bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poisson-saddlepoint approximation for Gibbs point processes with infinite-order interaction: in memory of Peter Hall
Authors: Baddeley Adrian , Nair Gopalan 
Published: November 2017

Abstract
We develop a computational approximation to the intensity of a Gibbs spatial point process having interactions of any order. Limit theorems from stochastic geometry, and small-sample probabilities estimated once and for all by an extensive simulation study, are combined with scaling properties to form an approximation to the moment generating function of the sufficient statistic under a Poisson process. The approximate intensity is obtained as the solution of a self-consistency equation.
Allosteric nanobodies uncover a role of hippocampal mGlu2 receptor homodimers in contextual fear consolidation
Authors: Scholler Pauline , Nevoltris Damien , de Bundel Dimitri , Bossi Simon , Moreno-Delgado David , Rovira Xavier , Møller Thor C. , El Moustaine Driss , Mathieu Michaël , Blanc Emilie , McLean Heather , Dupuis Elodie , Mathis Gérard , Trinquet Eric , Daniel Hervé , Valjent Emmanuel , Baty Daniel , Chames Patrick , Rondard Philippe , Pin Jean-Philippe 
Published: November 2017

AbstractAntibodies have enormous therapeutic and biotechnology potential. G protein-coupled receptors (GPCRs), the main targets in drug development, are of major interest in antibody development programs. Metabotropic glutamate receptors are dimeric GPCRs that can control synaptic activity in a multitude of ways. Here we identify llama nanobodies that specifically recognize mGlu2 receptors, among the eight subtypes of mGluR subunits. Among these nanobodies, DN10 and 13 are positive allosteric modulators (PAM) on homodimeric mGlu2, while DN10 displays also a significant partial agonist activity. DN10 and DN13 have no effect on mGlu2-3 and mGlu2-4 heterodimers. These PAMs enhance the inhibitory action of the orthosteric mGlu2/mGlu3 agonist, DCG-IV, at mossy fiber terminals in the CA3 region of hippocampal slices. DN13 also impairs contextual fear memory when injected in the CA3 region of hippocampal region. These data highlight the potential of developing antibodies with allosteric actions on GPCRs to better define their roles in vivo.
Warhead biosynthesis and the origin of structural diversity in hydroxamate metalloproteinase inhibitors
Authors: Leipoldt Franziska , Santos-Aberturas Javier , Stegmann Dennis P. , Wolf Felix , Kulik Andreas , Lacret Rodney , Popadić Désirée , Keinhörster Daniela , Kirchner Norbert , Bekiesch Paulina , Gross Harald , Truman Andrew W. , Kaysser Leonard 
Published: November 2017

AbstractMetalloproteinase inhibitors often feature hydroxamate moieties to facilitate the chelation of metal ions in the catalytic center of target enzymes. Actinonin and matlystatins are potent metalloproteinase inhibitors that comprise rare N-hydroxy-2-pentyl-succinamic acid warheads. Here we report the identification and characterization of their biosynthetic pathways. By gene cluster comparison and a combination of precursor feeding studies, heterologous pathway expression and gene deletion experiments we are able to show that the N-hydroxy-alkyl-succinamic acid warhead is generated by an unprecedented variation of the ethylmalonyl-CoA pathway. Moreover, we present evidence that the remarkable structural diversity of matlystatin congeners originates from the activity of a decarboxylase-dehydrogenase enzyme with high similarity to enzymes that form epoxyketones. We further exploit this mechanism to direct the biosynthesis of non-natural matlystatin derivatives. Our work paves the way for follow-up studies on these fascinating pathways and allows the identification of new protease inhibitors by genome mining.
Reversible silencing of lumbar spinal interneurons unmasks a task-specific network for securing hindlimb alternation
Authors: Pocratsky Amanda M. , Burke Darlene A. , Morehouse Johnny R. , Beare Jason E. , Riegler Amberly S. , Tsoulfas Pantelis , States Gregory J. R. , Whittemore Scott R. , Magnuson David S. K. 
Published: November 2017

AbstractNeural circuitry in the lumbar spinal cord governs two principal features of locomotion, rhythm and pattern, which reflect intra- and interlimb movement. These features are functionally organized into a hierarchy that precisely controls stepping in a stereotypic, speed-dependent fashion. Here, we show that a specific component of the locomotor pattern can be independently manipulated. Silencing spinal L2 interneurons that project to L5 selectively disrupts hindlimb alternation allowing a continuum of walking to hopping to emerge from the otherwise intact network. This perturbation, which is independent of speed and occurs spontaneously with each step, does not disrupt multi-joint movements or forelimb alternation, nor does it translate to a non-weight-bearing locomotor activity. Both the underlying rhythm and the usual relationship between speed and spatiotemporal characteristics of stepping persist. These data illustrate that hindlimb alternation can be manipulated independently from other core features of stepping, revealing a striking freedom in an otherwise precisely controlled system.
3D microniches reveal the importance of cell size and shape
Authors: Bao Min , Xie Jing , Piruska Aigars , Huck Wilhelm T. S. 
Published: November 2017

AbstractGeometrical cues have been shown to alter gene expression and differentiation on 2D substrates. However, little is known about how geometrical cues affect cell function in 3D. One major reason for this lack of understanding is rooted in the difficulties of controlling cell geometry in a complex 3D setting and for long periods of culture. Here, we present a robust method to control cell volume and shape of individual human mesenchymal stem cells (hMSCs) inside 3D microniches with a range of different geometries (e.g., cylinder, triangular prism, cubic, and cuboid). We find that the actin filaments, focal adhesions, nuclear shape, YAP/TAZ localization, cell contractility, nuclear accumulation of histone deacetylase 3, and lineage selection are all sensitive to cell volume. Our 3D microniches enable fundamental studies on the impact of biophysical cues on cell fate, and have potential applications in investigating how multicellular architectures organize within geometrically well-defined 3D spaces.
Contributions of Hamstring Stiffness to Straight-Leg-Raise and Sit-and-Reach Test Scores
Authors: Miyamoto Naokazu , Hirata Kosuke , Kimura Noriko , Miyamoto-Mikami Eri 
Published: November 2017

AbstractThe passive straight-leg-raise (PSLR) and the sit-and-reach (SR) tests have been widely used to assess hamstring extensibility. However, it remains unclear to what extent hamstring stiffness (a measure of material properties) contributes to PSLR and SR test scores. Therefore, we aimed to clarify the relationship between hamstring stiffness and PSLR and SR scores using ultrasound shear wave elastography. Ninety-eight healthy subjects completed the study. Each subject completed PSLR testing, and classic and modified SR testing of the right leg. Muscle shear modulus of the biceps femoris, semitendinosus, and semimembranosus was quantified as an index of muscle stiffness. The relationships between shear modulus of each muscle and PSLR or SR scores were calculated using Pearson’s product-moment correlation coefficients. Shear modulus of the semitendinosus and semimembranosus showed negative correlations with the two PSLR and two SR scores (absolute r value≤0.484). Shear modulus of the biceps femoris was significantly correlated with the PSLR score determined by the examiner and the modified SR score (absolute r value≤0.308). The present findings suggest that PSLR and SR test scores are strongly influenced by factors other than hamstring stiffness and therefore might not accurately evaluate hamstring stiffness.
Social media and political communication
Authors: Karlsson Martin , Åström Joachim 
Published: November 2017

Abstract
As the Internet has come to play a greater role in politics, there has been a
growing scholarly interest in how digital and social media are changing
politics. The competition between the innovation and normalization hypotheses
has been at the center of the debate. This article sets out to identify evidence
of innovation and normalization in terms of how politicians communicate in- and
the level of influence they are attaining within the political blogosphere. The
analyses conducted show paradoxical results as we find that those groups of
politicians who are utilizing political communication in the blogosphere in more
innovative and progressive ways – mirroring the hopes and expectations
about how social media might influence politicians and political
communication – have weaker positions within the blog network compared to
other politicians.
The Effects of Endotracheal Suctioning in the Pediatric Population
Authors: Fisk Anna C. 
Published: November 2017

Background:
Critically ill pediatric patients with endotracheal tubes routinely receive endotracheal tube suctioning to clear secretions and ensure tube patency. This common practice can result in adverse effects.

Objectives:
The aim of this study was to evaluate the research literature on the stressors of endotracheal suctioning and consequent effect on the pediatric patient.

Methods:
An integrative review was conducted using the Whittemore and Knafl modified framework for integrative reviews, and article selection was guided by the Preferred Reporting Items for Systematic Reviews and Meta-analyses flow diagram. A literature search was conducted via PubMed, the Cumulative Index to Nursing and Allied Health Literature, and Scopus. Selected articles were evaluated to present the current evidence on the stressors of endotracheal suctioning in the pediatric population.

Results:
This review includes 14 articles, with a total of 849 patients, ranging in age from premature neonates to 17 years of age. The available literature aligned into 3 categories: neurovascular effects, respiratory systems effects, and pain related to endotracheal tube suctioning. Pain was the most prevalent category, with half of the studies using endotracheal suctioning as a painful procedure to validate pain assessment tools rather than examining the effect of suctioning. A majority of the studies (67%) were conducted in the premature neonate population. Children with congenital cardiac or pulmonary defects, genetic syndromes, or neurological injuries were frequently excluded.

Conclusions:
Literature regarding the effects of endotracheal suctioning in children is limited. There are many extrapersonal, interpersonal, and intrapersonal stressors associated with endotracheal suctioning that merit future research.
Impact of an Ultrasonically Activated Device in Robot-Assisted Distal Gastrectomy
Authors: Hikage Makoto , Tokunaga Masanori , Makuuchi Rie , Tanizawa Yutaka , Bando Etsuro , Kawamura Taiichi , Terashima Masanori 
Published: November 2017

Objective Robot-assisted gastrectomy is increasingly used for the treatment of gastric cancer, although it remains a time-consuming procedure. An ultrasonically activated device might be useful to shorten operation times. This study therefore assessed the effect of ultrasonically activated device use on procedural times and on other early surgical outcomes. Methods Consecutive patients (N = 42) who underwent robot-assisted distal gastrectomy for gastric cancer were included. Clinicopathological characteristics and early surgical outcomes were compared between robotic-assisted gastrectomy procedures using an ultrasonically activated device (U group, n = 21) and those without it (NU group, n = 21). Results There were no significant differences in patient characteristics between the groups; however, the median operation time was significantly less in the U group than in the NU group (291 vs 351 minutes, P = 0.006). In detail, the median duration of console time until dividing the duodenum was less in the U group (70 vs 102 minutes, P < 0.001). Estimated blood loss, incidence of postoperative morbidity, and duration of postoperative hospital stay were not different between the groups. Conclusions An ultrasonically activated device reduced the operation time of robot-assisted gastrectomy without increasing blood loss and morbidity.
Success Rate of Tympanic Membrane Closure in the Elderly Compared to Younger Adults
Authors: Jolink Casper , Zwemstra Max R. , de Wolf Maarten J. F. , Ebbens Fenna A. , van Spronsen Erik 
Published: November 2017

Objective:
To assess the effectiveness and safety of tympanoplasty in elderly patients and the effect of frailty on the results.

Study Design:
Retrospective chart review.

Setting:
Tertiary referral center.

Patients:
Thirty-one ears in 30 patients aged 65 years and older were included and matched with 31 controls, based on the type of surgery, of a pool of 133 patients aged 35 to 55 years.

Intervention:
Therapeutic.

Main Outcome Measure:
Success was defined as tympanic membrane closure and resolution of presenting complaints. Complications were assessed. Frailty was defined by assessing multimorbidity and polypharmacy. Fisher's exact test was used to compare success and complication rates between the age groups. Linear logistic regression analysis using generalized linear models was performed on success and complication rate.

Results:
Success rates in both the groups were 84%. Complication rate in the elderly group was 16% versus 6% in the control group. This difference was not statistically significant in the Fisher's exact test. In the generalized linear model analysis age group, multimorbidity and polypharmacy had no significant influence on both success and complication rate.

Conclusion:
There was no difference in success and complication rate in elderly undergoing tympanoplasty compared with younger adults. Having multimorbidity or polypharmacy did not correlate with failure of the tympanic membrane closure or a higher complication rate.
A new sequence logo plot to highlight enrichment and depletion
Authors: Dey Kushal K. , Xie Dongyue , Stephens Matthew 
Published: November 2017

AbstractBackgroundSequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesting depletions. Current alternatives that try to highlight depletion often produce visually cluttered logos.ResultsWe introduce a new sequence logo plot, the EDLogo plot, that highlights both enrichment and depletion, while minimizing visual clutter. We provide an easy-to-use and highly customizable R package Logolas to produce a range of logo plots, including EDLogo plots. This software also allows elements in the logo plot to be strings of characters, rather than a single character, extending the range of applications beyond the usual DNA, RNA or protein sequences. We illustrate our methods and software on applications to transcription factor binding site motifs, protein sequence alignments and cancer mutation signature profiles.ConclusionOur new EDLogo plots, and flexible software implementation, can help data analysts visualize both enrichment and depletion of characters (DNA sequence bases, amino acids, etc) across a wide range of applications.
Enumerating all possible biosynthetic pathways from metabolic networks
Authors: Ravikrishnan Aarthi , Nasre Meghana , Raman Karthik 
Published: November 2017

AbstractExhaustive identification of all alternate possible pathways that exist within metabolic networks can provide valuable insights into cellular metabolism. With the growing number of metabolic reconstructions, there is a need for an efficient method to enumerate pathways, which can also scale well to large metabolic networks, such as those corresponding to microbial communities.We developed MetQuest, an efficient graph-theoretic algorithm to enumerate all possible pathways of a particular length between a given set of source and target molecules. Our algorithm employs aguidedbreadth-first search to identify all feasible reactions based on the availability of the precursor molecules, followed by a novel dynamic-programming based enumeration, which assembles these reactions into pathways producing the target from the source. We demonstrate several interesting applications of our algorithm, ranging from predicting amino acid biosynthesis pathways to identifying the most diverse pathways involved in degradation of complex molecules. We also illustrate the scalability of our algorithm, by studying larger graphs such as those corresponding to microbial communities, and identify several metabolic interactions happening therein.A Python-based implementation of MetQuest is available athttps://github.com/RamanLab/MetQuest
Conformational control of translation termination on the 70S ribosome
Authors: Svidritskiy Egor , Korostelev Andrei A. 
Published: November 2017

AbstractTranslation termination ensures proper lengths of cellular proteins. During termination, release factor (RF) recognizes a stop codon and catalyzes peptide release. Conformational changes in RF are thought to underlie accurate translation termination. If true, the release factor should bind the A-site codon in inactive (compact) conformation(s), but structural studies of ribosome termination complexes have only captured RFs in an extended, active conformation. Here, we identify a hyper-accurate RF1 variant, and present crystal structures of 70S termination complexes that suggest a structural pathway for RF1 activation. In the presence of blasticidin S, the catalytic domain of RF1 is removed from the peptidyl-transferase center, whereas the codon-recognition domain is fully engaged in stop-codon recognition in the decoding center. RF1 codon recognition induces decoding-center rearrangements that precede accommodation of the catalytic domain. Our findings suggest how structural dynamics of RF1 and the ribosome coordinate stop-codon recognition with peptide release, ensuring accurate translation termination.
To integrate or not to integrate? Understanding B2B social media communications
Authors: Gruner Richard L. , Power Damien 
Published: November 2017

PurposeSocial media communications on platforms such as Facebook and LinkedIn can allow managers to interact cost effectively with trading partners. However, although most firms have an online presence on multiple social media platforms, the question remains as to whether marketers’ widespread social media investments are beneficial for firms. The paper aims to discuss this issue.Design/methodology/approachThis paper presents competing hypotheses to explore how firms’ investment in one form of social media impacts activity on another form of social media. To do so, the authors draw on a data set of 208 large Australian organizations using objective social media activity metrics that measure business-to-business (B2B) audience engagement.FindingsThe findings suggest that widespread social media activity on LinkedIn, Twitter, and YouTube negatively affects a firm’s marketing activity on Facebook. The results indicate that having a social media preference whereby firms focus on a specific social media platform is more effective in forming successful inter-organizational relationships than a multiplatform approach.Originality/valueThe study contributes to the sparse research that seeks to leverage social media for audience engagement beyond a business-to-consumer context. The study’s findings provide insights into the key mechanisms that underlie firms’ B2B social media strategies, and in so doing, offer a fresh perspective on the importance of interactive marketing communication.
Representing Metro Manila on Wikipedia
Authors: Luyt Brendan 
Published: November 2017

PurposeThe advent and wide use of new digital technologies suggests that the internet is becoming a powerful new media for the imagination of city space. If this is the case then issues concerning urban representation on social media platforms such as Wikipedia provide an area of overlap and interest between urban studies and information studies. The purpose of this paper is to examine the representation of Manila, Philippines, one of the world’s major mega cities, on the popular online encyclopedia Wikipedia.Design/methodology/approachThe author’s broad approach to the study of Wikipedia is qualitative in nature. For this study the entire Metro Manila article was downloaded on March 16, 2015 and subjected to textual analysis.FindingsWhile the Wikipedia article on Manila cannot be classified as promotional, it is clear that much of the city remains invisible in this work. Such a puzzle becomes understandable when we examine the urban studies literature where we find that the spatial logic of the city itself helps conceal much from view, so that what we read on Wikipedia is a view from the islands of privilege rather than the oceans of marginalization that make up much of the city’s spatial form. If such a spatial structure is to change, representations such as found on Wikipedia need to be challenged.Originality/valueWikipedia is a key element of today’s information infrastructure yet despite its importance it remains relatively understudied within the field of information science. More specifically, the role of Wikipedia in representing cities, the dominant settlement form in the world today, has not been previously studied.