bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Signal Peptide Cleavage Sites with Subsite‐Coupled and Template Matching Fusion Algorithm
Authors: Zhang Shao‐Wu , Zhang Ting‐He , Zhang Jun‐Nan , Huang Yufei 
Published: March 2014

AbstractFast and effective prediction of signal peptides (SP) and their cleavage sites is of great importance in computational biology. The approaches developed to predict signal peptide can be roughly divided into machine learning based, and sliding windows based. In order to further increase the prediction accuracy and coverage of organism for SP cleavage sites, we propose a novel method for predicting SP cleavage sites called Signal‐CTF that utilizes machine learning and sliding windows, and is designed for N‐termial secretory proteins in a large variety of organisms including human, animal, plant, virus, bacteria, fungi and archaea. Signal‐CTF consists of three distinct elements: (1) a subsite‐coupled and regularization function with a scaled window of fixed width that selects a set of candidates of possible secretion‐cleavable segment for a query secretory protein; (2) a sum fusion system that integrates the outcomes from aligning the cleavage site template sequence with each of the aforementioned candidates in a scaled window of fixed width to determine the best candidate cleavage sites for the query secretory protein; (3) a voting system that identifies the ultimate signal peptide cleavage site among all possible results derived from using scaled windows of different width. When compared with Signal‐3L and SignalP 4.0 predictors, the prediction accuracy of Signal‐CTF is 4–12 %, 10–25 % higher than that of Signal‐3L for human, animal and eukaryote, and SignalP 4.0 for eukaryota, Gram‐positive bacteria and Gram‐negative bacteria, respectively. Comparing with PRED‐SIGNAL and SignalP 4.0 predictors on the 32 archaea secretory proteins of used in Bagos’s paper, the prediction accuracy of Signal‐CTF is 12.5 %, 25 % higher than that of PRED‐SIGNAL and SignalP 4.0, respectively. The predicting results of several long signal peptides show that the Signal‐CTF can better predict cleavage sites for long signal peptides than SignalP, Phobius, Philius, SPOCTOPUS, Signal‐CF and Signal‐3L. These results show that Signal‐CTF is more accurate and flexible in predicting signal peptides of different characteristics for many organisms. Signal‐CTF is freely available as a web‐server at http://darwin2.cbi.utsa.edu/minniweb/index.html.
Compact multiband antenna with CRLH‐TL ZOR for wireless USB dongle applications
Authors: Xing Jun , Li Long , Zhang Lu , Sun Hao , Shi Yan 
Published: March 2014

AbstractA compact multiband antenna with composite right‐ and left‐handed transmission line (CRLH‐TL) zeroth‐order resonator for wireless universal serial bus dongle applications is proposed in this article. The proposed antenna occupying a small volume of 12 × 28 × 5.8 mm3 comprises a folded monopole which can generate two resonant modes to cover the GSM850/900 (820–960 MHz) and the LTE2500 operation (2500–2690 MHz) and a CRLH‐TL ZOR structure which is capacitively excited by the folded monopole to generate zeroth‐order resonant mode to cover LTE700 (746–787 MHz). The proposed antenna offers nearly omnidirectional radiation patterns, the measured peak gain are obtained from 0.8 to 3.4 dBi, and measured antenna efficiency varies from about 40–56% in the whole operation band. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:1133–1138, 2014
Printed inverted‐L shaped monopole antenna with Parasitic Inverted‐F element for dual band applications
Authors: Verma Sudhanshu , Kumar Preetam 
Published: March 2014

ABSTRACTThis article presents a low‐profile dual band printed Inverted‐L (IL) shaped monopole antenna with Parasitic Inverted‐F (PIF) shaped element in the ground plane for 2.4/5.2/5.8 GHz wireless local area network applications simultaneously. Owing to coupling 006‐Ff microstrip line‐fed IL driven element and PIF element, a compact radiator of 8 × 12 mm2 is realized and tested. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:1163–1167, 2014
A new speech enhancement algorithm for millimeter‐wave radar speech sensor
Authors: Jiao Mingke , Lou Lin , Hu Jie , Geng Xiliang , Zhang Wenyuan , Zhang Peng , Wang Jianqi 
Published: March 2014

ABSTRACTA novel millimeter‐wave radar speech sensor based on vibration detection developed in our laboratory can penetrate nonmetal barriers to obtain speech signals, which expands traditional speech detection techniques. However, the radar speech signals are usually corrupted by nonuniform noises that include radar noise, electrocircuit noise, and so on. The article, therefore, proposed an improved Wiener filter method based on wavelet entropy (WE) to suppress the nonuniform noise. The utilization of WE contributes to the high efficiency of the algorithm for suppressing nonuniform radar noise. WE point detection can provide a basis through which radar noise can be accurately estimated and updated in an adaptive manner, resulting in accurate a priori signal‐to‐noise ratios obtained from updated noise estimations and reduction of nonuniform noise. The results from spectrogram and mean opinion score demonstrate that the radar nonuniform noise can be reduced efficiently, and the radar speech quality was improved effectively. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:1184–1189, 2014
Miniature dual‐mode dual‐band bandpass filter with improved passbands performance for 2.4/5.2 GHz WLAN application
Authors: Wu Yan‐liang , Liao Cheng , Xiong Xiang‐zheng , Zhou Hai‐jing 
Published: March 2014

ABSTRACTIn this article, a miniature dual‐mode dual‐band bandpass filter (BPF) based on novel complementary center‐stub‐loaded stepped‐impedance resonators has been presented. By loading an open stub at the center of stepped‐impedance resonator, the center frequency of the fundamental even‐mode could be independently controlled, whereas that of the fundamental odd‐mode is fixed. A dual‐mode dual‐band BPF using complementary configuration is implemented with three transmission zeros. To validate the design and analysis, a prototype filter has been designed and fabricated with its two bands located at 2.4/5.2 GHz for WLAN. The measured performances show good agreements with those of the coupling matrix analysis and electromagnetic simulation. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:1235–1238, 2014
Annealing of gold nanoparticles on GaP(111)B: initial stage of GaP nanowire growth
Authors: Eliáš Peter , Hasenöhrl Stanislav , Laurencíková Agáta , Rosová Alica , Novák Jozef 
Published: March 2014

AbstractGaP(111)B substrate was strewn with 30 nm colloidal Au nanoparticles. Organic residues were removed by: A) boiling in acetone and isopropylalcohol followed by a DI water rinse, B) treatment A + HF:H2O, C) treatment A + O2 plasma for 10 min, 20 min, and 40 min, and D) treatment A combined with O2 plasma (10 min) and HF:H2O. The substrate thus had original ‘epi‐ready' oxides (A), or fresh native oxides (B and D), or new added oxides (C). The samples were annealed at Ta = 650 °C for 10 min under PH3 and H2 in an MOVPE chamber. This resulted in the growth of GaP stumps along [111]B on each sample. Their length was <3 nm (B and D), ∼20 nm (A), and ∼220 nm (C 40 min). Elemental Ga is left as P2O5/Ga2O3 oxides form on etched GaP(111)B at room temperature. We believe that as the oxides disintegrated during annealing, they released the elemental Ga that combined with phosphorus from PH3, and this led to the growth of the GaP stumps. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nonlinear fractional‐order power system stabilizer for multi‐machine power systems based on sliding mode technique
Authors: Majidabad Sajjad Shoja , Shandiz Heydar Toosian , Hajizadeh Amin 
Published: March 2014

SummaryThis paper presents two novel nonlinear fractional‐order sliding mode controllers for power angle response improvement of multi‐machine power systems. First, a nonlinear block control is used to handle nonlinearities of the interconnected power system. In the second step, a decentralized fractional‐order sliding mode controller with a nonlinear sliding manifold is designed. Practical stability is achieved under the assumption that the upper bound of the fractional derivative of perturbations and interactions are known. However, when an unknown transient perturbation occurs in the system, it makes the evaluation of perturbation and interconnection upper bound troublesome. In the next step, an adaptive‐fuzzy approximator is applied to fix the mentioned problem. The fuzzy approximator uses adjacent generators relative speed as own inputs, which is known as semi‐decentralized control strategy. For both cases, the stability of the closed‐loop system is analyzed by the fractional‐order stability theorems. Simulation results for a three‐machine power system with two types of faults are illustrated to show the performance of the proposed robust controllers versus the conventional sliding mode. Additionally, the fractional parameter effects on the system transient response and the excitation voltage amplitude and chattering are demonstrated in the absence of the fuzzy approximator. Finally, the suggested controller is combined with a simple voltage regulator in order to keep the system synchronism and restrain the terminal voltage variations at the same time. Copyright © 2014 John Wiley & Sons, Ltd.
Analysis of compaction initiation in human embryos by using time-lapse cinematography
Authors: Iwata Kyoko , Yumoto Keitaro , Sugishima Minako , Mizoguchi Chizuru , Kai Yoshiteru , Iba Yumiko , Mio Yasuyuki 
Published: March 2014

Abstract

Purpose
To analyze the initiation of compaction in human embryos in vitro by using time-lapse cinematography (TLC), with the goal of determining the precise timing of compaction and clarifying the morphological changes underlying the compaction process.

Methods
One hundred and fifteen embryos donated by couples with no further need for embryo-transfer were used in this study. Donated embryos were thawed and processed, and then their morphological behavior during the initiation of compaction was dynamically observed via time-lapse cinematography (TLC) for 5 days.

Results
Although the initiation of compaction occurred throughout the period from the 4-cell to 16-cell stage, 99 (86.1 %) embryos initiated compaction at the 8-cell stage or later, with initiation at the 8-cell stage being most frequent (22.6 %). Of these 99 embryos, 49.5 % developed into good-quality blastocysts. In contrast, of the 16 (13.9 %) embryos that initiated compaction prior to the 8-cell stage, only 18.8 % developed into good-quality blastocysts. Embryos that initiated compaction before the 8-cell stage showed significantly higher numbers of multinucleated blastomeres, due to asynchronism in nuclear division at the third mitotic division resulting from cytokinetic failure.

Conclusions
The initiation of compaction primarily occurs at the third mitotic division or later in human embryos. Embryos that initiate compaction before the 8-cell stage are usually associated with aberrant embryonic development (i.e., cytokinetic failure accompanied by karyokinesis).
Direct evidence of central European forest refugia during the last glacial period based on mollusc fossils
Authors: Juřičková Lucie , Horáčková Jitka , Ložek Vojen 
Published: March 2014

AbstractAlthough there is evidence from molecular studies for the existence of central European last glacial refugia for temperate species, there is still a great lack of direct fossil records to confirm this theory. Here we bring such evidence in the form of fossil shells from twenty strictly forest land snail species, which were recorded in radiocarbon-dated late glacial or older mollusc assemblages of nine non-interrupted mollusc successions situated in the Western Carpathians, and one in the Bohemian Massif. We proposed that molluscs survived the last glacial period in central Europe in isolated small patches of broadleaf forest, which we unequivocally demonstrate for two sites of last glacial maximum age.
Primary undifferentiated high‐grade pleomorphic sarcoma/malignant fibrous histiocytoma arising from the mandible
Authors: Mori Yoshiyuki , Motoi Toru , Ida Komei , Shibahara Junji , Saijo Hideto , Susami Takafumi , Takato Tsuyoshi 
Published: March 2014

AbstractA patient who had a primary undifferentiated high‐grade pleomorphic sarcoma/malignant fibrous histiocytoma that apparently arose in the mandible, but showed uncertain differentiation on histopathological examination, is described. Our regimen, a combination of pre‐ and postoperative chemotherapy and surgical resection, produced a good outcome.
The gametogenic cycle and life history ofNicolea uspiana(Polychaeta: Terebellidae) on the south-east coast of Brazil
Authors: Garraffoni André Rinaldo Senna , Yokoyama Leonardo Querobim , Amaral Antonia Cecília Zacagnini 
Published: March 2014

The gametogenic cycle and life history ofNicolea uspiana(Nogueira, 2003) (Polychaeta: Terebellidae) was studied by taking monthly samples over a 13 month period. Each month, 10 females were sorted; 50 oocytes were removed from the coelom of each specimen, and the maximum diameter was determined. Additionally, 10 males were sorted and 100 gametes were randomly selected from each specimen to evaluate their shape and maturation stage. This species is gonochoric and exhibits slight external sexual dimorphism (in the shape of the nephridial papillae). The sex-ratio ofN. uspianawas 2.4 male for each female. The initial gametic stages of both sexes are produced in special structures called nephromixia. Oogenesis is extra-ovarian, and the germ cells are clumped and surrounded by follicle cells. These cells are ovulated into the coelomic fluid, and yolk synthesis occurs in this cavity. The maximum diameter of oocytes measured, 225 µm, showed that these eggs fall into the size-range for lecithotrophy. Furthermore,N. uspianais an iteroparous species, as the mature individuals can breed several times during their lifetime. Male gonads release germ cells early in development, and sperm maturation also occurs in the coelomic fluid. The male gametes consist of flattened plaques of germ cells attached on their anterior part by a cytophore assuming a rosette-like appearance. Following maturation of the male cells, the spermatids produce arrays of stiffly vibratile tails, assuming a morula shape. The reproductive patterns and life history of the terebellids are also discussed.
Investors prefer entrepreneurial ventures pitched by attractive men
Authors: Brooks Alison Wood , Huang Laura , Kearney Sarah Wood , Murray Fiona E. 
Published: March 2014

Significance
We identify a profound and consistent gender gap in entrepreneurship, a central path to job creation, economic growth, and prosperity. Across a field setting (three entrepreneurial pitch competitions in the United States) and two controlled experiments, we find that investors prefer entrepreneurial pitches presented by male entrepreneurs compared with pitches presented by female entrepreneurs, even when the content of the pitch is the same. This effect is moderated by male physical attractiveness: attractive males are particularly persuasive, whereas physical attractiveness does not matter among female entrepreneurs. These findings fundamentally advance the science related to gender, physical attractiveness, psychological persuasion, bias, role expectations, and entrepreneurship.
Testing Turing’s theory of morphogenesis in chemical cells
Authors: Tompkins Nathan , Li Ning , Girabawe Camille , Heymann Michael , Ermentrout G. Bard , Epstein Irving R. , Fraden Seth 
Published: March 2014

Significance
Turing proposed that intercellular reaction-diffusion of molecules is responsible for morphogenesis. The impact of this paradigm has been profound. We exploit an abiological experimental system of emulsion drops containing the Belousov–Zhabotinsky reactants ideally suited to test Turing’s theory. Our experiments verify Turing’s thesis of the chemical basis of morphogenesis and reveal a pattern, not previously predicted by theory, which we explain by extending Turing’s model to include heterogeneity. Quantitative experimental results obtained using this artificial cellular system establish the strengths and weaknesses of the Turing model, applicable to biology and materials science alike, and pinpoint which directions are required for improvement.
Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens
Authors: Franceschini Andrea , Meier Roger , Casanova Alain , Kreibich Saskia , Daga Neha , Andritschke Daniel , Dilling Sabrina , Rämö Pauli , Emmenlauer Mario , Kaufmann Andreas , Conde-Álvarez Raquel , Low Shyan Huey , Pelkmans Lucas , Helenius Ari , Hardt Wolf-Dietrich , Dehio Christoph , von Mering Christian 
Published: March 2014

SignificancePathogens can enter into human cells using a variety of specific mechanisms, often hitchhiking on naturally existing transport pathways. To uncover parts of the host machinery that are required for entry, scientists conduct infection screens in cultured cells. In these screens, human genes are systematically inactivated by short RNA oligos, designed to bind and inactivate mRNA molecules. Here, we show that many of these oligos additionally bind unintended mRNA targets as well, and that this effect overall dominates and complicates such screens. Focusing on the strong “off-target” signal, we design novel oligos that no longer bind any one gene specifically but nevertheless strongly and reproducibly block pathogen entry—pointing to pathogen/host interactions at a higher-order, pathway level.
Settlement length and temporal settlement patterns of juvenile cod (Gadus morhua), haddock (Melanogrammus aeglefinus), and whiting (Merlangius merlangus) in a northern North Sea coastal nursery area
Authors: Bastrikin Dorota K. , Gallego Alejandro , Millar Colin P. , Priede Imants G. , Jones Emma G. 
Published: March 2014

Abstract
Knowledge of settlement timing and duration, which has been identified as an important milestone for demersal fish, is critical to understanding population connectivity, relevant to the development of spatially—and temporally—resolved conservation measures, and recruitment variability, as important density-dependent dynamics may take place at this stage. To study the settlement ecology of cod haddock, and whiting, sampling was conducted over spring and summer 2004–2006 at the northern North Sea nursery area. Over 4000 0-group juveniles were collected. Settlement was associated with clear and progressive changes in the prey composition of these juveniles. The size of fish that could be considered settled was estimated as 49 (±3) mm for cod, 78 (±4) mm for haddock, and 85 (±6) mm for whiting. Clear differences in temporal settlement patterns were also apparent. Cod settled in a single pulse lasting about a month (mid-May to mid-June) and initially occupied shallower, inshore waters, whereas haddock settled in one pulse, lasting ∼2 weeks (second half of May), favouring deeper, farther offshore locations. Whiting settled much later in the season and over a more protracted period (early June to early August), and their depth preferences also changed over time and with increasing length.
Galaxy and Mass Assembly (GAMA): fine filaments of galaxies detected within voids
Authors: Alpaslan Mehmet , Robotham Aaron S. G. , Obreschkow Danail , Penny Samantha , Driver Simon , Norberg Peder , Brough Sarah , Brown Michael , Cluver Michelle , Holwerda Benne , Hopkins Andrew M. , van Kampen Eelco , Kelvin Lee S. , Lara-Lopez Maritza A. , Liske Jochen , Loveday Jon , Mahajan Smriti , Pimbblet Kevin 
Published: March 2014

Abstract
Based on data from the Galaxy and Mass Assembly (GAMA) survey, we report on the discovery of structures that we refer to as ‘tendrils’ of galaxies: coherent, thin chains of galaxies that are rooted in filaments and terminate in neighbouring filaments or voids. On average, tendrils contain six galaxies and span 10 h−1 Mpc. We use the so-called line correlation function to prove that tendrils represent real structures rather than accidental alignments. We show that voids found in the Sloan Digital Sky Survey, 7th data release survey that overlap with GAMA regions contain a large number of galaxies, primarily belonging to tendrils. This implies that void sizes are strongly dependent on the number density and sensitivity limits of a survey. We caution that galaxies in low-density regions, which may be defined as ‘void galaxies,’ will have local galaxy number densities that depend on such observational limits and are likely higher than those can be directly measured.
The effect of helium accretion efficiency on rates of Type Ia supernovae: double detonations in accreting binaries
Authors: Ruiter A. J. , Belczynski K. , Sim S. A. , Seitenzahl I. R. , Kwiatkowski D. 
Published: March 2014

Abstract
The double-detonation explosion scenario of Type Ia supernovae (SNe Ia) has gained increased support from the SN Ia community as a viable progenitor model, making it a promising candidate alongside the well-known single degenerate and double degenerate scenarios. We present delay times of double-detonation SNe, in which a sub-Chandrasekhar mass carbon–oxygen white dwarf (WD) accretes non-dynamically from a helium-rich companion. One of the main uncertainties in quantifying SN rates from double detonations is the (assumed) retention efficiency of He-rich matter. Therefore, we implement a new prescription for the treatment of accretion/accumulation of He-rich matter on WDs. In addition, we test how the results change depending on which criteria are assumed to lead to a detonation in the helium shell. In comparing the results to our standard case (Ruiter et al.), we find that regardless of the adopted He accretion prescription, the SN rates are reduced by only ∼25 per cent if low-mass He shells (≲0.05 M⊙) are sufficient to trigger the detonations. If more massive (0.1 M⊙) shells are needed, the rates decrease by 85 per cent and the delay time distribution is significantly changed in the new accretion model – only SNe with prompt (&lt;500 Myr) delay times are produced. Since theoretical arguments favour low-mass He shells for normal double-detonation SNe, we conclude that the rates from double detonations are likely to be high, and should not critically depend on the adopted prescription for accretion of He.
Mid-infrared period–luminosity relations of RR Lyrae stars derived from the AllWISE Data Release
Authors: Klein C. R. , Richards J. W. , Butler N. R. , Bloom J. S. 
Published: March 2014

Abstract
We use photometry from the recent AllWISE Data Release of the Wide-field Infrared Survey Explorer (WISE) of 129 calibration stars, combined with prior distances obtained from the established MV–[Fe/H] relation and Hubble Space Telescope trigonometric parallax, to derive mid-infrared period–luminosity relations for RR Lyrae pulsating variable stars. We derive relations in the W1, W2 and W3 wavebands (3.4, 4.6 and 12 μm, respectively), and for each of the two main RR Lyrae sub-types (RRab and RRc). We report an error on the period–luminosity relation slope for RRab stars of 0.2. We also fit posterior distances for the calibration catalogue and find a median fractional distance error of 0.8 per cent.