bluuebunny/crossref_metadata_2025_split huggingface dataset:
The sociophonetic orientation of the language learner
Authors: Labov William 
Published: May 2014

This paper is an effort to define the phonetic target of the language learner: what are the data that the child focuses on in becoming a native speaker? A number of studies are reviewed to show that children reject the idiosyncratic features of their parents’ phonetic system if they do not match the pattern of the larger speech community: in the acquisition of the Philadelphia and New York City dialects; the formation of a new dialect in Milton Keynes; the spread of the low back merger in eastern New England; the reduction of the future marker in Tok Pisin. The end result is a high degree of uniformity in both the categorical and variable aspects of language, where individual variation is reduced below the level of linguistic significance.
On the Pathology of the Enthymeme: Accounting for Hidden Visual Premises in Advertising Discourse
Authors: Rossolatos George 
Published: May 2014

AbstractOne of the key reasons that have been put forward for justifying the superior argumentative force of visuals over verbal arguments in advertising discourse is their immediacy. The immediate resonance of visuals and their forceful appeal bear considerable resemblance to the argumentative force of enthymemes as hidden premises in informal rhetorical argumentation. In this article an attempt is made at bridging the logical and pathemic appeals of enthymemes under the aegis of what may be called the pathology of the enthymeme, while demonstrating that what has been pejoratively tagged, since Freudian psychoanalytic discourse, as “the psychopathology of everyday life” in fact constitutes the very underpinning of enthymematic structures and a system of topoi of which such structures constitute an integral part. By assuming as the point of departure of this genealogico-pathological tracing Heidegger’s opening up of the meaning of logos and as destination Heidegger’s ontological reading of everydayness, the enthymematic embeddedness of cultural topoi is depathologized, while being reinserted in its “proper” pathological dimension. The exemplification of how visual enthymemes function and may be translated as hidden premises in advertising discourse seeks to demonstrate the pathology of the enthymeme as “unquestionable” major premises that underpin visual arguments.
Converting Knights: A Semiotic Reading of Spiritual Change in Four Italian Chivalric Poems
Authors: Leone Massimo 
Published: May 2014

AbstractThis essay compares representations of religious conversion in four Italian chivalric poems: Luigi Pulci’s Morgante, Matteo Maria Boiardo’s Orlando innamorato, Ludovico Ariosto’s Orlando furioso, and Torquato Tasso’s Gerusalemme liberata. Semiotically read, they cast new light on the Catholic idea of the religious self in its development from the late Middle Ages throughout the early modern era. In this evolution, the Council of Trent represents a fundamental watershed.
Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells
Authors: Aranda Sergi , Rutishauser Dorothea , Ernfors Patrik 
Published: May 2014

Abstract
Pluripotency of embryonic stem cells (ESCs) is maintained by transcriptional activities and chromatin modifying complexes highly organized within the chromatin. Although much effort has been focused on identifying genome-binding sites, little is known on their dynamic association with chromatin across cell divisions. Here, we used a modified version of the iPOND (isolation of proteins at nascent DNA) technology to identify a large protein network enriched at nascent DNA in ESCs. This comprehensive and unbiased proteomic characterization in ESCs reveals that, in addition to the core replication machinery, proteins relevant for pluripotency of ESCs are present at DNA replication sites. In particular, we show that the chromatin remodeller HDAC1–NuRD complex is enriched at nascent DNA. Interestingly, an acute block of HDAC1 in ESCs leads to increased acetylation of histone H3 lysine 9 at nascent DNA together with a concomitant loss of methylation. Consistently, in contrast to what has been described in tumour cell lines, these chromatin marks were found to be stable during cell cycle progression of ESCs. Our results are therefore compatible with a rapid deacetylation-coupled methylation mechanism during the replication of DNA in ESCs that may participate in the preservation of pluripotency of ESCs during replication.
Motions of the central objects in cD clusters of galaxies and transverse cooling flows
Authors: Inoue Hajime 
Published: May 2014

Abstract
We first study dynamical effects of dark matter sub-halos (optically observed as member galaxies) on the central object (optically observed as a cD galaxy) in a cD cluster of galaxies. The sub-halos come closest to the center in turn and cause the central object to be pulled to random directions.Thus, the central object tends to move with a velocity given from an equipartition of the kinetic energy of the central object with the averaged kinetic energy of the sub-halos. The dark matter particles in the halo around the central object, however, give the central object a drag force to suppress the motion. Under a balance between the energy input from the closest sub-halo and the output to the ambient dark matter halo, the average velocity of the central object is roughly estimated to be 107 cm s−1. We secondly investigate effects of radiative cooling on hot plasma when the central object moves relatively to the hot plasma. The current cooling flow hypothesis is based on the estimation that the radiative cooling time is sufficiently shorter than the age of the cluster of galaxies. In the present case, however, the cooling flow would be excited when the radiative cooling time is shorter than the plasma passage time across the central object. We perform such a time scale comparison in an approximate way, and find that only the plasma flowing to the central object with an impact parameter less than a critical one is trapped by the central object and falls on to the central object as the cooling flow. This transverse cooling flow scenario well explains several observational evidences which have been argued to be inconsistent with the current isotropic cooling flow hypothesis, when the relative velocity is ∼ 107 cm s−1.
A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
Authors: O’Geen Henriette , Henry Isabelle M. , Bhakta Mital S. , Meckler Joshua F. , Segal David J. 
Published: May 2014

ABSTRACTClustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most previous studies have examined predicted off-target binding sites that differ from the perfect target site by one to four mismatches, which represent only a subset of genomic regions. Here, we use ChIP-seq to examine genome-wide CRISPR binding specificity at gRNA-specific and gRNA-independent sites. For two guide RNAs targeting the murineSnurfgene promoter, we observed very high binding specificity at the intended target site while off-target binding was observed at 2- to 6-fold lower intensities. We also identified significant gRNA-independent off-target binding. Interestingly, we found that these regions are highly enriched in the PAM site, a sequence required for target site recognition by CRISPR. To determine the relationship between Cas9 binding and endonuclease activity, we used targeted sequence capture as a high-throughput approach to survey a large number of the potential off-target sites identified by ChIP-seq or computational prediction. A high frequency of indels was observed at both target sites and one off-target site, while no cleavage activity could be detected at other ChIP-bound regions. Our data is consistent with recent finding that most interactions between the CRISPR nuclease complex and genomic PAM sites are transient and do not lead to DNA cleavage. The interactions are stabilized by gRNAs with good matches to the target sequence adjacent to the PAM site, resulting in target cleavage activity.
Pluripotency in the light of the developmental hourglass
Authors: Kuijk Ewart , Geijsen Niels , Cuppen Edwin 
Published: May 2014

ABSTRACTThe hourglass model of development postulates divergence in early and late embryo development bridged by a period of developmental constraint at mid‐embryogenesis. Recently, molecular support for the hourglass model of development has accumulated, with the emphasis on studies using zebrafish and Drosophila species. Across mammals, the hourglass model and specifically divergence in early development has thus far received little attention. Divergence in mammalian pre‐implantation development is particularly interesting because of its potential impact on derivation of pluripotent embryonic stem cells. Here, we review recent findings that support the hourglass model of development. We provide striking examples of variation in key events in mammalian peri‐implantation development and their potential consequences for pluripotency of embryonic stem cell lines, including mechanisms of cell signalling and differentiation, gene regulatory networks, X‐chromosome inactivation, and epigenetic regulation. The variation in these processes indicates divergence in early mammalian development as was postulated by the hourglass model of development. We discuss the naive and primed states of pluripotency in light of this developmental divergence and their implications for human pluripotent stem cell states.
Impact of tillage intensity on carbon and nitrogen pools in surface and sub‐surface soils of three long‐term field experiments
Authors: Kaiser M. , Piegholdt C. , Andruschkewitsch R. , Linsler D. , Koch H.‐J. , Ludwig B. 
Published: May 2014

SummaryManagement options such as the intensity of tillage are known to influence the turnover dynamics of soil organic matter. However, less information is available about the influence of the tillage intensity on individual soil organic matter pools with different turnover dynamics in surface as compared with sub‐surface soils. This study aimed to analyse the impact of no tillage (NT), reduced tillage (RT) and conventional tillage (CT) on labile, intermediate and stable carbon (C) and nitrogen (N) pools in surface and sub‐surface soils. We took surface and sub‐surface soil samples from the three tillage systems in three long‐term field experiments in Germany. The labile, intermediate and stable C and N pool sizes were determined by using the combined application of a decomposition experiment and a physical‐chemical separation procedure. For the surface soils, we found larger stocks of the labile C and N pool under NT and RT (C, 1.7 and 1.3 t ha−1; N, 180 and 160 kg ha−1) than with CT (C, 0.5 t ha−1; N, 60 kg ha−1). In contrast, we found significantly larger stocks of the labile C pool under CT (2.7 t ha−1) than with NT and RT (2 t ha−1) for the sub‐surface soils. The intermediate pool accounted for 75–84% of the soil organic C and total N stocks. However, the stocks of the intermediate N and C pools were only distinctly larger for NT than for CT in the surface soils. The stocks of the stable C and N pools were not affected by the tillage intensity but were positively correlated with the stocks of the clay‐size fraction and oxalate soluble aluminum, indicating a strong influence of site‐specific mineral characteristics on the size of these pools. Our results indicate soil depth‐specific variations in the response of organic matter pools to tillage of different intensity. This means that the potential benefits of decreasing tillage intensity with respect to soil functions that are closely related to organic matter dynamics have to be evaluated separately for surface and sub‐surface soils.
Abnormal response to photic stimulation in Juvenile Myoclonic Epilepsy: An EEG‐fMRI study
Authors: Bartolini Emanuele , Pesaresi Ilaria , Fabbri Serena , Cecchi Paolo , Giorgi Filippo Sean , Sartucci Ferdinando , Bonuccelli Ubaldo , Cosottini Mirco 
Published: May 2014

SummaryObjectiveJuvenile myoclonic epilepsy (JME) is a young‐onset electroclinical syndrome, characterized by myoclonic, generalized tonic–clonic, and possibly typical absence seizures. Interictal electroencephalography (EEG) displays 3–6 Hz spike/polyspike and wave pattern. Photosensitivity is common. Our aim was to explore the blood oxygen level–dependent (BOLD) response evoked by a highly provocative photic stimulus in a cohort of people with JME compared to a group of nonphotosensitive healthy controls, and to investigate the hemodynamic phenomena seen in patients with photosensitive JME.MethodsWe studied 13 JME patients and 18 healthy controls using EEG–functional magnetic resonance imaging (fMRI) performed during low luminance intermittent photic stimulation (IPS). The BOLD response to IPS was investigated both in JME and control groups. In photosensitive JME subjects, we also performed a dynamic evaluation of BOLD signal changes evoked by the photoparoxysmal response (PPR) in a time frame ranging from 10 s before the onset of the EEG paroxysm up until 10 s afterward.ResultsThe IPS evoked a positive BOLD response in striate and extrastriate visual areas, which was less in JME patients than in controls. Moreover, people with JME had a reduced positive BOLD response in the frontoparietal areas and putamen but a stronger negative BOLD response in the primary sensorimotor cortex (SM1) and in cortical regions belonging to the default mode network (DMN). In JME, the dynamic evaluation of BOLD signal changes related to PPR revealed an early positive response in the putamen and SM1, followed by BOLD signal decrements in the putamen, caudate nuclei, thalami, and SM1.SignificanceOur results confirm the hypothesis that people with JME might have an altered interaction between the motor circuit and other neuronal networks, with prominent involvement of basal ganglia circuitry. The PPR could be a final expression of pathogenic phenomena occurring in the striato‐thalamocortical system, possibly a core feature of system epilepsy JME.A PowerPoint slide summarizing this article is available for download in the Supporting Information section here.
Biochemical characterization of the tandem HAMP domain from Natronomonas pharaonis as an intraprotein signal transducer
Authors: Natarajan Janani , Schultz Anita , Kurz Ursula , Schultz Joachim E. 
Published: May 2014

Available structures of HAMP domains suggest rotation as one potential mechanism in intraprotein signal transduction. It has been proposed that in poly‐HAMP modules the signal sign is inverted with each additional HAMP. We examined signal transduction through the HAMP tandem domain from the phototaxis transducer of the halophilic archaeon Natronomonas pharaonis in membrane‐bound chimeras consisting of the Escherichia coli chemotaxis receptor for serine, Tsr, as an input and the mycobacterial adenylyl cyclase Rv3645 as an output domain, i.e. the basic chimera was ‘Tsr–NpHAMP tandem–Rv3645 cyclase’. Neither of the NpHAMP units alone nor the NpHAMP tandem transduced a serine signal. After five targeted point mutations in the first α‐helix of NpHAMP1, the non‐functional NpHAMP modules combined into a functional HAMP tandem. 1 mm serine significantly inhibited cyclase activity (−35%; IC50 = 30 μm) in disagreement with the structure‐based predictions. Surprisingly, replacement of NpAS11 in the tandem by the respective AS1 from HAMPTsr resulted in signal inversion, i.e. serine activated cyclase (+129%; EC50 = 10 μm). Examination of 48 mutants of AS11 in the HAMP tandem including two residues of a putative N‐terminal control cable identified five residues in NpAS11 which probably define different ground states of the output domain and thus affect the sign of signal output. The data question the predicted HAMP rotation as the predominant mechanism of intraprotein signal transduction and point to as yet unrecognized conformational motions of HAMP domains in intraprotein signaling.
Apical extrusion of debris using ProTaper Universal and ProTaper Next rotary systems
Authors: Koçak M. M. , Çiçek E. , Koçak S. , Sağlam B. C. , Yılmaz N. 
Published: May 2014

AbstractAimTo assess and compare the amount of extruded debris after canal preparation using ProTaper Universal and ProTaper Next files.MethodologyForty extracted mandibular premolars with single canals and of similar lengths were instrumented using the ProTaper Universal F3 or the ProTaper Next X3. The extruded debris during instrumentation was collected into pre‐weighed Eppendorf tubes. The tubes were stored in an incubator for 5 days. The tubes were weighed to obtain the final dry weight of the extruded debris. The amount of apically extruded debris was calculated by subtracting the initial weight of the tube from the final weight. The distribution of the data was examined using the Shapiro–Wilks test. Continuous variables were compared with an independent‐samples t‐test for two groups.ResultsAll specimens were associated with apical debris extrusion. The ProTaper Universal group produced a significantly greater amount of debris extrusion (P < 0.001). The lowest and highest amounts of debris for PTU and PTN groups were recorded as 0.00117–0.00165 g and 0.00017–0.00067 g, respectively.ConclusionProTaper Next files was associated with significantly less extruded apical debris when compared to ProTaper Universal files.
Effect of surgical incision management on wound infections in a poststernotomy patient population
Authors: Grauhan Onnen , Navasardyan Artashes , Tutkun Baris , Hennig Felix , Müller Peter , Hummel Manfred , Hetzer Roland 
Published: May 2014

AbstractSkin breakdown and infiltration of skin flora are key causative elements in poststernotomy wound infections. We hypothesised that surgical incision management (SIM) using negative pressure wound therapy over closed surgical incisions for 6–7 days would reduce wound infections in a comprehensive poststernotomy patient population. ‘All comers’ undergoing median sternotomy at our institution were analysed prospectively from 1 September to 15 October 2013 (study group, n = 237) and retrospectively from January 2008 to December 2009 (historical control group, n = 3508). The study group had SIM (Prevena™ Therapy) placed immediately after skin suturing and applied at −125 mmHg for 6–7 days, whereas control group received conventional sterile wound tape dressings. Primary endpoint was wound infection within 30 days. Study group had a significantly lower infection rate than control group: 1·3% (3 patients) versus 3·4% (119 patients), respectively (P < 0·05; odds ratio 2·74). In the study group, when the foam dressing was removed after 6–7 days, the incision was primarily closed in 234 of 237 patients (98·7%). SIM over clean, closed incisions for the first 6‐7 postoperative days significantly reduced the incidence of wound infection after median sternotomy. Based on these data SIM may be cost‐effective in patients undergoing cardiac surgery.
A simple novel technique for enteroatmospheric fistulae: silicone fistula plug
Authors: Ozer M Tahir , Sinan Hüseyin , Zeybek Nazif , Peker Yusuf 
Published: May 2014

AbstractEnteroatmospheric fistulae (EAFs), a rare condition that develops in patients treated with an open abdomen, present serious problems for the surgeon. There are no fixed algorithms for treatment of EAF, and treatment options are determined based on the experience of the surgeon and status of the patient. We developed a ‘suspended silicone fistula plug’ for treating a patient who developed an EAF after undergoing multiple operations in a short period of time. Used in conjunction with negative pressure wound therapy, application of this novel therapy resulted in EAF closure and patient discharge.
Long‐term outcome of Guillain‐Barré syndrome in children
Authors: Roodbol Joyce , de Wit Marie‐Claire Y. , Aarsen Femke K. , Catsman‐Berrevoets Coriene E. , Jacobs Bart C. 
Published: May 2014

AbstractThe objective of this study is to determine the long‐term outcome and consequences of Guillain‐Barré syndrome (GBS) in children. This is an observational cross‐sectional cohort study of children diagnosed with GBS (0–18 years old) at the Sophia Children's Hospital in Rotterdam from 1987 to 2009. All patients were invited for a structured interview, questionnaires, and full neurologic exam to record their current clinical condition focused on complaints and symptoms, neurological deficits, disabilities, behavior, and quality of life. Thirty‐seven patients participated, 23 were now adults, with a median age of 20 years (range 4–39 years) and a median follow‐up time of 11 years (range 1–22 years). Residual complaints were reported by 24 (65%) patients, including paresthesias (38%), unsteadiness of gait in the dark (37%), painful hands or feet (24%), and severe fatigue (22%). Four patients had severe neurological deficits, including facial diplegia and limb weakness. Two patients had had a recurrence of GBS. In 10 patients (26%), GBS had a negative impact on their school career. Questionnaires identified a wide range of behavioral problems. Quality of life was below normal on the subscale vitality, and above normal on the subscales social functioning and positive emotions in the adult group. Most children show good recovery of neurological deficits after GBS, but many have persisting long‐term residual complaints and symptoms that may lead to psychosocial problems interfering with participation in daily life.
Design rules for efficient transgene expression in plants
Authors: Jackson Mark A. , Sternes Peter R. , Mudge Stephen R. , Graham Michael W. , Birch Robert G. 
Published: May 2014

SummarySustained expression of transgenes in specified developmental patterns is commonly needed in plant biotechnology, but obstructed by transgene silencing. Here, we present a set of gene design rules, tested on the silencing‐susceptible beetle luc and bacterial ims genes, expressed in sugarcane. Designs tested independently or in combination included removal of rare codons, removal of RNA instability sequences, blocking of likely endogenous sRNA binding sites and randomization of non‐rare codons. Stable transgene expression analyses, on multiple independent lines per construct, showed greatest improvement from the removal of RNA instability sequences, accompanied by greatly reduced transcript degradation evident in northern blot analysis. We provide a set of motifs that readily can be eliminated concurrently with rare codons and undesired structural features such as repeat sequences, using Gene Designer 2.0 software. These design rules yielded 935‐ and 5‐fold increased expression in transgenic callus, relative to the native luc and ims sequences; and gave sustained expression under the control of sugarcane and heterologous promoters over several years in greenhouse and field trials. The rules can be applied easily with codon usage tables from any plant species, providing a simple and effective means to achieve sustained expression of otherwise silencing‐prone transgenes in plants.