bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inter-residue coupling contributes to high-affinity subtype-selective binding of α-bungarotoxin to nicotinic receptors
Authors: Sine Steven M. , Huang Sun , Li Shu-Xing , daCosta Corrie J. B. , Chen Lin 
Published: June 2013

The crystal structure of a pentameric α7 ligand-binding domain chimaera with bound α-btx (α-bungarotoxin) showed that of the five conserved aromatic residues in α7, only Tyr184 in loop C of the ligand-binding site was required for high-affinity binding. To determine whether the contribution of Tyr184 depends on local residues, we generated mutations in an α7/5HT3A (5-hydroxytryptamine type 3A) receptor chimaera, individually and in pairs, and measured 125I-labelled α-btx binding. The results show that mutations of individual residues near Tyr184 do not affect α-btx affinity, but pairwise mutations decrease affinity in an energetically coupled manner. Kinetic measurements show that the affinity decreases arise through increases in the α-btx dissociation rate with little change in the association rate. Replacing loop C in α7 with loop C from the α-btx-insensitive α2 or α3 subunits abolishes high-affinity α-btx binding, but preserves acetylcholine-elicited single channel currents. However, in both the α2 and α3 construct, mutating either residue that flanks Tyr184 to its α7 counterpart restores high-affinity α-btx binding. Analogously, in α7, mutating both residues that flank Tyr184 to the α2 or α3 counterparts abolishes high-affinity α-btx binding. Thus interaction between Tyr184 and local residues contributes to high-affinity subtype-selective α-btx binding.
Writing Treatment for Aphasia: A Texting Approach
Authors: Beeson Pélagie M. , Higginson Kristina , Rising Kindle 
Published: June 2013

PurposeTreatment studies have documented the therapeutic and functional value of lexical writing treatment for individuals with severe aphasia. The purpose of this study was to determine whether such retraining could be accomplished using the typing feature of a cellular telephone, with the ultimate goal of using text messaging for communication.MethodA 31-year-old man with persistent Broca's aphasia, severe apraxia of speech, global dysgraphia, and right hemiparesis participated in this study. Using a multiple baseline design, relearning and maintenance of single-word spellings (and oral naming) of targeted items were examined in response to traditional Copy and Recall Treatment (CART) for handwriting and a new paradigm using 1-handed typing on a cell phone keyboard (i.e., a texting version of CART referred to as T-CART).ResultsMarked improvements were documented in spelling and spoken naming trained in either modality, with stronger maintenance for handwriting than cell phone typing. Training resulted in functional use of texting that continued for 2 years after treatment.ConclusionsThese results suggest that orthographic retraining using a cell phone keyboard has the potential to improve spelling knowledge and provide a means to improve functional communication skills. Combined training with both handwriting and cell phone typing should be considered in order to maximize the durability of treatment effects.
Influence of Analogy Instruction for Pitch Variation on Perceptual Ratings of Other Speech Parameters
Authors: Tse Andy C. Y. , Wong Andus W-K. , Ma Estella P-M. , Whitehill Tara L. , Masters Rich S. W. 
Published: June 2013

Purpose

Analogy
is the similarity of different concepts on which a comparison can be based. Recently, an analogy of “waves at sea” was shown to be effective in modulating fundamental frequency (F
0
) variation. Perceptions of intonation were not examined, as the primary aim of the work was to determine whether analogy instruction had a negative impact on other parameters of the speech signal compared with explicit instruction. The purpose of this study was (a) to determine whether changes in the standard deviation of F
0
, acoustically, resulted in similar changes in the perception of pitch variability and (b) to determine the perceptual influence of analogy vs. explicit instructions on speech naturalness, loudness, and rate.

Method
Ten speech-language pathologists were asked to listen to and rate pitch variation, speech naturalness, loudness, and rate for 74 Cantonese speech samples using a visual analogue scale, which allowed raters to indicate their subjective perceptions of each parameter.

Results
It is revealed that listeners perceived pitch variation to be greater and speech to be more natural in analogy-instructed, rather than explicitly instructed, speech. No differences were perceived for ratings of speech loudness or speech rate.

Conclusion
It is concluded that analogy instruction has a less negative impact on the naturalness of speech than explicit instruction and may provide a better method by which to manipulate desired pitch variation.
Gain enhancement for wide bandwidth endfire antenna with I‐shaped resonator (ISR) structures
Authors: Sun Y.H. , Wen G.J. , Jin H.Y. , Wang P. , Huang Y.J. 
Published: June 2013

A broadband gain enhancement endfire antenna is presented. The gain enhancement is achieved by loading with an I‐shaped resonator (ISR) structure in the endfire direction. Broad bandwidth is realised by using a microstrip‐to‐coplanar balun and bowtie dipole elements, while gain enhancement is achieved by loading the ISR structure in the endfire direction. The measurements show that the ISR‐loaded antenna presents a gain of about 4–8 dB in the whole working band (4.5–9.5 GHz), which is about 2 dB more than the unloaded one. The advantages of broad bandwidth and high gain make this antenna valuable in wireless communication systems.
Laterally‐coupled distributed feedback laser with first‐order gratings by interference lithography
Authors: Li Jingsi , Cheng Julian 
Published: June 2013

The first laterally‐coupled distributed feedback (DFB) laser with first‐order sidewall gratings fabricated by optical interference lithography is experimentally demonstrated. The gratings were first etched into a dielectric mask on the planar top surface of an InP/AlGaInAs laser epiwafer, and then transferred to both sidewalls of a 2 µm deep ridge‐waveguide structure using a novel self‐aligned process. DFB ridge‐waveguide lasers with a cavity length of 650 µm and width of 2.6 µm (with 300 nm gratings on both sidewalls) achieved single longitudinal mode continuous‐wave operation, with a sidemode suppression ratio of 37 dB. The threshold current density is 1.7 kA/cm2 at room temperature, and the slope efficiency is 0.14 mW/mA per facet (uncoated).
Piezoresistive bridge microcantilevers biosensor based on SOI wafer for glucose detecting
Authors: Wen Feng , Zhao Yuejin , Yu Xiaomei 
Published: June 2013

To measure glucose accurately, a high sensitivity piezoresistive four‐set Wheatstone bridge structure microcantilevers glucose biosensor was developed. The microcantilevers with a piezoresistor were fabricated using a series of bulk silicon processes based on a silicon‐on‐insulator wafer. An improved Wheatstone bridge readout circuit with voltage closed‐loop auto‐zero and high‐gain magnified functions is proposed. The sensing microcantilever gold‐coated surface was functionalised by immobilising a self‐assembled monolayer of 4‐mercaptophenylboronic acid, the reference cantilever was not functionalised. The relationship between a piezoresistive bridgeout caused by the microcantilevers bending and glucose solution concentration was obtained at 5 and 15 mM. Experimental results demonstrated that the output voltage induced by microcantilevers bending is proportional to the glucose concentrations and the sensitivity is up to 0.1 V/mM.
Solvent annealing induced phase separation and dewetting in PMMA/SAN blend film: Film thickness and solvent dependence
Authors: You Jichun , Zhang Shuangshuang , Huang Gang , Shi Tongfei , Li Yongjin 
Published: June 2013

The competition between “dewetting” and “phase separation” behaviors in polymer blend films attracts significant attention in the last decade. The simultaneous phase separation and dewetting in PMMA/SAN [poly(methyl methacrylate) and poly(styrene-ran-acrylonitrile)] blend ultrathin films upon solvent annealing have been observed for the first time in our previous work. In this work, film thickness and annealing solvent dependence of phase behaviors in this system has been investigated using atomic force microscopy and grazing incidence small-angle X-ray scattering (GISAXS). On one hand, both vertical phase separation and dewetting take place upon selective solvent vapor annealing, leading to the formation of droplet/mimic-film structures with various sizes (depending on original film thickness). On the other hand, the whole blend film dewets the substrate and produces dispersed droplets on the silicon oxide upon common solvent annealing. GISAXS results demonstrate the phase separation in the big dewetted droplets resulted from the thicker film (39.8 nm). In contrast, no period structure is detected in small droplets from the thinner film (5.1 nm and 9.7 nm). This investigation indicates that dewetting and phase separation in PMMA/SAN blend film upon solvent annealing depend crucially on the film thickness and the atmosphere during annealing.
Global patterns of terrestrial vertebrate diversity and conservation
Authors: Jenkins Clinton N. , Pimm Stuart L. , Joppa Lucas N. 
Published: June 2013

Significance
Identifying priority areas for biodiversity is essential for directing conservation resources. We mapped global priority areas using the latest data on mammals, amphibians, and birds at a scale 100 times finer than previous assessments. Priority areas have a higher—but still insufficient—rate of protection than the global average. We identify several important areas currently ignored by biodiversity hotspots, the current leading priority map. As the window of opportunity for expanding the global protected area network begins to close, identifying priorities at a scale practical for local action ensures our findings will help protect biodiversity most effectively.
Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields
Authors: Pruteanu-Malinici Iulian , Majoros William H. , Ohler Uwe 
Published: June 2013

AbstractMotivation: Computational approaches for the annotation of phenotypes from image data have shown promising results across many applications, and provide rich and valuable information for studying gene function and interactions. While data are often available both at high spatial resolution and across multiple time points, phenotypes are frequently annotated independently, for individual time points only. In particular, for the analysis of developmental gene expression patterns, it is biologically sensible when images across multiple time points are jointly accounted for, such that spatial and temporal dependencies are captured simultaneously.Methods: We describe a discriminative undirected graphical model to label gene-expression time-series image data, with an efficient training and decoding method based on the junction tree algorithm. The approach is based on an effective feature selection technique, consisting of a non-parametric sparse Bayesian factor analysis model. The result is a flexible framework, which can handle large-scale data with noisy incomplete samples, i.e. it can tolerate data missing from individual time points.Results: Using the annotation of gene expression patterns across stages of Drosophila embryonic development as an example, we demonstrate that our method achieves superior accuracy, gained by jointly annotating phenotype sequences, when compared with previous models that annotate each stage in isolation. The experimental results on missing data indicate that our joint learning method successfully annotates genes for which no expression data are available for one or more stages.Contact: uwe.ohler@duke.edu
Using state machines to model the Ion Torrent sequencing process and to improve read error rates
Authors: Golan David , Medvedev Paul 
Published: June 2013

Abstract
Motivation: The importance of fast and affordable DNA sequencing methods for current day life sciences, medicine and biotechnology is hard to overstate. A major player is Ion Torrent, a pyrosequencing-like technology which produces flowgrams – sequences of incorporation values – which are converted into nucleotide sequences by a base-calling algorithm. Because of its exploitation of ubiquitous semiconductor technology and innovation in chemistry, Ion Torrent has been gaining popularity since its debut in 2011. Despite the advantages, however, Ion Torrent read accuracy remains a significant concern.
Results: We present FlowgramFixer, a new algorithm for converting flowgrams into reads. Our key observation is that the incorporation signals of neighboring flows, even after normalization and phase correction, carry considerable mutual information and are important in making the correct base-call. We therefore propose that base-calling of flowgrams should be done on a read-wide level, rather than one flow at a time. We show that this can be done in linear-time by combining a state machine with a Viterbi algorithm to find the nucleotide sequence that maximizes the likelihood of the observed flowgram. FlowgramFixer is applicable to any flowgram-based sequencing platform. We demonstrate FlowgramFixer’s superior performance on Ion Torrent Escherichia coli data, with a 4.8% improvement in the number of high-quality mapped reads and a 7.1% improvement in the number of uniquely mappable reads.
Availability: Binaries and source code of FlowgramFixer are freely available at: http://www.cs.tau.ac.il/~davidgo5/flowgramfixer.html.
Contact: davidgo5@post.tau.ac.il
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution
Authors: Reinharz Vladimir , Ponty Yann , Waldispühl Jérôme 
Published: June 2013

Abstract
Motivations: The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity.
Results: In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure.
Availability: IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/
Contact: jeromew@cs.mcgill.ca or yann.ponty@lix.polytechnique.fr
Supplementary Information: Supplementary data are available at Bioinformatics online.
Predicting protein interactions via parsimonious network history inference
Authors: Patro Rob , Kingsford Carl 
Published: June 2013

Abstract
Motivation: Reconstruction of the network-level evolutionary history of protein–protein interactions provides a principled way to relate interactions in several present-day networks. Here, we present a general framework for inferring such histories and demonstrate how it can be used to determine what interactions existed in the ancestral networks, which present-day interactions we might expect to exist based on evolutionary evidence and what information extant networks contain about the order of ancestral protein duplications.
Results: Our framework characterizes the space of likely parsimonious network histories. It results in a structure that can be used to find probabilities for a number of events associated with the histories. The framework is based on a directed hypergraph formulation of dynamic programming that we extend to enumerate many optimal and near-optimal solutions. The algorithm is applied to reconstructing ancestral interactions among bZIP transcription factors, imputing missing present-day interactions among the bZIPs and among proteins from five herpes viruses, and determining relative protein duplication order in the bZIP family. Our approach more accurately reconstructs ancestral interactions than existing approaches. In cross-validation tests, we find that our approach ranks the majority of the left-out present-day interactions among the top 2 and 17% of possible edges for the bZIP and herpes networks, respectively, making it a competitive approach for edge imputation. It also estimates relative bZIP protein duplication orders, using only interaction data and phylogenetic tree topology, which are significantly correlated with sequence-based estimates.
Availability: The algorithm is implemented in C++, is open source and is available at http://www.cs.cmu.edu/ckingsf/software/parana2.
Contact: robp@cs.cmu.edu or carlk@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms
Authors: Xu Min , Alber Frank 
Published: June 2013

Abstract
Motivation: Cryo-electron tomography allows the imaging of macromolecular complexes in near living conditions. To enhance the nominal resolution of a structure it is necessary to align and average individual subtomograms each containing identical complexes. However, if the sample of complexes is heterogeneous, it is necessary to first classify subtomograms into groups of identical complexes. This task becomes challenging when tomograms contain mixtures of unknown complexes extracted from a crowded environment. Two main challenges must be overcomed: First, classification of subtomograms must be performed without knowledge of template structures. However, most alignment methods are too slow to perform reference-free classification of a large number of (e.g. tens of thousands) of subtomograms. Second, subtomograms extracted from crowded cellular environments, contain often fragments of other structures besides the target complex. However, alignment methods generally assume that each subtomogram only contains one complex. Automatic methods are needed to identify the target complexes in a subtomogram even when its shape is unknown.
Results: In this article, we propose an automatic and systematic method for the isolation and masking of target complexes in subtomograms extracted from crowded environments. Moreover, we also propose a fast alignment method using fast rotational matching in real space. Our experiments show that, compared with our previously proposed fast alignment method in reciprocal space, our new method significantly improves the alignment accuracy for highly distorted and especially crowded subtomograms. Such improvements are important for achieving successful and unbiased high-throughput reference-free structural classification of complexes inside whole-cell tomograms.
Contact: alber@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways
Authors: Abaka Gamze , Bıyıkoğlu Türker , Erten Cesim 
Published: June 2013

Abstract
Motivation: Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism.
Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.
Availability: Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/.
Contact: cesim@khas.edu.tr
Supplementary information: Supplementary data are available at Bioinformatics online.
Pipit: visualizing functional impacts of structural variations
Authors: Sakai Ryo , Moisse Matthieu , Reumers Joke , Aerts Jan 
Published: June 2013

Abstract
Summary: Pipit is a gene-centric interactive visualization tool designed to study structural genomic variations. Through focusing on individual genes as the functional unit, researchers are able to study and generate hypotheses on the biological impact of different structural variations, for instance, the deletion of dosage-sensitive genes or the formation of fusion genes. Pipit is a cross-platform Java application that visualizes structural variation data from Genome Variation Format files.
Availability: Executables, source code, sample data, documentation and screencast are available at https://bitbucket.org/biovizleuven/pipit.
Contact: ryo.sakai@esat.kuleuven.be
Supplementary information: Supplementary data are available at Bioinformatics online.