bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jagged-1 signaling suppresses the IL-6 and TGF-β treatment-induced Th17 cell differentiation via the reduction of RORγt/IL-17A/IL-17F/IL-23a/IL-12rb1
Authors: Wang Yuan , Xing Feiyue , Ye Siqi , Xiao Jia , Di Jingfang , Zeng Shan , Liu Jing 
Published: February 2015

AbstractJagged-1 signaling has recently been reported to be involved in the Th17 cell differentiation. However, little is known about its mechanisms. Soluble Jagged-1 was used to activate the Jagged-1–Notch signaling to interfere with the IL-6 and TGF-β-induced Th17 cell skewing. Genes relevant to the autoimmunity or inflammation were screened for the first time in this system by qPCR array for the differential expressions. The 18 genes out of 84, including Clec7a, Il12b, Il12rb1, Il12rb2, Csf3, Il15, Il17a, Il17f, Il17rc, Il17rd, Il17re, Il23a, Myd88, Socs1, Stat4, Stat5a, Sykb and Tbx21, were downregulated, but only Cxcl2, Cxcl12 and Mmp3 were upregulated. The expressions of the genes, Rorγt, Il17a, Il17f, Il12rb1 and Il23a, induced by simultaneous IL-6 and TGF-β treatment were significantly suppressed by Jagged-1, followed by the reduction of RORγt, IL-17A and IL-17F. Consistent with the attenuation of RORγt and the reduced production and secretion of IL-17A and IL-17F in the cell supernatant and the in situ stained cells, the number of CD4+IL-17+ cells was also diminished. It is concluded that the Jagged-1–Notch signaling can suppress the IL-6 and TGF-β treatment-induced Th17 cell skewing through the attenuation of RORγt and, hence by, the down-regulation of IL-17A, IL-17F, IL-23a and IL-12rb1.
The shift between the Red Queen and the Red King effects in mutualisms
Authors: Gao Lei , Li Yao-Tang , Wang Rui-Wu 
Published: February 2015

AbstractInterspecific mutualisms consist of partners trading services that yield common benefits to both species. Until now, understanding how the payoffs from mutualistic cooperation are allocated among the participants has been problematic. Two hypotheses have been proposed to resolve this problem. The Red Queen effect argues that faster-evolving species are favoured in co-evolutionary processes because they are able to obtain a larger share of benefits. Conversely, the Red King effect argues that the slower-evolving species gains a larger share of benefits. The model we propose shows that the allocations for a common benefit vary when the effect of a reward mechanism is included in the model. The outcome is a shift from the Red Queen effect to the Red King effect and vice versa. In addition, our model shows that either an asymmetry in payoff or an asymmetry in the number of cooperative partners causes a shift between the Red Queen effect and the Red King effect. Even in situations where the evolutionary rates are equal between the two species, asymmetries in rewards and in participant number lead to an uneven allocation of benefits among the partners.
Rab1A regulates anterograde melanosome transport by recruiting kinesin-1 to melanosomes through interaction with SKIP
Authors: Ishida Morié , Ohbayashi Norihiko , Fukuda Mitsunori 
Published: February 2015

AbstractMelanosomes are lysosome-related organelles in melanocytes that are transported from the perinucleus to the cell periphery by coordination between bidirectional (anterograde and retrograde) microtubule-dependent transport and unidirectional actin-dependent transport. Although the molecular machineries that mediate retrograde transport and actin-dependent transport have already been identified, little is known about the anterograde transport complex on microtubules in mammalian cells. Here we discovered that small GTPase Rab1A on melanosomes recruits SKIP/PLEKHM2 as a Rab1A-specific effector and that Rab1A, SKIP and a kinesin-1/(Kif5b+KLC2) motor form a transport complex that mediates anterograde melanosome transport in melanocytes. Interestingly, Arl8, Arf-like small GTPase that also interacts with SKIP, is specifically localized at lysosomes and regulates their anterograde transport in melanocytes. Our findings suggest that the anterograde microtubule-dependent transport of melanosomes and lysosomes are differently regulated by independent cargo receptors, i.e., Rab1A and Arl8, respectively, but that a SKIP–kinesin-1 mechanism is responsible for the transport of both.
Teaching Children Who Use Augmentative and Alternative Communication to Ask Inverted Yes/No Questions Using Aided Modeling
Authors: Kent-Walsh Jennifer , Binger Cathy , Buchanan Carolyn 
Published: February 2015

Purpose
This study investigated the effects of a direct intervention program involving aided modeling and the presentation of contrastive targets on the aided production of inverted yes/no questions and possible generalization to other sentence types by children using augmentative and alternative communication (AAC).

Method

A single-case, multiple-probe, experimental design across participants was used to evaluate the effects of the instructional program with 3 children who had motor speech disorders and used AAC (ages 4;10 [years;months], 6;2, and 4;9). The treatment involved aided modeling of treatment and contrastive targets through concentrated modeling and interactive play activities. Direct treatment outcomes were examined by measuring the accuracy of producing inverted yes/no questions and
to be
declaratives through probes.

Results

All 3 participants showed a direct treatment effect, producing a greater number of inverted yes/no questions and
to be
declaratives within the probes following treatment compared with before treatment. All 3 participants evidenced some generalization to novel sentences.

Conclusions
Results provide initial evidence that instruction involving aided modeling with contrastive targets holds promise in targeting specific linguistic rules with children using AAC. Patterns of generalization may depend on participants' specific language deficits and acquisition patterns during intervention.
The Role of Sentence Position, Allomorph, and Morpheme Type on Accurate Use of s-Related Morphemes by Children Who Are Hard of Hearing
Authors: Koehlinger Keegan , Van Horne Amanda Owen , Oleson Jacob , McCreery Ryan , Moeller Mary Pat 
Published: February 2015

Purpose
Production accuracy of s-related morphemes was examined in 3-year-olds with mild-to-severe hearing loss, focusing on perceptibility, articulation, and input frequency.

Method
Morphemes with /s/, /z/, and /ɪz/ as allomorphs (plural, possessive, third-person singular –s, and auxiliary and copula “is”) were analyzed from language samples gathered from 51 children (ages: 2;10 [years;months] to 3;8) who are hard of hearing (HH), all of whom used amplification. Articulation was assessed via the Goldman-Fristoe Test of Articulation–Second Edition, and monomorphemic word final /s/ and /z/ production. Hearing was measured via better ear pure tone average, unaided Speech Intelligibility Index, and aided sensation level of speech at 4 kHz.

Results
Unlike results reported for children with normal hearing, the group of children who are HH correctly produced the /ɪz/ allomorph more than /s/ and /z/ allomorphs. Relative accuracy levels for morphemes and sentence positions paralleled those of children with normal hearing. The 4-kHz sensation level scores (but not the better ear pure tone average or Speech Intelligibility Index), the Goldman-Fristoe Test of Articulation–Second Edition, and word final s/z use all predicted accuracy.

Conclusions
Both better hearing and higher articulation scores are associated with improved morpheme production, and better aided audibility in the high frequencies and word final production of s/z are particularly critical for morpheme acquisition in children who are HH.
Tunable control of antibody immobilization using electric field
Authors: Emaminejad Sam , Javanmard Mehdi , Gupta Chaitanya , Chang Shuai , Davis Ronald W. , Howe Roger T. 
Published: February 2015

Significance
We introduce a novel method for controlling orientation of proteins during immobilization on solid-state surfaces using electric fields. Atomic force microscopy measurements and fluorescence-based readout are used to confirm this phenomenon. This method of immobilization has broad implications for improvement in performance of both affinity-based protein assays and probe-free detection assays.
Noninvasive mapping of pancreatic inflammation in recent-onset type-1 diabetes patients
Authors: Gaglia Jason L. , Harisinghani Mukesh , Aganj Iman , Wojtkiewicz Gregory R. , Hedgire Sandeep , Benoist Christophe , Mathis Diane , Weissleder Ralph 
Published: February 2015

SignificanceWe describe a readily exportable method for noninvasive imaging of the pancreatic inflammation underlying type-1 diabetes (T1D), based on MRI of the clinically approved magnetic nanoparticle ferumoxytol. This approach, which reflects nanoparticle uptake by macrophages in the inflamed pancreatic lesion, has been validated rigorously in mouse T1D models. Methodological advances reported here include extensive optimization of image acquisition and improved MRI registration and visualization technologies. A proof-of-principle study revealed a clear difference in whole-pancreas nanoparticle accumulation in patients with recent-onset T1D versus healthy controls and pronounced intra- and interpancreatic signal heterogeneity in patients. Noninvasive generation of 3D, high-resolution maps of pancreatic inflammation should prove invaluable in assessing T1D progression and as an indicator of response to therapy.
Factor graph analysis of live cell–imaging data reveals mechanisms of cell fate decisions
Authors: Niederberger Theresa , Failmezger Henrik , Uskat Diana , Poron Don , Glauche Ingmar , Scherf Nico , Roeder Ingo , Schroeder Timm , Tresch Achim 
Published: February 2015

AbstractMotivation : Cell fate decisions have a strong stochastic component. The identification of the underlying mechanisms therefore requires a rigorous statistical analysis of large ensembles of single cells that were tracked and phenotyped over time.Results : We introduce a probabilistic framework for testing elementary hypotheses on dynamic cell behavior using time-lapse cell-imaging data. Factor graphs, probabilistic graphical models, are used to properly account for cell lineage and cell phenotype information. Our model is applied to time-lapse movies of murine granulocyte-macrophage progenitor (GMP) cells. It decides between competing hypotheses on the mechanisms of their differentiation. Our results theoretically substantiate previous experimental observations that lineage instruction, not selection is the cause for the differentiation of GMP cells into mature monocytes or neutrophil granulocytes.Availability and implementation : The Matlab source code is available at http://treschgroup.de/Genealogies.htmlContact : failmezger@mpipz.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.
mFASD: a structure-based algorithm for discriminating different types of metal-binding sites
Authors: He Wei , Liang Zhi , Teng Maikun , Niu Liwen 
Published: February 2015

Abstract
Motivation: A large number of proteins contain metal ions that are essential for their stability and biological activity. Identifying and characterizing metal-binding sites through computational methods is necessary when experimental clues are lacking. Almost all published computational methods are designed to distinguish metal-binding sites from non-metal-binding sites. However, discrimination between different types of metal-binding sites is also needed to make more accurate predictions.
Results: In this work, we proposed a novel algorithm called mFASD, which could discriminate different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction. mFASD captures the characteristics of a metal-binding site by investigating the local chemical environment of a set of functional atoms that are considered to be in contact with the bound metal. Then a distance measure defined on functional atom sets enables the comparison between different metal-binding sites. The algorithm could discriminate most types of metal-binding sites from each other with high sensitivity and accuracy. We showed that cascading our method with existing ones could achieve a substantial improvement of the accuracy for metal-binding site prediction.
Availability and implementation: Source code and data used are freely available from http://staff.ustc.edu.cn/∼liangzhi/mfasd/
Contact: liangzhi@ustc.edu.cn or hwkobe@mail.ustc.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of nanopore data using hidden Markov models
Authors: Schreiber Jacob , Karplus Kevin 
Published: February 2015

Abstract
Motivation: Nanopore-based sequencing techniques can reconstruct properties of biosequences by analyzing the sequence-dependent ionic current steps produced as biomolecules pass through a pore. Typically this involves alignment of new data to a reference, where both reference construction and alignment have been performed by hand.
Results: We propose an automated method for aligning nanopore data to a reference through the use of hidden Markov models. Several features that arise from prior processing steps and from the class of enzyme used can be simply incorporated into the model. Previously, the M2MspA nanopore was shown to be sensitive enough to distinguish between cytosine, methylcytosine and hydroxymethylcytosine. We validated our automated methodology on a subset of that data by automatically calculating an error rate for the distinction between the three cytosine variants and show that the automated methodology produces a 2–3% error rate, lower than the 10% error rate from previous manual segmentation and alignment.
Availability and implementation: The data, output, scripts and tutorials replicating the analysis are available at https://github.com/UCSCNanopore/Data/tree/master/Automation.
Contact: karplus@soe.ucsc.edu or jmschreiber91@gmail.com
Supplementary information: Supplementary data are available from Bioinformatics online.
KAPPA, a simple algorithm for discovery and clustering of proteins defined by a key amino acid pattern: a case study of the cysteine-rich proteins
Authors: Joly Valentin , Matton Daniel P. 
Published: February 2015

Abstract
Motivation: Proteins defined by a key amino acid pattern are key players in the exchange of signals between bacteria, animals and plants, as well as important mediators for cell–cell communication within a single organism. Their description and characterization open the way to a better knowledge of molecular signalling in a broad range of organisms, and to possible application in medical and agricultural research. The contrasted pattern of evolution in these proteins makes it difficult to detect and cluster them with classical sequence-based search tools. Here, we introduce Key Aminoacid Pattern-based Protein Analyzer (KAPPA), a new multi-platform program to detect them in a given set of proteins, analyze their pattern and cluster them by comparison to reference patterns ( ab initio search) or internal pairwise comparison ( de novo search).
Results: In this study, we use the concrete example of cysteine-rich proteins (CRPs) to show that the similarity of two cysteine patterns can be precisely and efficiently assessed by a quantitative tool created for KAPPA: the κ -score. We also demonstrate the clear advantage of KAPPA over other classical sequence search tools for ab initio search of new CRPs. Eventually, we present de novo clustering and subclustering functionalities that allow to rapidly generate consistent groups of CRPs without a seed reference.
Availability and implementation: KAPPA executables are available for Linux, Windows and Mac OS at http://kappa-sequence-search.sourceforge.net .
Contact: dp.matton@umontreal.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Methods for the detection and assembly of novel sequence in high-throughput sequencing data
Authors: Holtgrewe Manuel , Kuchenbecker Leon , Reinert Knut 
Published: February 2015

Abstract
Motivation: Large insertions of novel sequence are an important type of structural variants. Previous studies used traditional de novo assemblers for assembling non-mapping high-throughput sequencing (HTS) or capillary reads and then tried to anchor them in the reference using paired read information.
Results: We present approaches for detecting insertion breakpoints and targeted assembly of large insertions from HTS paired data: BASIL and ANISE. On near identity repeats that are hard for assemblers, ANISE employs a repeat resolution step. This results in far better reconstructions than obtained by the compared methods. On simulated data, we found our insert assembler to be competitive with the de novo assemblers ABYSS and SGA while yielding already anchored inserted sequence as opposed to unanchored contigs as from ABYSS/SGA. On real-world data, we detected novel sequence in a human individual and thoroughly validated the assembled sequence. ANISE was found to be superior to the competing tool MindTheGap on both simulated and real-world data.
Availability and implementation: ANISE and BASIL are available for download at http://www.seqan.de/projects/herbarium under a permissive open source license.
Contact: manuel.holtgrewe@fu-berlin.de or knut.reinert@fu-berlin.de
Supplementary information: Supplementary data are available at Bioinformatics online.
TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples
Authors: He Liye , Wennerberg Krister , Aittokallio Tero , Tang Jing 
Published: February 2015

Abstract
Summary: Network pharmacology-based prediction of multi-targeted drug combinations is becoming a promising strategy to improve anticancer efficacy and safety. We developed a logic-based network algorithm, called Target Inhibition Interaction using Maximization and Minimization Averaging (TIMMA), which predicts the effects of drug combinations based on their binary drug-target interactions and single-drug sensitivity profiles in a given cancer sample. Here, we report the R implementation of the algorithm (TIMMA-R), which is much faster than the original MATLAB code. The major extensions include modeling of multiclass drug-target profiles and network visualization. We also show that the TIMMA-R predictions are robust to the intrinsic noise in the experimental data, thus making it a promising high-throughput tool to prioritize drug combinations in various cancer types for follow-up experimentation or clinical applications.
Availability and implementation: TIMMA-R source code is freely available at http://cran.r-project.org/web/packages/timma/ .
Contact: jing.tang@helsinki.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
Into a rhythm: diel activity patterns and behaviour in Mediterranean slipper lobsters, Scyllarides latus
Authors: Goldstein Jason S. , Dubofsky Elizabeth A. , Spanier Ehud 
Published: February 2015

AbstractAlthough the natural history for Mediterranean slipper lobsters (Scyllarides latus) is well established, there exists a disproportionate lack of important biological and physiological data to verify many key traits, including to what extent endogenous rhythms modulate aspects of their behaviour. Although Scyllarids appear nocturnally active, few studies exist that quantify this tendency. Our overall objective was to test the hypothesis that adult slipper lobsters are nocturnal and to determine if their diel activity rhythms are under the influence of an endogenous circadian clock. In the laboratory, we exposed a total of 16 animals (CLavg = 92.6 ± 6.6 mm; CL, carapace length) to a 12 : 12 light : dark (LD) cycle for 7–10 d, followed by ***constant dark (DD) for 15–20 d. Activity was assessed using a combination of time-lapse video and accelerometers. Of a total of 16 lobsters, we analysed data from 15 (one mortality). All 15 lobsters were evaluated using video. Thirteen of these lobsters were also evaluated using accelerometers. All lobsters were more active during night-time than during daytime and synchronized their activity to the LD cycle, expressing a diel activity pattern (τ = 24.04 ± 0.13 h). In DD, lobsters maintained a circadian rhythm with a τ of 23.87 ± 0.07 h. These findings may provide insight into the behaviour of these animals in their natural habitat and help explain their ability to anticipate dawn and dusk.
Cell-SELEX-based aptamer-conjugated nanomaterials for cancer diagnosis and therapy
Authors: Meng Hong-Min , Fu Ting , Zhang Xiao-Bing , Tan Weihong 
Published: February 2015

Abstract
Nucleic acid aptamers, which are generated by a novel technique called SELEX (systematic evolution of ligands by exponential enrichment), have recently attracted significant attention in the field of early detection and treatment of cancer based on their numerous merits, such as high affinity, high specificity, small size, little immunogenicity, stable structures, and ease of chemical modification. Furthermore, aptamers can gain more flexibility as cancer cell targeting tools when conjugated to nanomaterials, including metallic nanoparticles, carbon nanomaterials, DNA nanodevices, and polymeric nanoparticles. We discuss the progress achieved in cancer diagnosis and therapy through the conjugation of cell-SELEX-based aptamers with different nanomaterials.
‘Remotely Global’ Village Life in Interior West Africa
Authors: Stahl Ann B. 
Published: February 2015

AbstractTo pursue the history of African village life through archaeological investigations was once considered an oxymoron. Viewed as ‘traditional’ locales apart from the core of modernity, ethnographic inquiry was thought to provide a picture of village life to which archaeological investigations could add little. But in the last few decades archaeological investigations at sites of recent centuries have yielded robust insights into the dynamics of daily practice as African villagers negotiated the shifting terrain of global networks. This chapter explores how archaeological sources contribute to our understanding of the dynamics of daily practice in ‘remotely global’ (Piot 1999) villages of interior West Africa.
Does “Second Impact Syndrome” Exist?
Authors: McCrory Paul , Davis Gavin , Makdissi Michael , Turner Michael 
Published: February 2015

Abstract
Second impact syndrome is a condition that is believed by some people to be a consequence of recurrent sports concussion. The only evidence to support its existence is anecdotal and, if it does exist, it is rare. The fear of this condition has driven the promulgation of concussion management guidelines and, more worryingly, the recent trend towards government regulation of the clinical management of concussion in the United States. Diffuse brain swelling following a single head injury, a well-recognized condition, is more common in children than in adults and usually has a poor outcome. It is posited that the so-called second impact syndrome simply represents diffuse brain swelling mistakenly attributed to repeated concussion.
Sex Differences in Sports-Related Concussion
Authors: Brand Jesse G. , Rossetti Heidi R. , Broshek Donna K. 
Published: February 2015

Abstract
Sex differences in sports-related concussion are the focus of a growing body of literature. This chapter discusses the increasing rates of female participation in sport, briefly addresses sex differences in traumatic brain injury (TBI), as well as physical sex differences and their impact on sports-related concussion. Several discrepancies in sports regulations and playing style between sexes that have been implicated in differing rates of sports-related concussion are also discussed. Variations in symptom reporting between the sexes and sex differences in cognitive outcomes of sports-related concussion are also addressed. Sex differences in symptom resolution and time to return to play are presented. Finally, limitations of this literature are identified and suggestions for future research are provided.