bluuebunny/crossref_metadata_2025 huggingface dataset:
The serial nature of the masked onset priming effect revisited
Authors: Mousikou Petroula , Coltheart Max
Published: May 2014

Reading aloud is faster when target words/nonwords are preceded by masked prime words/nonwords that share their first sound with the target (e.g., s ave-SINK) compared to when primes and targets are unrelated to each other (e.g., farm-SINK). This empirical phenomenon is the masked onset priming effect (MOPE) and is known to be due to serial left-to-right processing of the prime by a sublexical reading mechanism. However, the literature in this domain lacks a critical experiment. It is possible that when primes are real words their orthographic/phonological representations are activated in parallel and holistically during prime presentation, so any phoneme overlap between primes and targets (and not just initial-phoneme overlap) could facilitate target reading aloud. This is the prediction made by the only computational models of reading aloud that are able to simulate the MOPE, namely the DRC1.2.1, CDP+, and CDP++ models. We tested this prediction in the present study and found that initial-phoneme overlap ( b lip-BEST), but not end-phoneme overlap ( flat-BEST), facilitated target reading aloud compared to no phoneme overlap ( junk-BEST). These results provide support for a reading mechanism that operates serially and from left to right, yet are inconsistent with all existing computational models of single-word reading aloud.
Solution to a non-Archimedean Monge-Ampère equation
Authors: Boucksom Sébastien , Favre Charles , Jonsson Mattias
Published: May 2014

LetXXbe a smooth projective Berkovich space over a complete discrete valuation fieldKKof residue characteristic zero, and assume thatXXis defined over a function field admittingKKas a completion. Let furtherμ\mube a positive measure onXXandLLbe an ample line bundle such that the mass ofμ\muis equal to the degree ofLL. We prove the existence of a continuous semipositive metric whose associated measure is equal toμ\muin the sense of Zhang and Chambert-Loir. We do this under a technical assumption on the support ofμ\mu, which is, for instance, fulfilled if the support is a finite set of divisorial points. Our method draws on analogs of the variational approach developed to solve complex Monge-Ampère equations on compact Kähler manifolds by Berman, Guedj, Zeriahi, and the first named author, and of Kołodziej’sC0C^0-estimates. It relies in a crucial way on the compactness properties of singular semipositive metrics, as defined and studied in a companion article.
Fundamental groups of links of isolated singularities
Authors: Kapovich Michael , Kollár János
Published: May 2014

We study fundamental groups of projective varieties with normal crossing singularities and of germs of complex singularities. We prove that for every finitely-presented group

G
G

there is a complex projective surface

S
S

with simple normal crossing singularities only, so that the fundamental group of

S
S

is isomorphic to

G
G

. We use this to construct 3-dimensional isolated complex singularities so that the fundamental group of the link is isomorphic to

G
G

. Lastly, we prove that a finitely-presented group

G
G

is

Q

{\mathbb Q}

-superperfect (has vanishing rational homology in dimensions 1 and 2) if and only if

G
G

is isomorphic to the fundamental group of the link of a rational 6-dimensional complex singularity.
A comprehensive protein–protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1
Authors: DeMille Desiree , Bikman Benjamin T. , Mathis Andrew D. , Prince John T. , Mackay Jordan T. , Sowa Steven W. , Hall Tacie D. , Grose Julianne H.
Published: May 2014

Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein–protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expression, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase–deficient mice, identifying a possible molecular mechanism and solidifying the evolutionary importance of PAS kinase in the regulation of glucose homeostasis.
The family-specific K-loop influences the microtubule on-rate but not the superprocessivity of kinesin-3 motors
Authors: Soppina Virupakshi , Verhey Kristen J.
Published: May 2014

The kinesin-3 family (KIF) is one of the largest among the kinesin superfamily and an important driver of a variety of cellular transport events. Whereas all kinesins contain the highly conserved kinesin motor domain, different families have evolved unique motor features that enable different mechanical and functional outputs. A defining feature of kinesin-3 motors is the presence of a positively charged insert, the K-loop, in loop 12 of their motor domains. However, the mechanical and functional output of the K-loop with respect to processive motility of dimeric kinesin-3 motors is unknown. We find that, surprisingly, the K-loop plays no role in generating the superprocessive motion of dimeric kinesin-3 motors (KIF1, KIF13, and KIF16). Instead, we find that the K-loop provides kinesin-3 motors with a high microtubule affinity in the motor's ADP-bound state, a state that for other kinesins binds only weakly to the microtubule surface. A high microtubule affinity results in a high landing rate of processive kinesin-3 motors on the microtubule surface. We propose that the family-specific K-loop contributes to efficient kinesin-3 cargo transport by enhancing the initial interaction of dimeric motors with the microtubule track.
Aquinas and Calvin on Romans
Authors: Raith II Charles
Published: May 2014

Aquinas and Calvin on Romans is a comparative study of John Calvin’s and Thomas Aquinas’s commentaries on the first eight chapters of Paul’s letter to the Romans. Focusing on the role of human participation in God’s work of salvation, the book argues that Calvin’s critiques of the “schoolmen” arising from his reading of Romans fail to find a target in Aquinas’s theology while Calvin’s principal positive affirmations are embraced by Aquinas as well. Aquinas upholds many fundamental insights that Calvin would later also obtain in his reading of Romans, such as justification sola fide non merito (by faith alone and not by merit), the centrality of Christ for salvation, the ongoing imperfection of the sanctified life, the work of the Spirit guiding the believer along the path of sanctification, and the assurance of salvation that one obtains through the indwelling of the Spirit, to name only a few. Even more, numerous identical interpretations arising in their commentaries make it necessary to consider Calvin’s reading of Romans as appropriating a tradition of interpretation that includes Aquinas. At the same time, the nonparticipatory dimensions of Calvin’s reading of Romans become clear when set beside Aquinas’s reading, and these nonparticipatory dimensions create difficulties for Calvin’s interpretation, especially on Romans 8, that are not present in Aquinas’s account. The book therefore suggests how Calvin’s reading of Romans, especially as it pertains to justification and merit, should be augmented by the participatory framework reflected in Aquinas’s interpretation. The book concludes by revisiting Calvin’s criticisms of the Council of Trent in light of these suggestions.
Justification
Authors: Raith Charles
Published: May 2014

Chapter 1 concentrates on Aquinas’s and Calvin’s interpretations of justification in Romans 1–3. A central point of continuity between Aquinas and Calvin is the unmerited reception of justification. Aquinas’s interpretation is in agreement with what Calvin calls the “main and cardinal point” of the first part of Romans: “we are justified by faith through the mercy of God alone.” Yet Aquinas affirms, while Calvin denies, transformative dimensions to justification, and this impacts the role of participation in their reading of Romans 1–3: since for Calvin justification is strictly what God does for us, rather than also what God does in and through us (as with Aquinas), key sections of his commentary on Romans 1–3 highlight Calvin’s limited participatory vision.
Peace with God, the Hope of Salvation, and the Adam–Christ Typology
Authors: Raith Charles
Published: May 2014

Chapter 3 addresses Paul’s teaching on our peace with God, hope of salvation and eternal life, and the Adam–Christ typology. The chapter argues that since Aquinas believes that justification makes the believer a just person, peace with God is made possible on account of the new life the believer lives in grace; Calvin claims, however, that the believer is still condemnable in se, thus making peace a matter of the believer’s conscience resulting from contemplating Christ’s work on his or her behalf. Hope in future eternal life is not rooted in the life lived by the believer, as it is with Aquinas, but rather on having received Christ’s imputed justice extra nos. When Aquinas and Calvin turn to the Adam–Christ typology, Aquinas focuses on Christ’s restoration in the believer of that which was distorted by original sin; Calvin focuses on God’s judgment and contrasts it with God’s gift of Christ.
The Spirit’s Work of Transformation: Part 1
Authors: Raith Charles
Published: May 2014

This chapter analyzes the transformation caused by the Spirit’s indwelling in connection with being united with Christ’s death in baptism. For Aquinas, the transformation enables the believer to avoid mortal sin in the future and perform meritorious works in the present while the believer continues to struggle with the remaining disorder of the flesh. Calvin, too, presents his version of the “Christian struggle,” but he asserts that the believer and his or her works are condemnable in se while being accepted in Christo. This contributes to Calvin’s rejection of merit and leads to a different reading of 6:23 than that of Aquinas, who upholds eternal life as both a gift and an object of merit. Part of Calvin’s nonparticipatory framework of human activity becomes evident in Calvin`s appropriation of the Scotistic notion of “acceptance.”
Life in the Spirit
Authors: Raith Charles
Published: May 2014

This chapter focuses on Aquinas’s and Calvin’s explanations for why there is no condemnation for those in Christ Jesus (8:1). Since for Calvin the believer is still condemnable in se, the reason for no condemnation cannot be due to the Spirit’s sanctification; Paul must be turning back at 8:1 to the topic of justification, which for Calvin is something altogether distinct from transformation. “Suffering with Christ” becomes a necessary but extrinsic principle for obtaining the inheritance as sons in the Son, and the just requirements of the law are no longer fulfilled “in us” (8:4) but rather “for us” by Christ. Aquinas, however, interprets Romans 8:1 as speaking of two “conditions” for having no condemnation: being in Christ and walking by the Spirit. The justified believer is transformed so as to possess nothing damnable, and is enabled by the Spirit to live a life in avoidance of damnable activity.
Conclusion
Authors: Raith Charles
Published: May 2014

Since the present study will necessarily have implications for contemporary ecumenical dialogue, this chapter suggests some of these implications by rereading Calvin’s engagement with the sixth session of the Council of Trent—where we find many of the same soteriological issues being engaged that appeared throughout Calvin’s and Aquinas’s commentaries on Romans, such as competitive causality, justification and merit, and imputation versus transformation—in light of the findings of this study. While the focus will necessarily shift more exclusively to Calvin, Aquinas is still present in the teachings of the Council, and anyone interested in soteriological participation and ecumenical engagement will benefit from the interaction between Calvin’s comments, Trent’s teachings, and the suggestions I offer. I conclude with some observations on understanding this present book as a work of ecumenical ressourcement and how this form of ecumenical engagement leads to a fruitful ecumenical future.
Phonetics in phonology
Authors: Ladd D. Robert
Published: May 2014

At least since Trubetzkoy it has been customary to distinguish phonology from phonetics. This is an important distinction, but it is not truly made by most linguists. Rather, IPA-based phonetic representations have played a crucial role in shaping assumptions and theoretical ideas in phonology since the emergence of the phonemic principle. First, the segmental idealization embodied in IPA representation entrenches a strongly sequential notion of phonological structure, which marginalizes ‘prosody’. Second, IPA phonetics implies the existence of universal categories, an idea that is poorly supported by instrumental phonetic data. True separation of phonology and phonetics can be achieved if surface segmental representations are defined separately for each language and therefore treated as part of phonology. Phonetics must be treated in quantitative terms.
Three Kinds of Moral Imagination
Authors: Chappell Sophie Grace
Published: May 2014

An examination of three kinds of case that are interesting for the notion of the moral imagination. The first is ‘ticking-bomb scenarios’, and the topical question whether we should torture in them. Answering ‘Yes’ to this typically just displays a failure of moral imagination. The second is imaginary cases as these often come up in contemporary moral philosophy, to which we may apply a distinction between what we may call ‘open’ and ‘closed’ deliberation. The third kind of case is ‘encounters with The Other’. Two particular actual examples are contrasted: Hitler and the Jews in pre-WWI Vienna in Mein Kampf, and Patrick Leigh Fermor and a Rabbi and his sons in the forests of Rumania in 1938. The differences between Hitler’s and Fermor’s reactions to ‘the other’ that they encounter can revealingly be treated as differences in their moral imaginations.
Intuition, System, and the ‘Paradox’ of Deontology
Authors: Chappell Sophie Grace
Published: May 2014

Deontological views in ethics have been thought by many recent commentators to face ‘the paradox of deontology’. The way to resolve the paradox is simply to see the diversity of the roles that our agency can play, and hence the diversity of our reasons. But systematic moral thinkers such as Kantians are not always hospitable to ‘untidy’ thoughts about diversity, even when, as in this case, such untidiness crucially helps their cause; they have also displayed a tendency, which we can trace in Kant himself, to look for ways of complicating the story in directions that are at best of dubious help to them.
On the Very Idea of Criteria for Personhood
Authors: Chappell Sophie Grace
Published: May 2014

This chapter examines the familiar criterial view of personhood, according to which the possession of personal properties such as self-consciousness, emotionality, sentience, and so forth is necessary and sufficient for the status of a person. This view confuses criteria for personhood with components of an ideal of personhood. In normal cases, we have already identified a creature as a person before we start looking for it to manifest the personal properties, indeed this pre-identification is part of what makes it possible for us to see and interpret the creature as a person in the first place. This pre-identification is typically based on biological features. Except in some interesting special or science-fiction cases, it is human animals that we identify as persons.
Moral Certainties
Authors: Chappell Sophie Grace
Published: May 2014

This chapter considers, and largely endorses, the thesis that there is no sceptical argument which entails that we don’t know that, for example, murder is bad which is as certain as our knowledge that murder is bad. For some ethical claims—the moral certainties—any reason that might be produced for doubting one of these claims will get into a ‘credibility contest’ with that claim; and it will lose. Insofar as we are rational, any witness or argument who tells us that any of these action-types, or any paradigm instance of any of them, is not in fact bad, will not undermine our confidence that they are bad, but our confidence in that witness or argument. Along the way consequences of this Moorean argument for realism and for moral epistemology are noticed and considered.
The Varieties of Knowledge in Plato and Aristotle
Authors: Chappell Sophie Grace
Published: May 2014

This chapter develops the relatively familiar idea of a variety of forms of knowledge: not just propositional knowledge but also knowledge-how and experiential knowledge. It presents arguments against reductive projects aimed at showing that ‘really’ only one of these kinds of knowledge counts, or is basic. And it shows how this variety can be used to make interesting sense of Plato’s and Aristotle’s philosophy, sense which can feed into our overall understanding of ethics. The chapter then adds to this threefold analysis of knowledge a less familiar fourth variety, objectual knowledge, and suggests that this is also interesting and important both in the understanding of Plato and Aristotle, and in the understanding of ethics in general.
Technology Fundamentals
Authors: Bauer William I.
Published: May 2014

An understanding of various technologies is an important component of one’s TPACK. This chapter presents the essential technological knowledge and skill necessary for a music educator to successfully begin to utilize technology for music learning. Topics include explanation of the key components of computers and their operating systems, description and comparison of MIDI and digital audio, discussion of graphic and video media, identification of types of music software and the evaluation of software titles, and exploration of Internet resources that may be used for music learning. Free and low cost implementations of these technologies are emphasized; using technology to facilitate music learning does not require excessive amounts of money. Since technologies are always being refined and improved, with new technologies that may be applicable to music learning constantly emerging, music educators need to maintain a mindset of ongoing professional learning in this area.
Performing Music
Authors: Bauer William I.
Published: May 2014

Grounded in the research and best practice literature, chapter 4 discusses concepts and skills, pedagogies, and technology related to musical performance. Technologies may be of assistance in learning psychomotor knowledge and skills, and in accomplishing effective musical practice. Models of exemplary performances and performers, along with feedback on performance may also be augmented through technology. The aural and visual skills necessary to read and write music with fluency, and the identification and selection of musical literature can be enhanced via technology. Technology can assist with traditional ensemble rehearsals and new technologies are creating new performance opportunities, even for people without a formal musical background. Technology facilitated learning in music performance classrooms has the potential to benefit both teachers and their students, and to allow more individuals to experience the joy and benefits of active musical participation through performance.
Assessment for Music Learning
Authors: Bauer William I.
Published: May 2014

Assessment is an essential aspect of teaching and learning. Not only is assessment necessary to determine if students have learned what teachers think they have taught, but it also informs the design of instruction and is used to adjust the specific teaching and learning strategies that are used over time. Numerous technological tools are available that enable teachers to be more efficient and effective with this process. This chapter is primarily concerned with the assessment of musical achievement in creative, psychomotor, and cognitive domains. It outlines essential assessment principles, discusses the technology-assisted development of assessments, explores technologies helpful to the process of assessing specific music learning outcomes, and describes new assessment approaches enabled by technology. The management of assessment data and processes via technology is also examined.
Pluralist Congregations
Authors: Marti Gerardo , Ganiel Gladys
Published: May 2014

The book characterizes the congregations of the Emerging Church Movement (ECM) as pluralist congregations, seeing them as rare examples of religious institutions that—rather than failing to recognize or trying to suppress diversity—instead try to facilitate it. Pluralist congregations are social spaces that permit and even foster direct interaction between people with religiously contradictory perspectives and value systems. Pluralist congregations are distinct in promoting individualism while at the same time providing a basis for community around shared experiences and relationships. Pluralist congregations exemplify what sociologist Ulrich Beck has called “cooperative egoism,” striving to form the basis for a religious orientation that straddles the tension between individualism and collective identity. In short, even within the loosest of emerging churches, the ECM is a congregational faith, one that relies on relationships, regular gatherings, and involvement.
Faith as Conversation
Authors: Marti Gerardo , Ganiel Gladys
Published: May 2014

Emerging Christians have taken to calling their movement a conversation. This chapter emphasizes the value placed on dialogue and discussion within the Emerging Church Movement (ECM). Drawing on the literature on institutional entrepreneurship, the chapter argues that understanding how religious institutional entrepreneurs use discourses helps explain the effectiveness of the faith as conversation approach of the ECM. The conversation of the ECM is an almost paradigmatic example of the type of meaning work that includes theorizing, mythologizing, valorizing, and demonizing to undermine previously held assumptions and beliefs and to justify change, activity central to studies of institutional entrepreneurship. We also analyze the content of the ECM conversation, focusing on the importance placed on asking questions and distinct ideas about the nature of truth, embracing doubt, and the nature of God, exploring how these ideas shape Emerging Christians’ religious orientations. Ongoing conversation is in itself a mechanism or a strategy to maintain a plurality of identities and positions within emerging congregations. Emerging Christians are collective institutional entrepreneurs, using religious discourses to interrogate conventional Christianity and to create congregations where they can say what’s really on their minds.
FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads
Authors: Wang Meng , Lin Shili
Published: May 2014

Motivation: In recent years, there has been an increasing interest in using common single-nucleotide polymorphisms (SNPs) amassed in genome-wide association studies to investigate rare haplotype effects on complex diseases. Evidence has suggested that rare haplotypes may tag rare causal single-nucleotide variants, making SNP-based rare haplotype analysis not only cost effective, but also more valuable for detecting causal variants. Although a number of methods for detecting rare haplotype association have been proposed in recent years, they are population based and thus susceptible to population stratification.

Results: We propose family-triad-based logistic Bayesian Lasso (famLBL) for estimating effects of haplotypes on complex diseases using SNP data. By choosing appropriate prior distribution, effect sizes of unassociated haplotypes can be shrunk toward zero, allowing for more precise estimation of associated haplotypes, especially those that are rare, thereby achieving greater detection power. We evaluate famLBL using simulation to gauge its type I error and power. Compared with its population counterpart, LBL, highlights famLBL’s robustness property in the presence of population substructure. Further investigation by comparing famLBL with Family-Based Association Test (FBAT) reveals its advantage for detecting rare haplotype association.

Availability and implementation: famLBL is implemented as an R-package available at http://www.stat.osu.edu/∼statgen/SOFTWARE/LBL/ .

Contact:  shili@stat.osu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Minimally Invasive Surgery in Patients With Adolescent Idiopathic Scoliosis
Authors: Sarwahi Vishal , Horn Jonathan J. , Kulkarni Preethi M. , Wollowick Adam L. , Lo Yungtai , Gambassi Melanie , Amaral Terry D.
Published: May 2014

Study Design:

This is a retrospective controlled study.

Objective:

To compare the safety and efficacy of minimally invasive surgery (MIS) for the surgical management of adolescent idiopathic scoliosis (AIS) to the standard open posterior approach (PSF).

Summary of Background Data:

MIS approaches offer the potential to reduce soft-tissue trauma, intraoperative blood loss, and surgical-site infection. Thus far, MIS has been successfully utilized for the surgical correction of multilevel spine pathology in adults. It is not yet known if these results can be replicated in the surgical management of AIS.

Materials and Methods:

Seven MIS patients were compared with 15 PSF patients using minimum 2-year follow-up data. Parameters studied included preoperative patient and deformity characteristics, perioperative details, extent of deformity correction, and complications. Data were compared using Mann-Whitney tests for continuous variables and Fisher exact tests for categorical variables.

Results:

The MIS and PSF groups were similar for all preoperative characteristics collected (P>0.05). MIS patients had fewer fixation points (P=0.015), but a longer median operative time (P=0.011). There was no significant difference in estimated blood loss (EBL) (P=0.051), EBL/fixation point (P=0.204), or amount of fluids administered (P=0.888). Postoperative recovery did not differ between the 2 groups in number of intensive care unit days (P=0.362), length of hospital stay (P=0.472), time to mobilization (P=1.00), Visual Analogue Scale pain scores (P=0.698), or patient-controlled analgesia (P=1.00). The MIS technique had similar deformity correction, screw placement accuracy, and fusion status when compared with the PSF group. MIS patients had lower blood transfusion rate (P=0.02), shorter fusion (P=0.046) and fewer pedicle screws (P=0.015).

Conclusions:

The short-term advantages seen in MIS for adult scoliosis were not as obvious in our series. We found similar deformity correction and adequate fusion, however shortcomings related to learning curve, and instrumentation persist. MIS surgery is an innovative treatment for AIS that is technically feasible with significantly lower transfusion rate, shorter fusion lenghts and lesser pedicle screw fixation. Despite these advanatges, its role in AIS is currently difficut to define.
The distribution of deleterious genetic variation in human populations
Authors: Lohmueller Kirk E.
Published: May 2014

Population genetic studies suggest that most amino-acid changing mutations are deleterious. Such mutations are of tremendous interest in human population genetics as they are important for the evolutionary process and may contribute risk to common disease. Genomic studies over the past 5 years have documented differences across populations in the number of heterozygous deleterious genotypes, numbers of homozygous derived deleterious genotypes, number of deleterious segregating sites and proportion of sites that are potentially deleterious. These differences have been attributed to population history affecting the ability of natural selection to remove deleterious variants from the population. However, recent studies have suggested that the genetic load may not differ across populations, and that the efficacy of natural selection has not differed across human populations. Here I show that these observations are not incompatible with each other and that the apparent differences are due to examining different features of the genetic data and differing definitions of terms.
Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders
Authors: Konietzny S. G. A. , Pope P. B. , Weimann A. , McHardy A. C.
Published: May 2014

Background

Efficient industrial processes for converting plant lignocellulosic materials into biofuels are a key challenge in global efforts to use alternative energy sources to fossil fuels. Novel cellulolytic enzymes have been discovered from microbial genomes and metagenomes of microbial communities. However, the identification of relevant genes without known homologs, and elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain a challenge.

Results

We describe a new computational method for the targeted discovery of functional modules of plant biomass-degrading protein families based on their co-occurrence patterns across genomes and metagenome datasets, and the strength of association of these modules with the genomes of known degraders. From more than 6.4 million family annotations for 2884 microbial genomes and 332 taxonomic bins from 18 metagenomes, we identified five functional modules that are distinctive for plant biomass degraders, which we call plant biomass degradation modules (PDMs). These modules incorporated protein families involved in the degradation of cellulose, hemicelluloses and pectins, structural components of the cellulosome and additional families with potential functions in plant biomass degradation. The PDMs could be linked to 81 gene clusters in genomes of known lignocellulose degraders, including previously described clusters of lignocellulolytic genes. On average, 70% of the families of each PDM mapped to gene clusters in known degraders, which served as an additional confirmation of their functional relationships. The presence of a PDM in a genome or taxonomic metagenome bin allowed us to predict an organism’s ability for plant biomass degradation accurately. For 15 draft genomes of a cow rumen metagenome, we validated by cross-linking with confirmed cellulolytic enzymes that the PDMs identified plant biomass degraders within a complex microbial community.

Conclusions

Functional modules of protein families that realize different aspects of plant cell wall degradation can be inferred from co-occurrence patterns across (meta)genomes with a probabilistic topic model. The PDMs represent a new resource of protein families and candidate genes implicated in microbial plant biomass degradation. They can be used to predict the ability to degrade plant biomass for a genome or taxonomic bin. The method would also be suitable for characterizing other microbial phenotypes.
Colletotrichum orbiculare Secretes Virulence Effectors to a Biotrophic Interface at the Primary Hyphal Neck via Exocytosis Coupled with SEC22-Mediated Traffic
Authors: Irieda Hiroki , Maeda Hitomi , Akiyama Kaoru , Hagiwara Asuka , Saitoh Hiromasa , Uemura Aiko , Terauchi Ryohei , Takano Yoshitaka
Published: May 2014

The hemibiotrophic pathogen Colletotrichum orbiculare develops biotrophic hyphae inside cucumber (Cucumis sativus) cells via appressorial penetration; later, the pathogen switches to necrotrophy. C. orbiculare also expresses specific effectors at different stages. Here, we found that virulence-related effectors of C. orbiculare accumulate in a pathogen–host biotrophic interface. Fluorescence-tagged effectors accumulated in a ring-like region around the neck of the biotrophic primary hyphae. Fluorescence imaging of cellular components and transmission electron microscopy showed that the ring-like signals of the effectors localized at the pathogen–plant interface. Effector accumulation at the interface required induction of its expression during the early biotrophic phase, suggesting that transcriptional regulation may link to effector localization. We also investigated the route of effector secretion to the interface. An exocytosis-related component, the Rab GTPase SEC4, localized to the necks of biotrophic primary hyphae adjacent to the interface, thereby suggesting focal effector secretion. Disruption of SEC4 in C. orbiculare reduced virulence and impaired effector delivery to the ring signal interface. Disruption of the v-SNARE SEC22 also reduced effector delivery. These findings suggest that biotrophy-expressed effectors are secreted, via the endoplasmic reticulum-to-Golgi route and subsequent exocytosis, toward the interface generated between C. orbiculare and the host cell.
A point mutation in the [2Fe–2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties
Authors: Tamir Sagi , Eisenberg-Domovich Yael , Conlan Andrea R. , Stofleth Jason T. , Lipper Colin H. , Paddock Mark L. , Mittler Ron , Jennings Patricia A. , Livnah Oded , Nechushtai Rachel
Published: May 2014

NAF-1 is an important [2Fe–2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, and suppression of NAF-1 expression by knockdown significantly suppresses tumor growth. Key to NAF-1 function is the NEET fold with its [2Fe–2S] cluster. In this work, the high-resolution structure of native NAF-1 was determined to 1.65 Å resolution (Rfactor = 13.5%) together with that of a mutant in which the single His ligand of its [2Fe–2S] cluster, His114, was replaced by Cys. The NAF-1 H114C mutant structure was determined to 1.58 Å resolution (Rfactor = 16.0%). All structural differences were localized to the cluster binding site. Compared with native NAF-1, the [2Fe–2S] clusters of the H114C mutant were found to (i) be 25-fold more stable, (ii) have a redox potential that is 300 mV more negative and (iii) have their cluster donation/transfer function abolished. Because no global structural differences were found between the mutant and the native (wild-type) NAF-1 proteins, yet significant functional differences exist between them, the NAF-1 H114C mutant is an excellent tool to decipher the underlying biological importance of the [2Fe–2S] cluster of NAF-1in vivo.
A complement to the modern crystallographer's toolbox: caged gadolinium complexes with versatile binding modes
Authors: Stelter Meike , Molina Rafael , Jeudy Sandra , Kahn Richard , Abergel Chantal , Hermoso Juan A.
Published: May 2014

A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd3+ion into protein crystals in order to provide strong anomalous scattering forde novophasing. The complexes contained multidentate ligand molecules with different functional groups to provide a panel of possible interactions with the protein. An exhaustive crystallographic analysis showed them to be nondisruptive to the diffraction quality of the prepared derivative crystals, and as many as 50% of the derivatives allowed the determination of accurate phases, leading to high-quality experimental electron-density maps. At least two successful derivatives were identified for all tested proteins. Structure refinement showed that the complexes bind to the protein surface or solvent-accessible cavities, involving hydrogen bonds, electrostatic and CH–π interactions, explaining their versatile binding modes. Their high phasing power, complementary binding modes and ease of use make them highly suitable as a heavy-atom screen for high-throughputde novostructure determination, in combination with the SAD method. They can also provide a reliable tool for the development of new methods such as serial femtosecond crystallography.
The structure ofPlasmodium falciparumserine hydroxymethyltransferase reveals a novel redox switch that regulates its activities
Authors: Chitnumsub Penchit , Ittarat Wanwipa , Jaruwat Aritsara , Noytanom Krittikar , Amornwatcharapong Watcharee , Pornthanakasem Wichai , Chaiyen Pimchai , Yuthavong Yongyuth , Leartsakulpanich Ubolsree
Published: May 2014

Plasmodium falciparumserine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutantPfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. ThePfSHMT-F292E structure is a good representation ofPfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure ofPfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.
Two-dimensional coordination polymeric structures in caesium complexes with ring-substituted phenoxyacetic acids
Authors: Smith Graham , Lynch Daniel E.
Published: May 2014

The two-dimensional polymeric structures of the caesium complexes with the phenoxyacetic acid analogues (4-fluorophenoxy)acetic acid, (3-chloro-2-methylphenoxy)acetic acid and the herbicidally active (2,4-dichlorophenoxy)acetic acid (2,4-D), namely poly[[μ5-(4-fluorophenoxy)acetato][μ4-(4-fluorophenoxy)acetato]dicaesium], [Cs2(C8H6FO3)2]n, (I), poly[aqua[μ5-(3-chloro-2-methylphenoxy)acetato]caesium], [Cs(C9H8ClO3)(H2O)]n, (II), and poly[[μ7-(2,4-dichlorophenoxy)acetato][(2,4-dichlorphenoxy)acetic acid]caesium], [Cs(C8H5Cl2O3)(C8H6Cl2O3)]n, (III), are described. In (I), the Cs+cations of the two individual irregular coordination polyhedra in the asymmetric unit (one CsO7and the other CsO8) are linked by bridging carboxylate O-atom donors from the two ligand molecules, both of which are involved in bidentate chelateOcarboxy,Ophenoxyinteractions, while only one has a bidentate carboxylateO,O′-chelate interaction. Polymeric extension is achieved through a number of carboxylate O-atom bridges, with a minimum Cs...Cs separation of 4.3231 (9) Å, giving layers which lie parallel to (001). In hydrated complex (II), the irregular nine-coordination about the Cs+cation comprises a single monodentate water molecule, a bidentateOcarboxy,Ophenoxychelate interaction and six bridging carboxylate O-atom bonding interactions, giving a Cs...Cs separation of 4.2473 (3) Å. The water molecule forms intralayer hydrogen bonds within the two-dimensional layers, which lie parallel to (100). In complex (III), the irregular centrosymmetric CsO6Cl2coordination environment comprises two O-atom donors and two ring-substituted Cl-atom donors from two hydrogen bis[(2,4-dichlorophenoxy)acetate] ligand species in a bidentate chelate mode, and four O-atom donors from bridging carboxyl groups. The duplex ligand species lie across crystallographic inversion centres, linked through a short O—H...O hydrogen bond involving the single acid H atom. Structure extension gives layers which lie parallel to (001). The present set of structures of Cs salts of phenoxyacetic acids show previously demonstrated trends among the alkali metal salts of simple benzoic acids with no stereochemically favourable interactive substituent groups for formation of two-dimensional coordination polymers.
An organic–inorganic hybrid compound containing imidazolium cations and a one-dimensional lithium hexacyanidocobaltate-based anionic framework
Authors: Shao Xiu-Dan , Yu Chun-Hua
Published: May 2014

An organic–inorganic hybrid compound,catena-poly[bis(3H-imidazol-1-ium) [[tetracyanido-κ4C-cobalt(III)]-μ-cyanido-κ2C:N-[diaqualithium(I)]-μ-cyanido-κ2N:C]], {(C3H5N2)2[CoLi(CN)6(H2O)2]}n, was synthesized by the reaction of Li3[Co(CN)6] with imidazolium chloride in aqueous solution. The compound crystallizes in the monoclinic space groupC2/c(data collected at 273 K). In the crystal structure, neighbouring [Co(CN)6]3−anionic units are linked by Li+cations through the cyanide groups in atransmode, forming a one-dimensional zigzag chain structure extending along thecaxis. A three-dimensional supramolecular network is formed through hydrogen-bonding interactions and is further stabilized by weak CN...π interactions between the cyanide groups and the imidazolium cations.
How loan interest rate liberalization affects firms’ loan maturity structure
Authors: Zhou Jianfang , Wang Jingjing , Ding Jianping
Published: May 2014

Purpose

– After loan interest rate upper limit deregulation in October 2004, the financing environment in China changed dramatically, and the banks were eligible for risk compensation. The purpose of this paper is to focus on the influence of the loan interest rate liberalization on firms’ loan maturity structure.

Design/methodology/approach

– Based on Rajan's (1992) model, the authors constructed a trade-off model of how the banks choose long-term and short-term loans scales, and further analyzed banks’ loan term decisions under the loan interest rate upper limit deregulation or collateral cases. Then the authors used an unbalanced panel data set of 586 Chinese listed manufacturing companies and 9,376 observations during the period 1996-2011 to testify the theoretical conclusion. Furthermore, the authors studied the effect on firms with different characteristics of ownership or scale.

Findings

– The results show that the loan interest rate liberalization significantly decreases the private companies’ reliance on short-term loans and increases sensitivity to interest rates of state-owned companies’ long-term loans. But the results also show that the companies’ ownership still plays a key role on the long-term loans availability. When monetary policy tightened, small companies still have to borrow short-term loans for long-term purposes. As the bank industry is still dominated by state-owned banks and the deposit interest rate has upper limits, the effect of the loan interest rate liberalization on easing long-term credit constraints is limited.

Originality/value

– From a new perspective, the content and findings of this paper contribute to the study of the effect of the interest rate liberalization on China economy.
Ant colony optimization for the topological design of interior permanent magnet (IPM) machines
Authors: S. Batista Lucas , Campelo Felipe , G. Guimarães Frederico , A. Ramírez Jaime , Li Min , A. Lowther David
Published: May 2014

Purpose

– The purpose of this paper is to apply an Ant colony optimization approach for the solution of the topological design of interior permanent magnet (IPM) machines.

Design/methodology/approach

– The IPM motor design domain is discretized into a suitable equivalent graph representation and an Ant System (AS) algorithm is employed to achieve an efficient distribution of materials into this graph.

Findings

– The single-objective problems associated with the maximization of the torque and with the maximization of the shape smoothness of the IPM are investigated. The rotor of the device is discretized into a 9×18 grid in both cases, and three different materials are considered: air, iron and permanent magnet.

Research limitations/implications

– The graph representation used enables the solution of topological design problems with an arbitrary number of materials, which is relevant for 2 and 3D problems.

Originality/value

– From the numerical experiments, the AS algorithm was able to achieve reasonable shapes and torque values for both design problems. The results show the relevance of the mechanism for multi-domain topology optimization of electromagnetic devices.
Decomposition based least squares iterative estimation algorithm for output error moving average systems
Authors: Zhang Wenge
Published: May 2014

Purpose

– The purpose of this paper is to solve the heavy computational problem of parameter estimation algorithm.

Design/methodology/approach

– Presents a decomposition least squares based iterative identification algorithm.

Findings

– Can estimate the parameters for linear or pseudo-linear systems and have lower computational burden.

Originality/value

– This paper adopts a decomposition technique to solve engineering computation problems and offers a potential and efficient algorithm.
Mixed convection boundary layer flow past a vertical flat plate embedded in a non-Darcy porous medium saturated by a nanofluid
Authors: C. Roşca Natalia , V. Roşca Alin , Groşan Teodor , Pop Ioan
Published: May 2014

Purpose

– The purpose of this paper is to numerically solve the problem of steady mixed convection boundary layer flow past a vertical flat plate embedded in a fluid-saturated porous medium filled by a nanofluid. The non-Darcy equation model along with the mathematical nanofluid model proposed by Tiwari and Das (2007) has been used.

Design/methodology/approach

– Using appropriate similarity transformations, the basic partial differential equations are transformed into ordinary differential equations. These equations have been solved numerically for different values of the nanoparticle volume fraction, the mixed convection and the non-Darcy parameters using the bvp4c function from Matlab. A stability analysis has been also performed.

Findings

– Numerical results are obtained for the reduced skin-friction, heat transfer and for the velocity and temperature profiles. The results indicate that dual solutions exist for the opposing flow case (λ<0). The stability analysis indicates that for the opposing flow case, the lower solution branch is unstable, while the upper solution branch is stable. In addition, it is shown that for a regular fluid (φ=0) a very good agreement exists between the present numerical results and those reported in the open literature.

Research limitations/implications

– The problem is formulated for three types of nanoparticles, namely, copper (Cu), alumina (Al2O3) and titania (TiO2). However, the paper present results here only for the Cu nanoparticles. The analysis reveals that the boundary layer separates from the plate. Beyond the turning point it is not possible to get the solution based on the boundary-layer approximations. To obtain further solutions, the full basic partial differential equations have to be solved.

Practical implications

– Nanofluids have many practical applications, for example, the production of nanostructured materials, engineering of complex fluids, for cleaning oil from surfaces due to their excellent wetting and spreading behavior, etc.

Social implications

– Nanofluids could be applied to almost any disease treatment techniques by reengineering the nanoparticle properties.

Originality/value

– The present results are original and new for the boundary-layer flow and heat transfer past a vertical flat plate embedded in a porous medium saturated by a nanofluid. Therefore, this study would be important for the researchers working in porous media in order to become familiar with the flow behavior and properties of such nanofluids.