component. Performing the assay for PA-inhibitory activity in plasma both in the presence and absence of saturating concentrations of anti-endothelial cell PA-inhibitor antibodies, allows the determination of endothelial cell type PA-inhibitor in plasma. The assay gives a linear dose-response curve of amount of plasma added versus t-PA neutralised.

Values for endothelial cell type PA-inhibitor in plasma of a group of 20 healthy individuals are in the range of 0.0-16.8 IU/ml and are not normally distributed (median value 3.0 IU/ml).

This method also reveals a second, so far unidentified, PA-inhibitory component in human plasma.
Isolation and Preliminary Characterisation of Active B-Chain of Recombinant Tissue-Type Plasminogen Activator
Authors: Dodd I , Fears R , Robinson J H
Published: July 2018

Purified 2-chain recombinant tissue-type plasminogen activator (t-PA) was reduced under mild conditions - 10 mM dithiothreitol/ 5° C/1.5 h - and the two chains were separated by chromatography on lysine Sepharose. The t-PA B chain was fully active as determined by its activity towards the chromogenic substrate S-2288 (H-D-ile-pro-arg p-nitroanilide). Analysis by sodium dodecyl sulphate polyacrylamide gel electrophoresis under reducing or non-reducing conditions revealed a single polypeptide at Mr = 35,000 or 29,000 respectively. In addition, under non-reducing conditions a fibrinolytic band at apparent Mr = 29,000 was present after fibrin zymography. The N-terminal sequence was confirmed as ile-lys-gly. The t-PA B chain had a specific amidolytic activity, using S-2288, of 170,000 to 210,000 SU/mg protein. (This compares to a specific activity of the native 2-chain t-PA of 170,000 SU/mg). It resembles urokinase-type plasminogen activator in its inability to be stimulated by fibrin and its dose response on human fibrin plates. However, t-PA B-chain was stimulated to almost the same extent as t-PA by poly-D-lysine. The isoelectric points, at pH 5.6 and 5.7, fall outside the range generally quoted for t-PA preparations (pH 7.8-8.8).
Inertial Sensors are a Valid Tool to Detect and Consistently Quantify Jumping
Authors: Spangler Rhys , Rantalainen Timo , Gastin Paul , Wundersitz Daniel
Published: July 2018

Considering the large and repetitive loads associated with jumping in team sports, automatic detection and quantification of jumping may show promise in reducing injury risks. The aim of this study was to validate commercially available inertial-movement analysis software to detect and quantify jumping in team sports. In addition, the test-retest reliability of the software to quantify jumping was assessed. Seventy-six healthy male participants completed a team sport circuit six times containing seven common movements (including three countermovement and two single-leg jumps) whilst wearing an inertial sensor (Catapult Sports, Australia). Jump detection accuracy was assessed by comparing the known number of jumps to the number recorded by the inertial movement analysis software. A further 27 participants separately performed countermovement and single-leg jumps at 33%, 66% and 100% of maximal jump height over two sessions. Jump height quantification accuracy was assessed by comparing criterion three-dimensional motion analysis-derived heights to that recorded by the inertial movement analysis software. Test-retest reliability was assessed by comparing recorded jump heights between both testing sessions. Catapult’s inertial movement analysis software displayed excellent jump detection accuracy (96.9%) and test-retest jump height quantification reliability (ICC: 0.86 [countermovement jump], 0.88 [single-leg jump]). However, significant mean bias (–2.74 cm [95% LoA –10.44 – 4.96]) was observed for jump height quantification. Overall, Catapult’s inertial movement analysis software appears to be a suitable method of automatically detecting jumping in team sports, and although reliable, caution is advised when using the IMA software to quantify jump height.
An analysis of high-frequency cryptocurrencies prices dynamics using permutation-information-theory quantifiers
Authors: Bariviera Aurelio F. , Zunino Luciano , Rosso Osvaldo A.
Published: July 2018

This paper discusses the dynamics of intraday prices of 12 cryptocurrencies during the past months’ boom and bust. The importance of this study lies in the extended coverage of the cryptoworld, accounting for more than 90% of the total daily turnover. By using the complexity-entropy causality plane, we could discriminate three different dynamics in the data set. Whereas most of the cryptocurrencies follow a similar pattern, there are two currencies (ETC and ETH) that exhibit a more persistent stochastic dynamics, and two other currencies (DASH and XEM) whose behavior is closer to a random walk. Consequently, similar financial assets, using blockchain technology, are differentiated by market participants.
Theory of alpha heating in inertial fusion: Alpha-heating metrics and the onset of the burning-plasma regime
Authors: Christopherson A. R. , Betti R. , Howard J. , Woo K. M. , Bose A. , Campbell E. M. , Gopalaswamy V.
Published: July 2018

A detailed and comprehensive 1-dimensional theory of alpha-heating metrics is developed to determine the onset of burning plasma regimes in inertial fusion implosions. The analysis uses an analytic model of the deceleration, stagnation, and burn phases of inertial confinement fusion implosions combined with the results from a database of radiation-hydrodynamic simulations. The onset of the burning-plasma regime occurs when the alpha-heating rate in the hot spot exceeds the compression power input and is represented by the parameter Qα=1/2 α energy/PdV work. A second burning plasma regime is also identified, where the alpha-heating rate exceeds the compression input to the entire stagnated plasma, including the hot spot and confining shell, and is represented by Qαtot. It is shown that progress towards the burning-plasma regime is correlated with the yield enhancement caused by alpha-heating but is more accurately related to the fractional alpha energy fα=1/2 α energy/hot-spot energy. In the analysis presented here, we develop a method to infer these intermediate metrics from experiments and show that the alpha power produced in National Ignition Facility High-Foot implosions is approximately 50% of the external input power delivered to the hot spot and 25% of the total external power (from compression) delivered to the stagnated core.
Many-particle mobility and diffusion tensors for objects in viscous sheets
Authors: Sokolov Yulia , Diamant Haim
Published: July 2018

We derive a mobility tensor for many cylindrical objects embedded in a viscous sheet. This tensor guarantees a positive dissipation rate for any configuration of particles and forces, analogous to the Rotne-Prager-Yamakawa tensor for spherical particles in a three-dimensional viscous fluid. We test our result for a ring of radially driven particles, demonstrating the positive-definite property at all particle densities. The derived tensor can be utilized in Brownian dynamics simulations with hydrodynamic interactions for such systems as proteins in biomembranes and inclusions in free-standing liquid films.
Passivation and thickness control of highly efficient kesterite solar cells
Authors: Antunez Priscilla D. , Li Siming , Bishop Douglas M. , Farmer Damon B. , Gershon Talia S. , Baxter Jason B. , Haight Richard
Published: July 2018

Kesterite Cu2ZnSn(SxSe1−x)4 (CZTSSe) is an attractive photovoltaic absorber material because of its tunable bandgap, earth abundance, and low toxicity. However, efficiency and open circuit voltage remain significantly below theoretical limits. We recently showed that back-contact engineering with MoO3/Au on exfoliated vapor-deposited kesterite solar cells can improve device performance. Here, we demonstrate more promising results, which translate into high power conversion efficiencies of up to 12.2% for solution-deposited CZTSe with thicknesses as low as 1.1 μm. Time-resolved terahertz spectroscopy of exfoliated films showed significantly faster recombination at the back surface than at the front. When atomic layer deposited Al2O3 was used to passivate the exposed back surface of exfoliated films, front and back surfaces showed nearly identical recombination dynamics. After thermally depositing high work function MoO3 and reflective Au as the back contact on the Al2O3-passivated absorber, we obtained devices with efficiencies of up to 11.6%. Applying the same strategy of exfoliating working devices and engineering the back contact resulted in efficiencies of up to 12.2% for passivation with a 10 nm layer of Se instead of Al2O3. Further development of such passivation and back-contact engineering approaches may lead to higher efficiency devices with absorber thicknesses below 1 μm.
Coalescence delay of microbubbles on superhydrophobic/superhydrophilic surfaces underwater
Authors: Tenjimbayashi Mizuki , Kawase Yudai , Doi Kotaro , Ng Chen Xian , Naito Masanobu
Published: July 2018

Inspired by penguins, the formation of an air film on surfaces underwater has been well-researched for the potential reduction of drag. However, the features that contribute to drag reduction of penguins are not only the formation of an air layer but also the flow of bubbles along the air layer; basic investigation of the wetting dynamics of a bubble scattered in an underwater environment has been overlooked. The focus of our research was microbubble contact on superhydrophobic/superhydrophilic surfaces underwater. Unlike the adhesion of mist in air, a “coalescence delay” is observed when bubbles make contact, which influences the deposition dynamics of an air film. The “coalescence delay” is proportional to the size of the bubbles. This study is helpful to understand air/solid/water systems as well as the drag reduction.
Measuring femtometer lattice displacements driven by free carrier diffusion in a polycrystalline semiconductor using time-resolved x-ray scattering
Authors: Jo Wonhyuk , Landahl Eric C. , DiChiara Anthony D. , Walko Donald A. , Lee Sooheyong
Published: July 2018

We show that time-resolved x-ray scattering can be applied to polycrystalline materials for the measurement of carrier diffusion. A polycrystalline indium antimonide sample is prepared by high-intensity ultrafast laser surface melting and re-solidification under vacuum to create randomly oriented grains with an average size of 13 nm. Two static diffraction rings are simultaneously observed on a gated pixel array detector. Their centroids move following lower-intensity laser excitation, and utilizing an in-situ angular calibration, the transient lattice spacing is determined with femtometer accuracy, thereby allowing the measurement of charge carrier dynamics. Compared to bulk calculations, we find that carrier diffusion slows by more than one order of magnitude. This result provides evidence for the formation of potential energy barriers at the grain boundaries and demonstrates the capability of time-resolved x-ray scattering to probe nanoscale charge transport in materials other than near-perfect crystals.
Phonon-assisted anti-Stokes excitation: Mechanism for the unusual temperature dependence of the Ce3+ luminescence in yttrium aluminum garnet
Authors: Yan Lin , Li Bo , Song Yunfei , Zhang Wei , Wang Zanhao , Lv Zhe , Zheng Xianxu , Wu Qiang , Yang Yanqiang
Published: July 2018

Luminescence emission spectra and decay kinetics of Ce3+ in YAG were investigated as a function of temperature (300–800 K) under excitation in the long wavelength tail of the lowest 4f–5d absorption spectrum. Both the anti-Stokes and Stokes emission intensity were found to exhibit an unusual non-monotonic temperature dependence compared to those commonly excited in the absorption band, where luminescence intensity decreases monotonically with increasing temperature. This phenomenon is well explained by a phonon-assisted anti-Stokes excitation model with strong vibronic interaction. It reveals that the intensity enhancement of Ce3+ anti-Stokes and Stokes emission is caused by the anti-Stokes excitation efficiency. Excitation efficiency is enhanced with increasing temperature, and thermal ionization of the 5d electron into the conduction band remains as the quenching mechanism of Ce3+ anti-Stokes and Stokes luminescence at high temperatures.
Note: Optimization and calibration for auto-cumulative flowmeter in horizontal oil-water two-phase flow
Authors: Kong D. M. , Xie B. B. , Kong L. F. , Xie R. H.
Published: July 2018

This note presented the optimization and calibration for a novel auto-cumulative flowmeter (ACF) to measure the oil flow rate in horizontal oil-water two-phase segregated flow. By using the finite element method, the electrode geometry of the probe in the ACF was designed, optimized, and simulated for oil accumulation measurement. Considering the practical application of ACF, a novel circuit for ACF with the optimized geometry of the probe was designed, simulated, and analyzed. The experiment for oil-water two-phase segregated flow with the novel circuit was carried out to calibrate the ACF. The calibration results can provide a theoretical basis and technical reference for the practical application of ACF.
Energy spectra and passive tracer cascades in turbulent flows
Authors: Jolly M. S. , Wirosoetisno D.
Published: July 2018

We study the influence of the energy spectrum on the extent of the cascade range of a passive tracer in turbulent flows. The interesting cases are when there are two different spectra over the potential range of the tracer cascade (in 2D when the tracer source is in the inverse energy cascade range and in 3D when the Schmidt number Sc is large). The extent of the tracer cascade range is then limited by the width of the range for the shallower of the two energy spectra. Nevertheless, we show that in dimension d = 2, 3, the tracer cascade range extends (up to a logarithm) to κdDp, where κdD is the wavenumber beyond which diffusion should dominate and p is arbitrarily close to 1, provided Sc is larger than a certain power (depending on p) of the Grashof number. We also derive estimates which suggest that in 2D, for Sc ∼ 1, a wide tracer cascade can coexist with a significant inverse energy cascade at Grashof numbers large enough to produce a turbulent flow.
Population ecology of a cryptic arboreal snake (Hoplocephalus bitorquatus)
Authors: Shelton Michael B. , Goldingay Ross L. , Phillips Stephen S.
Published: July 2018

Biologists have traditionally been reluctant to study arboreal snakes due to low rates of capture. Overlooking such taxa can mislead interpretations of population trends for data-deficient species. We used regularly spaced transect searches and standard capture–mark–recapture techniques to describe population structure, growth rates, survival and capture probability in a population of the pale-headed snake (Hoplocephalus bitorquatus) in southern Queensland. We obtained data from 194 captures of 113 individual snakes between 2009 and 2015. Using the Cormack–Jolly–Seber method, we estimated apparent annual survival in subadult snakes at 0.23 ± 0.01 (s.e.) and 0.81 ± 0.08 for adults. Capture probability was estimated at 0.16 ± 0.14 per session in subadult snakes and 0.33 ± 0.06 for adults. Within the red gum forests of our study site, we estimate pale-headed snake density at ~13 ± 7 ha–1. Using von Bertalanffy growth modelling, we predict that snakes reach sexual maturity after about four years and may live for up to 20. Our results suggest that the species is a ‘k’ strategist, characterised by slow maturation and low fecundity. These traits suggest that populations will recover slowly following decline, exacerbating the risk of local extinction.
Rates of cavity filling by liquids
Authors: Seo Dongjin , Schrader Alex M. , Chen Szu-Ying , Kaufman Yair , Cristiani Thomas R. , Page Steven H. , Koenig Peter H. , Gizaw Yonas , Lee Dong Woog , Israelachvili Jacob N.
Published: July 2018

Significance

In engineering and natural phenomena, various fluids contact rough/textured surfaces, e.g., wicking, facial creams, corrosion-preventive paints, and rain on plant leaves. Liquids on rough surfaces, especially those with cavities, pits, or pores, may or may not transit from the unfilled or partially filled (wetted) state to the fully filled (fully wetted) state. Either one of these states may be desired for a given application (compare superhydrophobicity) or even survival (compare oil-soaked feathers). In this article, we present five variables that control the wetting behavior (cavity filling) of water on intrinsically hydrophilic surfaces with micrometer-sized cavities. Our experimental results and theoretical analysis provide criteria for maintaining either the partially filled state, or quickly transiting to the fully filled state, and insights into other related wetting phenomena.
Prosodic separation of postverbal material in Georgian
Authors: Skopeteas Stavros , Féry Caroline , Asatiani Rusudan
Published: July 2018

A striking property of Georgian intonation is that focused postverbal material is prosodically separated from the core clause. The challenge of the present study is to assess the external validity of this experimental result by means of a corpus study. Corpus data is known to contain immense variability due to uncontrolled factors related to spontaneous speech production, such as segmental effects, intra-speaker variation, etc. The corpus study confirmed that the right edge of the verb is frequently associated with a prosodic boundary that separates the prosodic constituent encompassing the verb and the preverbal material from the postverbal domain. This boundary can be overwritten by information structure, in particular by postfocal dephrasing.
Macrosyntactic corpus annotation
Authors: Caron Bernard
Published: July 2018

This paper argues for a minimal annotation representing in a simple and concise way the interface between information structure and syntax. The article uses the concept of macrosyntax, based on illocutionary units, for a new level of annotation using existing morphosyntactic tiers in Elan. One of the main assets of this system of annotation lies in the notion of piles it uses to represent the oral discursive flow and account for dysfluencies, discontinuities and ellipses. A pilot 15,000 words corpus has been annotated in Elan to run a preliminary study of the information structure of illocutionary components in Zaar, a Chadic language spoken in Nigeria. Their micro- and macro-syntactic properties are represented using Universal Dependencies Grammar.
Focus marking and differential argument marking
Authors: Nikitina Tatiana
Published: July 2018

Wan makes use of a bidirectional case marker that does not attach to either the subject or the object but serves to separate core arguments that would otherwise be adjacent. The use of this optional marker depends on factors that are known to condition alignment splits in other languages (such as pronominality). Bidirectional case marking is but one strategy employed by speakers of Wan to avoid dispreferred combinations of adjacent subjects and objects. It is closely related to the marking of information structure: the same marker is also used to mark focus. The study presents an Optimality-Theoretic account of this relationship and draws parallels between the bidirectional case marking of Wan and systems of optional or pragmatic ergativity.
Information structure in the Neo-Aramaic dialect of Telkepe
Authors: Coghill Eleanor
Published: July 2018

This paper describes the expression of information structure in the North-Eastern Neo-Aramaic dialect of Telkepe, a town in northern Iraq. Based on the author’s fieldwork data, it looks at the various ways in which information structure is given linguistic expression in the dialect, in particular indexing on the verb, differential object flagging, word order, and the position of the nuclear stress. It is then shown that the findings for Telkepe provide supportive evidence for some of the universals of information structure proposed by Gundel (1988).
Information structure in a spoken corpus of Cameroon Pidgin English
Authors: Green Melanie , Ozón Gabriel
Published: July 2018

We explore information structure in a spoken corpus of Cameroon Pidgin English, addressing the broad question of how far the corpus method addresses the needs of research in this area. Focusing on marked pronouns used in focus/topic constructions and the copula/focus marker na, we detail a method for investigating information structure in the corpus. Corpus analysis not only confirms but elaborates an emergent description allowed by the elicitation stage, demonstrating that while elicitation reveals what is possible, corpus analysis reveals what is preferred. However, we conclude that qualitative analysis is still required to identify instances of focus in the absence of marked morphosyntactic features, as well as interpretations governed by context.
Annotation guidelines for Questions under Discussion and information structure
Authors: Riester Arndt , Brunetti Lisa , De Kuthy Kordula
Published: July 2018

We present a detailed manual for a pragmatic, i.e. meaning-based, method for the information-structural analysis of naturally attested data, which is built on the idea that for any assertion contained in a text (or transcript of spoken discourse) there is an implicit Question under Discussion (QUD) that determines which parts of the assertion are focused or backgrounded (and which ones are not at issue, i.e. not part of the assertion at all). We formulate a number of constraints, which allow the analyst/annotator to derive QUDs from the previous or upcoming discourse context, and demonstrate the method using corpus examples (of French, German, and English). Since we avoid making reference to language-specific morphosyntactic or prosodic properties, we claim that our method is also cross-linguistically applicable beyond our example languages.
Impression creep behaviour of TiB2 particles reinforced steel matrix composites
Authors: Sahoo S. , Jha B. B. , Mahata T.S. , Sharma J. , Murthy T. S. R. Ch. , Mandal A.
Published: July 2018

Impression creep behaviour of the powder metallurgy processed steel matrix composites was investigated under constant stress at different temperatures in the range of 873–973 K. By using the power-law relationship, the estimated activation energy for unreinforced steel was found to be 149 kJ mol−1 and steel reinforced with 2 and 4 vol.-% TiB2 was found to be 298 and 338 kJ mol−1, respectively indicating better creep resistance of the reinforced steel matrix composites. Dislocation creep is the dominant creep mechanism based on the calculated values of stress exponent and activation energy. Hence, this method can be used to assess the potential of steel matrix composites for use as structural materials for high-temperature application.
Mechanical behaviour and microstructure of heat-treated Cu–Ni–Si alloy
Authors: Stavroulakis Paul , Toulfatzis Anagnostis , Vazdirvanidis Athanasios , Pantazopoulos George , Papaefthymiou Spyros
Published: July 2018

Cu–Ni–Si alloys exhibit a good combination of strength and electrical conductivity and may be a potential candidate for utilisation in electrotechnical applications. In this work, the mechanical behaviour and its relation to the microstructure of a Cu–Ni–Si alloy, subjected to different solution heat treatment cycles, were investigated. Tensile, bend and hardness testing, in addition to Optical and Scanning Electron Microscopy, were employed, as the main analytical techniques, in the context of the present investigation.

This paper is part of a Thematic Issue on Copper and its Alloys.
The proliferation of colorectal cancer cells is suppressed by silencing of EIF3H
Authors: Yu Genhua , Liao Jiaqun , Wu Junlan , Ding Jun , Zhang Lin
Published: July 2018

Colorectal cancer is one of the most common causes of cancer-related deaths worldwide. Eukaryotic translation initiation factor 3, subunit H (EIF3H) is a subunit of EIF3, which is involved in mRNA recruitment and ribosomal complex disassembly and is known to be a driver of cell proliferation and survival in cancer. To investigate its function in colorectal cancer, the Oncomine database was used to evaluate the expression of EIF3H in human colorectal cancer and normal tissues. Then, we constructed a Lentivirus shorthair EIF3H vector (Lv-shEIF3H) to silence EIF3H expression in the colorectal cancer cell lines HCT116 and SW1116. We observed impaired cell growth and colony formation in these silenced cell lines. In addition, we showed that EIF3H knock-down led to cell apoptosis. In conclusion, EIF3H plays key roles in the apoptosis in colorectal cancer cells, which suggests EIF3H as a potential diagnostic biomarker in colorectal cancer.
SOBIR1 and AGB1 independently contribute to nonhost resistance to Pyricularia oryzae (syn. Magnaporthe oryzae) in Arabidopsis thaliana
Authors: Takahashi Toshiharu , Murano Tomoya , Ishikawa Atsushi
Published: July 2018

Rice blast caused by Pyricularia oryzae (syn. Magnaporthe oryzae) is a disease devastating to rice. We have studied the Arabidopsis-P. oryzae pathosystem as a model system for nonhost resistance (NHR) and found that SOBIR1, but not BAK1, is a positive regulator of NHR to P. oryzae in Arabidopsis. AGB1 is also involved in NHR. However, the genetic interactions between SOBIR1, BAK1, and AGB1 are uncharacterized. In this study, we delineated the genetic interactions between SOBIR1, BAK1, and AGB1 in NHR to P. oryzae in Arabidopsis and found SOBIR1 and AGB1 independently control NHR to P. oryzae in Arabidopsis pen2-1 mutant plants. Furthermore, XLG2, but not TMM, has a positive role in penetration resistance to P. oryzae in Arabidopsis pen2-1 mutant plants. Our study characterized genetic interactions in Arabidopsis NHR.

Abbreviations: PRR: pattern recognition receptor, RLK: receptor-like kinase, RLP: receptor-like protein, BAK1: BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1, BIR1: BAK1-INTERACTING RECEPTOR-LIKE KINASE 1, SOBIR1: SUPPRESSOR OF BIR1-1-1, AGB1: ARABIDOPSIS G PROTEIN ß-SUBUNIT 1, XLG2: EXTRA-LARGE G PROTEIN 2
Nde1 promotes diverse dynein functions through differential interactions and exhibits an isoform-specific proteasome association
Authors: Monda Julie K. , Cheeseman Iain M.
Published: July 2018

Nde1 is a key regulator of cytoplasmic dynein, binding directly to both dynein itself and the dynein adaptor, Lis1. Nde1 and Lis1 are thought to function together to promote dynein function, yet mutations in each result in distinct neurodevelopment phenotypes. To reconcile these phenotypic differences, we sought to dissect the contribution of Nde1 to dynein regulation and explore the cellular functions of Nde1. Here we show that an Nde1–Lis1 interaction is required for spindle pole focusing and Golgi organization but is largely dispensable for centrosome placement, despite Lis1 itself being required. Thus, diverse functions of dynein rely on distinct Nde1- and Lis1-mediated regulatory mechanisms. Additionally, we discovered a robust, isoform-specific interaction between human Nde1 and the 26S proteasome and identify precise mutations in Nde1 that disrupt the proteasome interaction. Together, our work suggests that Nde1 makes unique contributions to human neurodevelopment through its regulation of both dynein and proteasome function.
Periodic Limb Movements During Sleep Are Not Associated With Hypertension in a Clinical Cohort of Korean Adults
Authors: Shin Dae-Seop , Yang Kwang Ik , Kim Doh-Eui , Hwangbo Young , Koo Brian B , Cho Yong Won
Published: July 2018

BACKGROUND

There is growing evidence of increased cardiovascular risk including hypertension in patients with periodic limb movements during sleep (PLMS). In a multiethnic cohort study, the association between prevalent hypertension and PLMS varied according to ethnicity. We evaluated whether PLMS are associated with hypertension in Koreans.

METHODS

We enrolled 1,163 subjects who had polysomnography (PSG) from 2 tertiary hospitals. All subjects completed a sleep questionnaire before the PSG study. Coincidental hypertension was recorded according to past medical history. We analyzed the association between periodic limb movement index (PLMI), periodic limb movement associated with arousal index (PLMAI), and coincidental hypertension. Covariates were age, sex, body mass index (BMI), restless legs syndrome, apnea−hypopnea index (AHI), arousal index, and average oxygen saturation.

RESULTS

A total of 304 subjects (26.1%) had hypertension. The proportion of subjects with hypertension in the PLMI ≥ 15 category was higher than that in the PLMI < 15 category (32.4% vs. 25.0%; P = 0.04). The proportion of subjects with hypertension in the PLMAI ≥ 1 category was 32.6%, which was higher than that in the PLMAI < 1 category (24.6%; P = 0.02). In a multivariate regression model, neither PLMI (odds ratio [OR], 1.12; 95% confidence interval [CI] 0.75–1.68) nor PLMAI (OR, 1.21; 95% CI 0.83–1.76) were associated with hypertension. Statistical significance was found between coincidental hypertension and the following variables: age, smoking history, BMI, and AHI.

CONCLUSIONS

In a retrospective hospital-based study, there was no association between coincidental hypertension and PLMI/PLMAI in Koreans.
Prioritising candidate genes causing QTL using hierarchical orthologous groups
Authors: Warwick Vesztrocy Alex , Dessimoz Christophe , Redestig Henning
Published: July 2018

Motivation

A key goal in plant biotechnology applications is the identification of genes associated to particular phenotypic traits (for example: yield, fruit size, root length). Quantitative Trait Loci (QTL) studies identify genomic regions associated with a trait of interest. However, to infer potential causal genes in these regions, each of which can contain hundreds of genes, these data are usually intersected with prior functional knowledge of the genes. This process is however laborious, particularly if the experiment is performed in a non-model species, and the statistical significance of the inferred candidates is typically unknown.

Results

This paper introduces QTLSearch, a method and software tool to search for candidate causal genes in QTL studies by combining Gene Ontology annotations across many species, leveraging hierarchical orthologous groups. The usefulness of this approach is demonstrated by re-analysing two metabolic QTL studies: one in Arabidopsis thaliana, the other in Oryza sativa subsp. indica. Even after controlling for statistical significance, QTLSearch inferred potential causal genes for more QTL than BLAST-based functional propagation against UniProtKB/Swiss-Prot, and for more QTL than in the original studies.

Availability and implementation

QTLSearch is distributed under the LGPLv3 license. It is available to install from the Python Package Index (as qtlsearch), with the source available from https://bitbucket.org/alex-warwickvesztrocy/qtlsearch.

Supplementary information

Supplementary data are available at Bioinformatics online.
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations
Authors: Tang Haiming , Finn Robert D , Thomas Paul D
Published: July 2018

TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable to any annotations that have been made to internal nodes of a reference phylogenetic tree. TreeGrafter takes each input query protein sequence, finds the best matching homologous family in a library of pre-calculated, pre-annotated gene trees, and then grafts it to the best location in the tree. It then annotates the sequence by propagating annotations from ancestral nodes in the reference tree. We show that TreeGrafter outperforms subfamily HMM scoring for correctly assigning subfamily membership, and that it produces highly specific annotations of GO terms based on annotated reference phylogenetic trees. This method will be further integrated into InterProScan, enabling an even broader user community.

Availability and implementation

TreeGrafter is freely available on the web at https://github.com/pantherdb/TreeGrafter, including as a Docker image.

Supplementary information

Supplementary data are available at Bioinformatics online.
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics
Authors: Sun Chen , Medvedev Paul
Published: July 2018

Motivation

Genotyping a set of variants from a database is an important step for identifying known genetic traits and disease-related variants within an individual. The growing size of variant databases as well as the high depth of sequencing data poses an efficiency challenge. In clinical applications, where time is crucial, alignment-based methods are often not fast enough. To fill the gap, Shajii et al. propose LAVA, an alignment-free genotyping method which is able to more quickly genotype single nucleotide polymorphisms (SNPs); however, there remains large room for improvements in running time and accuracy.

Results

We present the VarGeno method for SNP genotyping from Illumina whole genome sequencing data. VarGeno builds upon LAVA by improving the speed of k-mer querying as well as the accuracy of the genotyping strategy. We evaluate VarGeno on several read datasets using different genotyping SNP lists. VarGeno performs 7–13 times faster than LAVA with similar memory usage, while improving accuracy.

Availability and implementation

VarGeno is freely available at: https://github.com/medvedevgroup/vargeno.

Supplementary information

Supplementary data are available at Bioinformatics online.
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples
Authors: Yu Hua , Lu Lu , Jiao Bingke , Liang Chengzhi
Published: July 2018

Motivation

The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism.

Results

Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding.

Availability and implementation

The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from ftp://47.94.193.106/pub.

Supplementary information

Supplementary data are available at Bioinformatics online.
Re-identification of individuals in genomic data-sharing beacons via allele inference
Authors: von Thenen Nora , Ayday Erman , Cicek A Ercument
Published: July 2018

Motivation

Genomic data-sharing beacons aim to provide a secure, easy to implement and standardized interface for data-sharing by only allowing yes/no queries on the presence of specific alleles in the dataset. Previously deemed secure against re-identification attacks, beacons were shown to be vulnerable despite their stringent policy. Recent studies have demonstrated that it is possible to determine whether the victim is in the dataset, by repeatedly querying the beacon for his/her single-nucleotide polymorphisms (SNPs). Here, we propose a novel re-identification attack and show that the privacy risk is more serious than previously thought.

Results

Using the proposed attack, even if the victim systematically hides informative SNPs, it is possible to infer the alleles at positions of interest as well as the beacon query results with very high confidence. Our method is based on the fact that alleles at different loci are not necessarily independent. We use linkage disequilibrium and a high-order Markov chain-based algorithm for inference. We show that in a simulated beacon with 65 individuals from the European population, we can infer membership of individuals with 95% confidence with only 5 queries, even when SNPs with MAF <0.05 are hidden. We need less than 0.5% of the number of queries that existing works require, to determine beacon membership under the same conditions. We show that countermeasures such as hiding certain parts of the genome or setting a query budget for the user would fail to protect the privacy of the participants.

Availability and implementation

Software is available at http://ciceklab.cs.bilkent.edu.tr/beacon_attack.

Supplementary information

Supplementary data are available at Bioinformatics online.
StackDPPred: a stacking based prediction of DNA-binding protein from sequence
Authors: Mishra Avdesh , Pokhrel Pujan , Hoque Md Tamjidul
Published: July 2018

Motivation

Identification of DNA-binding proteins from only sequence information is one of the most challenging problems in the field of genome annotation. DNA-binding proteins play an important role in various biological processes such as DNA replication, repair, transcription and splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus, prediction of DNA-binding proteins from sequences alone using computational methods can be useful to quickly annotate and guide the experimental process. Most of the methods developed for predicting DNA-binding proteins use the information from the evolutionary profile, called the position-specific scoring matrix (PSSM) profile, alone and the accuracies of such methods have been limited. Here, we propose a method, called StackDPPred, which utilizes features extracted from PSSM and residue specific contact-energy to help train a stacking based machine learning method for the effective prediction of DNA-binding proteins.

Results

Based on benchmark sequences of 1063 (518 DNA-binding and 545 non DNA-binding) proteins and using jackknife validation, StackDPPred achieved an ACC of 89.96%, MCC of 0.799 and AUC of 94.50%. This outcome outperforms several state-of-the-art approaches. Furthermore, when tested on recently designed two independent test datasets, StackDPPred outperforms existing approaches consistently. The proposed StackDPPred can be used for effective prediction of DNA-binding proteins from sequence alone.

Availability and implementation

Online server is at http://bmll.cs.uno.edu/add and code-data is at http://cs.uno.edu/∼tamjid/Software/StackDPPred/code_data.zip.

Supplementary information

Supplementary data are available at Bioinformatics online.
Posterior Fusiform and Midfusiform Contribute to Distinct Stages of Facial Expression Processing
Authors: Li Yuanning , Richardson R Mark , Ghuman Avniel Singh
Published: July 2018

Though the fusiform is well-established as a key node in the face perception network, its role in facial expression processing remains unclear, due to competing models and discrepant findings. To help resolve this debate, we recorded from 17 subjects with intracranial electrodes implanted in face sensitive patches of the fusiform. Multivariate classification analysis showed that facial expression information is represented in fusiform activity and in the same regions that represent identity, though with a smaller effect size. Examination of the spatiotemporal dynamics revealed a functional distinction between posterior fusiform and midfusiform expression coding, with posterior fusiform showing an early peak of facial expression sensitivity at around 180 ms after subjects viewed a face and midfusiform showing a later and extended peak between 230 and 460 ms. These results support the hypothesis that the fusiform plays a role in facial expression perception and highlight a qualitative functional distinction between processing in posterior fusiform and midfusiform, with each contributing to temporally segregated stages of expression perception.
IgE repertoire and immunological memory: compartmental regulation and antibody function
Authors: Gould Hannah J , Wu Yu-Chang Bryan
Published: July 2018

It is now generally recognized that bone marrow is the survival niche for antigen-specific plasma cells with long-term immunological memory. These cells release antibodies into the circulation, needed to prime effector cells in the secondary immune response. These antibodies participate in the surveillance for antigen and afford immune defence against pathogens and toxins previously encountered in the primary immune response. IgE antibodies function together with their effector cells, mast cells, to exert ‘immediate hypersensitivity’ in mucosal tissues at the front line of immune defence. The constant supply of IgE antibodies from bone marrow plasma cells allows the rapid ‘recall response’ by mast cells upon re-exposure to antigen even after periods of antigen absence. The speed and sensitivity of the IgE recall response and potency of the effector cell functions are advantageous in the early detection and elimination of pathogens and toxins at the sites of attack. Local antigen provocation also stimulates de novo synthesis of IgE or its precursors of other isotypes that undergo IgE switching in the mucosa. This process, however, introduces a delay before mast cells can be sensitized and resume activity; this is terminated shortly after the antigen is eliminated. Recent results from adaptive immune receptor repertoire sequencing of immunoglobulin genes suggest that the mucosal IgE+ plasmablasts, which have undergone affinity maturation in the course of their evolution in vivo, are a source of long-lived IgE+ plasma cells in the bone marrow that are already fully functional.
Clinical and Genomic Features of the First Cases of Elizabethkingia anophelis Infection in New York, Including the First Case in a Healthy Infant Without Previous Nosocomial Exposure
Authors: Snesrud Erik , McGann Patrick , Walsh Edward , Ong Ana , Maybank Rosslyn , Kwak Yoon , Campbell Jean , Jones Anthony , Vore Kelly , Hinkle Mary , Lesho Emil
Published: July 2018

Elizabethkingia spp are Gram-negative bacteria associated with neonatal meningitis. In 2015–2016, an outbreak of Elizabethkingia anophelis infection that involved 63 patients and 18 deaths occurred in Wisconsin. Despite a multistate investigation, as of September 2016 the source remained undetermined, and experts warned of reemergence. We describe here the first cases of E anophelis infection in New York, including the case of a healthy infant without previous healthcare contact.
Comforts, Clubs, and the Casino: Food and the Perpetuation of the British Class System in First World War Civilian Internment Camps
Authors: Durbach Nadja
Published: July 2018

Internment in camps for enemy aliens during the First World War might have led to a commonality of experience given that all civilian prisoners of war (POWs) were theoretically enduring the same material conditions. However, the privileges associated with social rank and with wealth led to profoundly different bodily regimes within these camps. The British class system was in fact perpetuated within the civilian internment camps established in the United Kingdom and among British subjects interned by the enemy, particularly in relation to the consumption of additional and superior food and drink that arrived in parcels from home and was provided at camp facilities for the privileged. These class distinctions had tangible material consequences for the interned, as not all bodies were equally subjected to the privations of the camp regime. That some POWs had access to more and better food throughout much of the First World War underscores the British state’s lack of commitment to the ideal of equality of bodily sacrifice. Instead the British government was complicit in perpetuating class inequalities both among its own subjects and those it had interned, even during a moment of international crisis when the social order was clearly being upended.
Plasma potassium ranges associated with mortality across stages of chronic kidney disease: the Stockholm CREAtinine Measurements (SCREAM) project
Authors: Gasparini Alessandro , Evans Marie , Barany Peter , Xu Hairong , Jernberg Tomas , Ärnlöv Johan , Lund Lars H , Carrero Juan-Jesús
Published: July 2018

Background

Small-scale studies suggest that hyperkalaemia is a less threatening condition in chronic kidney disease (CKD), arguing adaptation/tolerance to potassium (K+) retention. This study formally evaluates this hypothesis by estimating the distribution of plasma K+ and its association with mortality across CKD stages.

Methods

This observational study included all patients undergoing plasma K+ testing in Stockholm during 2006–11. We randomly selected one K+ measurement per patient and constructed a cross-sectional cohort with mortality follow-up. Covariates included demographics, comorbidities, medications and estimated glomerular filtration rate (eGFR). We estimated K+ distribution and defined K+ ranges associated with 90-, 180- and 365-day mortality.

Results

Included were 831 760 participants, of which 70 403 (8.5%) had CKD G3 (eGFR <60–30 mL/min) and 8594 (1.1%) had CKD G4–G5 (eGFR <30 mL/min). About 66 317 deaths occurred within a year. Adjusted plasma K+ increased across worse CKD stages: from median 3.98 (95% confidence interval 3.49–4.59) for eGFR >90 to 4.43 (3.22–5.65) mmol/L for eGFR ≤15 mL/min/1.73 m2. The association between K+ and mortality was U-shaped, but it flattened at lower eGFR strata and shifted upwards. For instance, the range where the 90-day mortality risk increased by no more than 100% was 3.45–4.94 mmol/L in eGFR >60 mL/min, but was 3.36–5.18  in G3 and 3.26–5.53 mmol/L in G4–G5. In conclusion, CKD stage modifies K+ distribution and the ranges that predict mortality in the community.

Conclusion

Although this study supports the view that hyperkalaemia is better tolerated with worse CKD, it challenges the current use of a single optimal K+ range for all patients.