bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of the TgrB1–TgrC1 cell adhesion complex during Dictyostelium discoideum development
Authors: Chen Gong , Xu Xiaoqun , Wu Xiangfu , Thomson Alexander , Siu Chi-Hung 
Published: February 2014

In Dictyostelium discoideum, TgrB1 and TgrC1 are partners of a heterophilic cell-adhesion system. To investigate its assembly process, the split GFP complementation assay was used to track the oligomeric status of both proteins. The ability of TgrC1 to form cis-homodimers spontaneously was demonstrated by fluorescence complementation studies and confirmed by chemical cross-linking. In contrast, TgrB1 failed to form cis-homodimers in the absence of TgrC1. Treatment of cell aggregates with antibodies against TgrB1 or TgrC1 did not affect TgrC1 dimerization, but inhibited TgrB1 dimer formation, suggesting that TgrB1 cis-homodimerization is dependent on trans-interaction with TgrC1. When TgrB1 and TgrC1 conjugated with the complementary halves of GFP were co-expressed in cells, cis-heterodimers were not detected. However, weak FRET signals were detected in cells expressing TgrB1–RFP and TgrC1–GFP, suggesting that TgrB1 dimers and TgrC1 dimers were arranged juxtapose to each other in the adhesion complex. The results of the present study suggest that the assembly process is initiated upon trans-interaction of monomeric TgrB1 with TgrC1 homodimers on adjacent cells, which triggers the formation of TgrB1 dimers. The homodimerization of TgrB1 in turn induces the clustering of TgrB1 and TgrC1, and the coalescence of TgrB1–TgrC1 clusters results in the formation of large adhesion complexes.
Phonological Assessment and Analysis of Bilingual Preschoolers' Spanish and English Word Productions
Authors: Prezas Raúl Francisco , Hodson Barbara Williams , Schommer-Aikins Marlene 
Published: February 2014

Purpose
The major purpose of this study was to examine Spanish and English phonological productions (patterns/deviations) of typically developing bilingual preschool children. Phonological scores were compared in order to determine if significant differences exist between (a) boys and girls, (b) 4- and 5-year-olds, and/or (c) their productions of Spanish and English words.

Method
Fifty-six bilingual 4- and 5-year-old children (27 boys and 29 girls) who attended Head Start programs named stimulus items for Spanish and English phonological assessment instruments that were similar in procedures and analyses.

Results
Multivariate analyses indicated no significant differences for phonological scores between boys and girls or between the 2 languages. Differences between the 4- and 5-year-olds, however, were significant, with the 5-year-olds performing better than the 4-year-olds. Liquid deviations and omissions of consonants in clusters/sequences were the most frequently occurring phonological deviations.

Conclusions
Phonological score differences between typically developing bilingual Spanish–English-speaking preschool boys and girls from similar backgrounds are not likely to be significant. Better phonological scores, however, can be expected for 5-year-olds than for 4-year-olds. Moreover, phonological deviation percentage scores of typically developing bilingual children for comparable Spanish and English assessment instruments are likely to be similar.
Inferring Speaker Attributes in Adductor Spasmodic Dysphonia: Ratings From Unfamiliar Listeners
Authors: Isetti Derek , Xuereb Linnea , Eadie Tanya L. 
Published: February 2014

Purpose
To determine whether unfamiliar listeners' perceptions of speakers with adductor spasmodic dysphonia (ADSD) differ from control speakers on the parameters of relative age, confidence, tearfulness, and vocal effort and are related to speaker-rated vocal effort or voice-specific quality of life.

Method
Twenty speakers with ADSD (including 6 speakers with ADSD plus tremor) and 20 age- and sex-matched controls provided speech recordings, completed a voice-specific quality-of-life instrument (Voice Handicap Index; Jacobson et al., 1997), and rated their own vocal effort. Twenty listeners evaluated speech samples for relative age, confidence, tearfulness, and vocal effort using rating scales.

Results

Listeners judged speakers with ADSD as sounding significantly older, less confident, more tearful, and more effortful than control speakers (
p
< .01). Increased vocal effort was strongly associated with decreased speaker confidence (
r
s = .88–.89) and sounding more tearful (
r
s = .83–.85). Self-rated speaker effort was moderately related (
r
s = .45–.52) to listener impressions. Listeners' perceptions of confidence and tearfulness were also moderately associated with higher Voice Handicap Index scores (
r
s = .65–.70).

Conclusion
Unfamiliar listeners judge speakers with ADSD more negatively than control speakers, with judgments extending beyond typical clinical measures. The results have implications for counseling and understanding the psychosocial effects of ADSD.
FeCoSiBNbCu bulk metallic glass with large compressive deformability studied by time-resolved synchrotron X-ray diffraction
Authors: Stoica Mihai , Scudino Sergio , Bednarčik Jozef , Kaban Ivan , Eckert Jürgen 
Published: February 2014

By adding 0.5 at. % Cu to the strong but brittle [(Fe0.5Co0.5)0.75Si0.05B0.20]96Nb4 bulk metallic glass, fully amorphous rods with diameters up to 2 mm were obtained. The monolithic samples with 1 mm diameter revealed a fracture strain of 3.80% and a maximum stress of 4143 MPa upon compression, together with a slight work-hardening behavior. SEM micrographs of fractured samples did neither reveal any shear bands on the lateral surface nor the typical vein patterns which characterize ductile fracture. However, some layers appear to have flowed and this phenomenon took place before the brittle final fracture. An estimate of the temperature rise ΔT in the shear plane gives 1039 K, which is large enough to melt a layer of 120 nm. The overall performance and the macroscopic plastic strain depend on the interaction between cleavage-like and viscous flow-like features. Mechanical tests performed in-situ under synchrotron radiation allowed the calculation of the strain tensor components, using the reciprocal-space data and analyzing the shift of the first (the main) and the second broad peak positions in the X-ray diffraction patterns. The results revealed that each atomic shell may have a different stiffness, which may explain the macroscopic compressive plastic deformation. Also, there were no signs of (nano) crystallization induced by the applied stress, but the samples preserve a monolithic amorphous structure until catastrophic failure occurs.
Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2–V3 interaction and modulates neutralization sensitivity
Authors: Cimbro Raffaello , Gallant Thomas R. , Dolan Michael A. , Guzzo Christina , Zhang Peng , Lin Yin , Miao Huiyi , Van Ryk Donald , Arthos James , Gorshkova Inna , Brown Patrick H. , Hurt Darrell E. , Lusso Paolo 
Published: February 2014

Significance
Despite intensive efforts, the structure of the native HIV-1 envelope trimer—the sole relevant target for vaccine design—has remained elusive. Our work identifies a key structural constraint that stabilizes the native envelope conformation and modulates its sensitivity to neutralization. We show that this constraint is established by previously unrecognized sulfated tyrosines within the second variable loop (V2) of the envelope glycoprotein subunit gp120, which mediate intramolecular interaction with the base of the third variable loop, V3. Strikingly, the V2 sulfotyrosines functionally mimic those present in the N terminus of the CCR5 coreceptor, which bind to the same V3 region. Our results shed light on the mechanisms adopted by HIV-1 to elude immunologic control and open new perspectives for vaccine design.
Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression
Authors: Rogier Eric W. , Frantz Aubrey L. , Bruno Maria E. C. , Wedlund Leia , Cohen Donald A. , Stromberg Arnold J. , Kaetzel Charlotte S. 
Published: February 2014

SignificanceAn experimental system was developed in mice to study the long-term benefits of early exposure to secretory antibodies of the IgA class (SIgA) in breast milk. We found that breast milk-derived SIgA promoted intestinal epithelial barrier function in suckling neonates, preventing systemic infection by potential pathogens. Long-term benefits of early exposure to SIgA included maintenance of a healthy gut microbiota and regulation of gene expression in intestinal epithelial cells. These findings suggest that maternal antibodies provide benefits to the intestinal immune system of the breast-fed infant, which persist into adulthood.
Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling
Authors: Kasperkiewicz Paulina , Poreba Marcin , Snipas Scott J. , Parker Heather , Winterbourn Christine C. , Salvesen Guy S. , Drag Marcin 
Published: February 2014

SignificanceThe exploration of protease substrate specificity is generally restricted to naturally occurring amino acids, limiting the degree of conformational space that can be surveyed. We substantially enhanced this by incorporating 102 unnatural amino acids to explore the S1–S4 pockets of human neutrophil elastase. This approach provides hybrid natural and unnatural amino acid sequences, and thus we termed it the Hybrid Combinatorial Substrate Library. Using this approach, we have designed an extremely active substrate of NE and subsequently converted it into an ultrasensitive activity-based probe for imaging active elastase during the process of neutrophil extracellular trap formation. Our study could have a substantial effect on the design of substrates, inhibitors, and probes for any endopeptidase.
Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign
Authors: Tran Karen , Poulsen Christian , Guenaga Javier , de Val Natalia , Wilson Richard , Sundling Christopher , Li Yuxing , Stanfield Robyn L. , Wilson Ian A. , Ward Andrew B. , Karlsson Hedestam Gunilla B. , Wyatt Richard T. 
Published: February 2014

Significance
The development of broadly neutralizing antibodies (bNAbs) to HIV-1 is often thought to be a key component of a successful vaccine. A common target of bNAbs is the conserved CD4 binding site (CD4bs) on the HIV envelope glycoprotein (Env) trimeric spike. Although CD4bs-directed bNAbs have been isolated from infected individuals, elicitation of such bNAbs by Env vaccination has proven difficult. To help understand the limitations of current immunogens, we structurally characterized two vaccine-elicited, CD4bs-directed non-bNAbs from primates. We demonstrate that these vaccine-elicited Abs attempt a vertical approach to the CD4bs, thereby clashing with the variable region of the trimeric spike cap, whereas CD4bs-directed bNAbs adopt angles of approach that avoid such clashes. This analysis can inform future vaccine redesign.
Functional and genetic studies of isolated cells from parathyroid tumors reveal the complex pathogenesis of parathyroid neoplasia
Authors: Shi Yuhong , Hogue Joyce , Dixit Darshana , Koh James , Olson John A. 
Published: February 2014

Significance
Parathyroid adenomas, the main cause of primary hyperparathyroidism (PHPT), are thought to result from clonal expansion of tumor cells and to be insensitive to normal calcium feedback due to the loss of the calcium-sensing receptor (CASR). Utilizing flow cytometric analysis to isolate and individually study oxyphil cells, chief cells, and lymphocytes from resected parathyroid tumors and glands, we now report previously unrecognized heterogeneity in these tissues with respect to calcium responsiveness, CASR expression, and clonal origin of parathyroid tumors. Such heterogeneity of parathyroid adenomas likely reflects the complex etiopathogenesis and clinical heterogeneity of PHPT.
BMP signaling requires retromer-dependent recycling of the type I receptor
Authors: Gleason Ryan J. , Akintobi Adenrele M. , Grant Barth D. , Padgett Richard W. 
Published: February 2014

Significance
The mechanisms that mediate bone morphogenetic protein (BMP) receptor recycling, and the importance of such recycling for signaling in vivo, have remained poorly understood. We find that the retromer complex functions as a linchpin in the recycling of the BMP type I receptor SMA-6 (small-6). In the absence of retromer-dependent recycling, retromer mutants result in the missorting of SMA-6 to lysosomes and a loss of BMP-mediated signaling. Surprisingly, we find that the BMP type II receptor, DAF-4 (dauer formation-defective-4), recycles through a distinct recycling pathway. Taken together, our results indicate a mechanism that separates the type I and type II receptors during receptor recycling, potentially terminating signaling while preserving both receptors for further rounds of activation.
UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs
Authors: Pirooz Sara Dolatshahi , He Shanshan , Zhang Tian , Zhang Xiaowei , Zhao Zhen , Oh Soohwan , O’Connell Douglas , Khalilzadeh Payam , Amini-Bavil-Olyaee Samad , Farzan Michael , Liang Chengyu 
Published: February 2014

Significance
Negative-strand RNA viruses are highly pathogenic and cause many severe diseases in humans and animals. These viruses generally use existing cellular pathways to enter cells, which involves intensive interaction with the endomembrane network, offering the endocytic pathway as an attractive scheme for therapeutic intervention. Molecular mechanisms governing virus entry remain incompletely understood. We found that UV-radiation resistance-associated gene, well known for regulating autophagy and intracellular trafficking, is a critical factor for virus entry through combinatorial interactions with a tether and endosomal SNAREs. Understanding the mechanism that allows the virus to interact with late endocytic organelles could identify the specific set of proteins that have a role in virus entry, which will help us to design specific therapeutic agents against endocytic virus entries.
Structural basis for the electron transfer from an open form of NADPH-cytochrome P450 oxidoreductase to heme oxygenase
Authors: Sugishima Masakazu , Sato Hideaki , Higashimoto Yuichiro , Harada Jiro , Wada Kei , Fukuyama Keiichi , Noguchi Masato 
Published: February 2014

Significance
Heme oxygenase (HO) is a key enzyme for heme degradation that is deeply involved in iron homeostasis, defensive reaction against oxidative stress, and signal transduction mediated by carbon monoxide. To complete a single HO reaction, seven electrons supplied from NADPH-cytochrome P450 reductase (CPR) are required. Based on crystallography, X-ray scattering, and NMR analyses of CPR, it has been proposed that CPR has a dynamic equilibrium of the “closed-open transition.” The crystal structure of the transient complex of CPR with heme-bound HO clearly demonstrated that it is the open form of CPR that can interact with and transfer electrons to heme-bound HO. Moreover, the complex structure provides a scaffold to research the protein–protein interactions between CPR and other redox partners.
Long-distance mechanism of neurotransmitter recycling mediated by glial network facilitates visual function in
Drosophila
Authors: Chaturvedi Ratna , Reddig Keith , Li Hong-Sheng 
Published: February 2014

Significance
Neurons communicate at synapses through neurotransmitters. For sustained neuronal signaling, neurotransmitters are recycled after release from neuronal terminals. During this process, perisynaptic glial cells take in and convert neurotransmitters such as glutamate, GABA, and histamine into inactive metabolites for transport. It has been assumed that inactive metabolites are delivered directly into neighboring neuronal terminals for neurotransmitter regeneration. Our work in the fruit fly, however, demonstrates that a gap junction-dependent multicellular glial network transports metabolites of histamine between perisynaptic glia and cell bodies of photoreceptor neurons, and this is required for visual signal transmission and alert behavior. Thus, by mediating this novel, long-distance recycling of neurotransmitters, intercellular glial networks play an important role in the maintenance of neuronal functions.
IgH
class switching exploits a general property of two DNA breaks to be joined
in cis
over long chromosomal distances
Authors: Gostissa Monica , Schwer Bjoern , Chang Amelia , Dong Junchao , Meyers Robin M. , Marecki Gregory T. , Choi Vivian W. , Chiarle Roberto , Zarrin Ali A. , Alt Frederick W. 
Published: February 2014

Significance
During an immune response, B lymphocytes generate different classes of antibodies better suited to protect against particular pathogens by making two chromosomal cuts that are joined to replace one type of antibody gene with a different one. These cuts happen in widely separated segments of the chromosome that must be physically adjacent to be joined. We have asked how this happens. The surprising answer is that genes and gene segments lying certain distances apart on any chromosome may actually be packaged such that both are frequently touching or nearly touching and, if broken, can be efficiently joined by general processes that repair breaks in all our genes. The joining mechanisms we describe also may contribute to genetic deletions in cancers.
Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification
Authors: Alekseyenko Artyom A. , Gorchakov Andrey A. , Kharchenko Peter V. , Kuroda Mitzi I. 
Published: February 2014

Significance
The fidelity of gene expression is regulated by chromosome-associated protein complexes. A traditional approach to characterizing complexes bound to chromosomes requires their release from the DNA to solubilize them. Here we develop an alternative approach, BioTAP-XL, that allows identification of protein–protein interactions while complexes remain linked to the DNA. We focus on protein interactions and genome localization of human EZH2 and two of its relatively uncharacterized interactors, C10orf12 and C17orf96. Our results provide strong evidence for diversity in human Polycomb repressive complexes, which are composed of factors essential for gene silencing during development in higher organisms. We propose that BioTAP-XL is an effective general approach for investigating the composition and subunit diversity of chromosome-associated complexes.
Measuring analyticity and syntheticity in creoles
Authors: Siegel Jeff , Szmrecsanyi Benedikt , Kortmann Bernd 
Published: February 2014

Creoles (here including expanded pidgins) are commonly viewed as being more analytic than their lexifiers and other languages in terms of grammatical marking. The purpose of the study reported in this article was to examine the validity of this view by measuring the frequency of analytic (and synthetic) markers in corpora of two different English-lexified creoles — Tok Pisin and Hawai‘i Creole — and comparing the quantitative results with those for other language varieties.To measure token frequency, 1,000 randomly selected words in each creole corpus were tagged with regard to word class, and categorized as being analytic, synthetic, both analytic and synthetic, or purely lexical. On this basis, an Analyticity Index and a Syntheticity Index were calculated. These were first compared to indices for other languages and then to L1 varieties of English (e.g. standard British and American English and British dialects) and L2 varieties (e.g. Singapore English and Hong Kong English). Type frequency was determined by the size of the inventories of analytic and synthetic markers used in the corpora, and similar comparisons were made.The results show that in terms of both token and type frequency of grammatical markers, the creoles are not more analytic than the other varieties. However, they are significantly less synthetic, resulting in much higher ratios of analytic to synthetic marking. An explanation for this finding relates to the particular strategy for grammatical expansion used by individuals when the creoles were developing.
On the origins of Chota Valley Spanish
Authors: Sessarego Sandro 
Published: February 2014

Chota Valley Spanish (CVS) is an Afro-Hispanic dialect spoken in the provinces of Imbabura and Carchi, Ecuador. The structure of CVS is relatively similar to Spanish, even though the conditions that characterized colonial Chota Valley seem — at a first glance — to have been ideal for a creole language to develop: a low white/black ratio, harsh working conditions on sugarcane plantations, massive introduction of African-born workers, and minimal contact with the outside Spanish speaking world (Schwegler 1999: 240; McWhorter 2000: 10–11). Two main hypotheses have been proposed to account for this fact: (a) the Monogenesis Hypothesis (Schwegler 1999); (b) the Afrogenesis Hypothesis (McWhorter 2000).In the present paper, the linguistic and sociohistorical evidence available for CVS is analyzed. Findings indicate that the long assumed creolizing conditions for CVS were not in place in colonial Chota Valley and therefore hypotheses (a) and (b) do not accurately explain the true nature and evolution of this language. The present study suggests that CVS can be better analyzed as the result of intermediate and advanced second language acquisition processes, which do not imply a previous creole stage.
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities
Authors: Klus Petr , Bolognesi Benedetta , Agostini Federico , Marchese Domenica , Zanzoni Andreas , Tartaglia Gian Gaetano 
Published: February 2014

Abstract
Motivation: The recent shift towards high-throughput screening is posing new challenges for the interpretation of experimental results. Here we propose the cleverSuite approach for large-scale characterization of protein groups.
Description: The central part of the cleverSuite is the cleverMachine (CM), an algorithm that performs statistics on protein sequences by comparing their physico-chemical propensities. The second element is called cleverClassifier and builds on top of the models generated by the CM to allow classification of new datasets.
Results: We applied the cleverSuite to predict secondary structure properties, solubility, chaperone requirements and RNA-binding abilities. Using cross-validation and independent datasets, the cleverSuite reproduces experimental findings with great accuracy and provides models that can be used for future investigations.
Availability: The intuitive interface for dataset exploration, analysis and prediction is available at http://s.tartaglialab.com/clever_suite.
Contact: gian.tartaglia@crg.es
Supplementary information: Supplementary data are available at Bioinformatics online.
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Authors: Paulsen Jonas , Sandve Geir Kjetil , Gundersen Sveinung , Lien Tonje G. , Trengereid Kai , Hovig Eivind 
Published: February 2014

Abstract
Summary: Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models.
Availability and implementation: HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site.
Contact: jonaspau@ifi.uio.no
Supplementary Information: Supplementary data are available at Bioinformatics online.