bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of a novel cellular model for myxofibrosarcoma heterogeneity
Authors: Lohberger Birgit , Stuendl Nicole , Leithner Andreas , Rinner Beate , Sauer Stefan , Kashofer Karl , Liegl-Atzwanger Bernadette 
Published: March 2017

AbstractHuman cancers frequently display substantial intra-tumoural heterogeneity in virtually all distinguishable phenotypic features, such as cellular morphology, gene expression, and metastatic potential. In order to investigate tumour heterogeneity in myxofibrosarcoma, we established a novel myxofibrosarcoma cell line with two well defined sub-clones named MUG-Myx2a and MUG-Myx2b. The parental tumour tissue and both MUG-Myx2 cell lines showed the same STR profile. The fact that MUG-Myx2a showed higher proliferation activity, faster migration and enhanced tumourigenicity was of particular interest. NGS mutation analysis revealed corresponding mutations in the FGFR3, KIT, KDR and TP53 genes. In contrast, the MUG-Myx2a cell lines showed an additional PTEN mutation. Analysis of CNV uncovered a highly aberrant karyotype with frequent losses and gains in the tumour sample. The two MUG-Myx2 cell lines share several CNV features of the tumour tissue, while some CNVs are present only in the two cell lines. Furthermore, certain CNV gains and losses that are exclusive to either MUG-Myx2a or MUG-Myx2b, distinguish the two cell lines. As it is currently not possible to purchase two different sarcoma cell lines derived from the same patient, the novel myxofibrosarcoma cell lines MUG-Myx2a and MUG-Myx2b will be useful tools to study pathogenesis, tumour heterogeneity and treatment options.
Effects of collision cascade density on radiation defect dynamics in 3C-SiC
Authors: Bayu Aji L. B. , Wallace J. B. , Kucheyev S. O. 
Published: March 2017

AbstractEffects of the collision cascade density on radiation damage in SiC remain poorly understood. Here, we study damage buildup and defect interaction dynamics in 3C-SiC bombarded at 100 °C with either continuous or pulsed beams of 500 keV Ne, Ar, Kr, or Xe ions. We find that bombardment with heavier ions, which create denser collision cascades, results in a decrease in the dynamic annealing efficiency and an increase in both the amorphization cross-section constant and the time constant of dynamic annealing. The cascade density behavior of these parameters is non-linear and appears to be uncorrelated. These results demonstrate clearly (and quantitatively) an important role of the collision cascade density in dynamic radiation defect processes in 3C-SiC.
Multiscale microenvironmental perturbation of pluripotent stem cell fate and self-organization
Authors: Tabata Yoji , Lutolf Matthias P. 
Published: March 2017

AbstractThe combination of microfluidics with engineered three-dimensional (3D) matrices can bring new insights into the fate regulation of stem cells and their self-organization into organoids. Although there has been progress in 3D stem cell culturing, most existing in vitro methodologies do not allow for mimicking of the spatiotemporal heterogeneity of stimuli that drive morphogenetic processes in vivo. To address this, we present a perfusion-free microchip concept for the in vitro 3D perturbation of stem cell fate. Stem cells are encapsulated in a hydrogel compartment that is flanked by open reservoirs for the diffusion-driven generation of biomolecule gradients. Juxtaposing additional compartments bearing supportive cells enables investigating the influence of long range cell-cell communication. We explore the utility of the microchips in manipulating early fate choices and self-organizing characteristics of 3D-cultured mouse embryonic stem cells (mESCs) under neural differentiation conditions and exposure to gradients of leukemia inhibitory factor (LIF). mESCs respond to LIF gradients in a spatially dependent manner. At higher LIF concentrations, multicellular colonies maintain pluripotency in contrast, at lower concentrations, mESCs develop into apicobasally polarized epithelial cysts. This versatile system can help to systematically explore the role of multifactorial microenvironments in promoting self-patterning of various stem cell types.
Organic Power Electronics: Transistor Operation in the kA/cm2 Regime
Authors: Klinger Markus P. , Fischer Axel , Kaschura Felix , Widmer Johannes , Kheradmand-Boroujeni Bahman , Ellinger Frank , Leo Karl 
Published: March 2017

AbstractIn spite of interesting features as flexibility, organic thin-film transistors have commercially lagged behind due to the low mobilities of organic semiconductors associated with hopping transport. Furthermore, organic transistors usually have much larger channel lengths than their inorganic counterparts since high-resolution structuring is not available in low-cost production schemes. Here, we present an organic permeable-base transistor (OPBT) which, despite extremely simple processing without any high-resolution structuring, achieve a performance beyond what has so far been possible using organic semiconductors. With current densities above 1 kA cm−2 and switching speeds towards 100 MHz, they open the field of organic power electronics. Finding the physical limits and an effective mobility of only 0.06 cm2 V−1 s−1, this OPBT device architecture has much more potential if new materials optimized for its geometry will be developed.
Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
Authors: Yu Jian , Ciaudo Constance 
Published: March 2017

AbstractForward genetic screens using retroviral (or transposon) gene-trap vectors in a haploid genome revolutionized the investigation of molecular networks in mammals. However, the sequencing data generated by Phenotypic interrogation followed by Tag sequencing (PhiT-seq) were not well characterized. The analysis of human and mouse haploid screens allowed us to describe PhiT-seq data and to define quality control steps. Moreover, we identified several blind spots in both haploid genomes where gene-trap vectors can hardly integrate. Integration of transcriptomic data improved the performance of candidate gene identification. Furthermore, we experimented with various statistical tests to account for biological replicates in PhiT-seq and investigated the effect of normalization methods and other parameters on the performance. Finally, we developed: VISITs, a dedicated pipeline for analyzing PhiT-seq data (https://sourceforge.net/projects/visits/).
The processing of body expressions during emotional scenes: the modulation role of attachment styles
Authors: Ma Yuanxiao , Chen Xu , Ran Guangming , Ma Haijing , Zhang Xing , Liu Guangzeng 
Published: March 2017

AbstractThere is broad evidence indicating that contextual information influence the processing of emotional stimuli. However, attachment theory suggests that attachment styles contribute to the ways in which people perceive emotional events. To shed light on whether the processing of body expressions during different emotional scenes is modulated by attachment styles, attachment-related electrophysiological differences were measured using event-related potentials. For avoidantly attached group, our results suggested that larger N170 amplitudes were educed by neutral bodies than angry bodies, which was found only in neutral scene. Moreover, significant differences were found in P300 amplitudes in response to angry bodies compared with neutral ones only during angry scene. However, securely and anxiously attached individuals were associated with larger P300 amplitudes in response to angry bodies versus neutral ones in both emotional scenes. The current study highlights the characteristics of cognitive processing of attachment styles on body expressions during different emotional scenes, with the variation of N170 and P300 amplitude in different emotional scenes as the best example.
E6/E7-P53-POU2F1-CTHRC1 axis promotes cervical cancer metastasis and activates Wnt/PCP pathway
Authors: Zhang Rong , Lu Huan , Lyu Yuan-yuan , Yang Xiao-mei , Zhu Lin-yan , Yang Guang-dong , Jiang Peng-cheng , Re Yuan , Song Wei-wei , Wang Jin-hao , Zhang Can-can , Gu Fei , Luo Tian-jiao , Wu Zhi-yong , Xu Cong-jian 
Published: March 2017

AbstractCervical cancer is an infectious cancer and the most common gynecologic cancer worldwide. E6/E7, the early genes of the high-risk mucosal human papillomavirus type, play key roles in the carcinogenic process of cervical cancer. However, little was known about its roles in modulating tumor microenvironment, particular extracellular matrix (ECM). In this study, we found that E6/E7 could regulate multiple ECM proteins, especially collagen triple helix repeat containing 1 (CTHRC1). CTHRC1 is highly expressed in cervical cancer tissue and serum and closely correlated with clinicopathological parameters. CTHRC1 promotes cervical cancer cell migration and invasion in vitro and metastasis in vivo. E6/E7 regulates the expression of CTHRC1 in cervical cancer by E6/E7-p53-POU2F1 (POU class 2 homeobox 1) axis. Futhermore, CTHRC1 activates Wnt/PCP signaling pathway. Take together, E6/E7-p53-POU2F1-CTHRC1 axis promotes cervical cancer cell invasion and metastasis and may act as a potential therapeutic target for interventions against cervical cancer invasion and metastasis.
Exposure to selenomethionine causes selenocysteine misincorporation and protein aggregation in Saccharomyces cerevisiae
Authors: Plateau Pierre , Saveanu Cosmin , Lestini Roxane , Dauplais Marc , Decourty Laurence , Jacquier Alain , Blanquet Sylvain , Lazard Myriam 
Published: March 2017

AbstractSelenomethionine, a dietary supplement with beneficial health effects, becomes toxic if taken in excess. To gain insight into the mechanisms of action of selenomethionine, we screened a collection of ≈5900 Saccharomyces cerevisiae mutants for sensitivity or resistance to growth-limiting amounts of the compound. Genes involved in protein degradation and synthesis were enriched in the obtained datasets, suggesting that selenomethionine causes a proteotoxic stress. We demonstrate that selenomethionine induces an accumulation of protein aggregates by a mechanism that requires de novo protein synthesis. Reduction of translation rates was accompanied by a decrease of protein aggregation and of selenomethionine toxicity. Protein aggregation was supressed in a ∆cys3 mutant unable to synthetize selenocysteine, suggesting that aggregation results from the metabolization of selenomethionine to selenocysteine followed by translational incorporation in the place of cysteine. In support of this mechanism, we were able to detect random substitutions of cysteinyl residues by selenocysteine in a reporter protein. Our results reveal a novel mechanism of toxicity that may have implications in higher eukaryotes.
Altered microstructure rather than morphology in the corpus callosum after lower limb amputation
Authors: Li Zhichao , Li Chuanming , Fan Lingzhong , Jiang Guangyao , Wu Jixiang , Jiang Tianzi , Yin Xuntao , Wang Jian 
Published: March 2017

AbstractThe corpus callosum (CC) has been implicated in the reorganization of the brain following amputation. However, it is unclear which regions of the CC are involved in this process. In this study, we explored the morphometric and microstructural changes in CC subregions in patients with unilateral lower limb amputation. Thirty-eight patients and 38 age- and gender-matched normal controls were included. The CC was divided into five regions, and the area, thickness and diffusion parameters of each region were investigated. While morphometric analysis showed no significant differences between the two groups, amputees showed significant higher values in axial diffusivity, radial diffusivity and mean diffusivity in region II of the CC, which connects the bilateral premotor and supplementary motor areas. In contrast, the mean fractional anisotropy value of the fibers generated by these cortical areas, as measured by tractography, was significantly smaller in amputees. These results demonstrate that the interhemispheric pathways contributing to motor coordination and imagery are reorganized in lower limb amputees.
HIF1α in aortic aneurysms and beyond
Authors: Hashimoto Tomoki , Rizzo Victor 
Published: March 2017

Abdominal aortic aneurysm (AAA) is a permanent expansion of the vessel wall with a high prevalence in those 65 years of age and older. Aneurysms are prone to dissection and rupture that carry a mortality rate of over 85%. Currently, surgical repair is the only option to treat this disease. The need to intervene prior to these events has set off a flurry of basic studies in an effort to understand the cellular and molecular mechanisms that govern AAA formation, progression and rupture. In the present study, the role of myeloid cells in contributing to AAA development has been confirmed. More specifically, the transcription factor, hypoxia-inducible factor-1α (HIF1α), was demonstrated to be a necessary component for regulating the expression of extracellular matrix modifying enzymes and their endogenous inhibitors in these cells. This new discovery may lead to therapeutic targets to prohibit the degradation and weakening of the vessel wall with the hope of limiting AAA formation and/or growth.
Practice Patterns of Speech-Language Pathologists in Pediatric Vocal Health
Authors: Hartley Naomi A. , Braden Maia , Thibeault Susan L. 
Published: March 2017

Purpose
The purpose of this study was to investigate current practices of speech-language pathologists (SLPs) in the management of pediatric vocal health, with specific analysis of the influence of clinical specialty and workplace setting on management approaches.

Method
American Speech-Language-Hearing Association–certified clinicians providing services within the United States (1%–100% voice caseload) completed an anonymous online survey detailing clinician demographics; employment location and service delivery models; approaches to continuing professional development; and specifics of case management, including assessment, treatment, and discharge procedures.

Results
Current practice patterns were analyzed for 100 SLPs (0–42 years of experience; 77 self-identifying as voice specialists) providing services in 34 U.S. states across a range of metropolitan and nonmetropolitan workplace settings. In general, SLPs favored a multidisciplinary approach to management; included perceptual, instrumental, and quality of life measures during evaluation; and tailored intervention to the individual using a combination of therapy approaches. In contrast with current practice guidelines, only half reported requiring an otolaryngology evaluation prior to initiating treatment. Both clinical specialty and workplace setting were found to affect practice patterns. SLPs in school settings were significantly less likely to consider themselves voice specialists compared with all other work environments. Those SLPs who considered themselves voice specialists were significantly more likely to utilize voice-specific assessment and treatment approaches.

Conclusion
SLP practice largely mirrors current professional practice guidelines; however, potential exists to further enhance client care. To ensure that SLPs are best able to support children in successful communication, further research, education, and advocacy are required.
The Relationship Between Executive Functions and Language Abilities in Children: A Latent Variables Approach
Authors: Kaushanskaya Margarita , Park Ji Sook , Gangopadhyay Ishanti , Davidson Meghan M. , Weismer Susan Ellis 
Published: March 2017

Purpose
We aimed to outline the latent variables approach for measuring nonverbal executive function (EF) skills in school-age children, and to examine the relationship between nonverbal EF skills and language performance in this age group.

Method
Seventy-one typically developing children, ages 8 through 11, participated in the study. Three EF components, inhibition, updating, and task-shifting, were each indexed using 2 nonverbal tasks. A latent variables approach was used to extract latent scores that represented each EF construct. Children were also administered common standardized language measures. Multiple regression analyses were conducted to examine the relationship between EF and language skills.

Results
Nonverbal updating was associated with the Receptive Language Index on the Clinical Evaluation of Language Fundamentals–Fourth Edition (CELF-4). When composites denoting lexical–semantic and syntactic abilities were derived, nonverbal inhibition (but not shifting or updating) was found to predict children's syntactic abilities. These relationships held when the effects of age, IQ, and socioeconomic status were controlled.

Conclusions
The study makes a methodological contribution by explicating a method by which researchers can use the latent variables approach when measuring EF performance in school-age children. The study makes a theoretical and a clinical contribution by suggesting that language performance may be related to domain-general EFs.
CPW‐to‐SL transition in LTCC technology
Authors: Bhutani A. , Goettel B. , Thelemann T. , Zwick T. 
Published: March 2017

A coplanar waveguide (CPW)‐to‐stripline (SL) via‐based signal transition operating from DC to 150 GHz is presented. The signal transition is manufactured using low‐temperature co‐fired ceramic (LTCC) technology and it is the largest‐bandwidth LTCC vertical signal transition published to date, according to the best of the authors’ knowledge. Probe‐based S‐parameter measurements of the transition show that the single‐ended CPW‐to‐SL signal transition has below 1 dB insertion loss for frequencies up to 150 GHz, thereby demonstrating it as a suitable component for realisation of a low‐cost, fully integrated, surface‐mountable millimetre‐wave system‐in‐package.
Complications after Hypospadias Correction: Prognostic Factors and Impact on Final Clinical Outcome
Authors: Mouës Chantal , Rooij Iris , Biezen Jan , Dokter Elisabeth 
Published: March 2017

Purpose The purpose of this study was to analyze the influence of patient and treatment characteristics on the occurrence of complications after hypospadias correction and the impact of complications on final clinical outcome.
Materials and Methods The study cohort consisted of 205 hypospadias patients who had surgery in the Medical Centre Leeuwarden (1996–2011). Patient and treatment characteristics were hypospadias severity (preoperative meatal location and chordee), number of planned surgeries, reconstruction technique, operation year, and patient's age at the time of surgery. The final clinical outcome was measured with the Hypospadias Objective Scoring Evaluation (HOSE) (maximum score = 16) and compared between patients with and without complications.
Results Sixty-four patients (31%) had complications, most of which were fistulas (n = 40). An increased complication risk was seen in patients with severe hypospadias (preoperative proximal meatus or chordee), multistage reconstruction, reconstruction techniques other than Mathieu, and surgeries performed before 2005. Uncomplicated treatment resulted only in a marginally higher HOSE (15.7) compared with complicated treatment (15.4). Fistulas and multiple complications reduced clinical outcome more (15.3 and 14.9, respectively), while urinary tract infections, wound dehiscence, or prepuce related complications did not (16.0, 16.0, and 15.8, respectively).
Conclusion The complication risk after hypospadias correction is influenced by hypospadias severity and type and year of reconstruction. Certain, but not all complications diminish final clinical outcome.
Symptomatic Parietal Intradiploic Encephalocele—A Case Report and Literature Review
Authors: Shi Chen , Flores Bruno , Fisher Stephen , Barnett Samuel 
Published: March 2017

AbstractEncephalocele is a rare condition that consists of herniation of cerebral matter through openings of dura and skull. A majority of encephaloceles are congenital and manifest in childhood. We present a case of a 45-year-old man presenting with contralateral hemiparesis and found to have an extremely rare phenomenon of a symptomatic posttraumatic parietal intradiploic encephalocele (IE) manifesting 36 years following pediatric traumatic head injury. Computed tomography and magnetic resonance imaging confirmed herniation of brain tissue into the intradiploic space. Surgical treatment with reduction of the encephalocele achieved near resolution of preoperative hemiparesis on follow-up. The pathogenesis and a literature review of IE are discussed.
GenomeScope: fast reference-free genome profiling from short reads
Authors: Vurture Gregory W , Sedlazeck Fritz J , Nattestad Maria , Underwood Charles J , Fang Han , Gurtowski James , Schatz Michael C 
Published: March 2017

Abstract

Summary
GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates.

Availability and Implementation
http://genomescope.org, https://github.com/schatzlab/genomescope.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Thomas Carlyle and Political Economy: The ‘Dismal Science’ in Context
Authors: Jordan Alexander 
Published: March 2017

Abstract
Thomas Carlyle (1795–1881) is notorious for his description of economics as ‘the dismal science’. In the existing literature, Carlyle is portrayed as an ignorant and philistine critic, who rejected the science from the outside, on purely ‘moral’ grounds.
In contrast, the current article offers a close, comprehensive, and contextualised reading of Carlyle’s oeuvre, continually following up his sources, interlocutors, and reception. In short, it argues that Carlyle was relatively well-informed, participating in some key debates within political economy.
The article begins by situating Carlyle in 1820s Edinburgh. Whereas Smith had understood political economy as a subordinate branch of the ‘science of the legislator’, Stewart and McCulloch drew a sharp distinction between political economy and politics. Having established political economy as an independent science, they called upon the legislator to withdraw from economic life. Having expressed severe misgivings, Carlyle found an alternative in Sismondi and the Saint-Simonians, who sought to shift the emphasis away from the production of material wealth, and towards distribution, morality, and ethics.
Having reconstructed the controversies in which Carlyle engaged with specific political economists, the article argues that it was not altogether unreasonable for Carlyle to consider certain strands of political economy a ‘dismal science’.
The article then examines the reception of Carlyle’s writings amongst Owenites, Chartists, and scholars of ancient Greek. It also shows how Carlyle won over some political economists, notably John Stuart Mill. Finally, the article explores the influence of Carlyle upon advocates of a ‘social science’, and upon some later nineteenth-century economists.