bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of HGF in epithelial–stromal cell interactions during progression from benign breast disease to ductal carcinoma in situ
Authors: Casbas-Hernandez Patricia , D’Arcy Monica , Roman-Perez Erick , Brauer Heather Ann , McNaughton Kirk , Miller Samantha M , Chhetri Raghav K , Oldenburg Amy L , Fleming Jodie M , Amos Keith D , Makowski Liza , Troester Melissa A 
Published: September 2013

Abstract
Introduction
Basal-like and luminal breast cancers have distinct stromal–epithelial interactions, which play a role in progression to invasive cancer. However, little is known about how stromal–epithelial interactions evolve in benign and pre-invasive lesions.

Methods
To study epithelial–stromal interactions in basal-like breast cancer progression, we cocultured reduction mammoplasty fibroblasts with the isogenic MCF10 series of cell lines (representing benign/normal, atypical hyperplasia, and ductal carcinoma in situ). We used gene expression microarrays to identify pathways induced by coculture in premalignant cells (MCF10DCIS) compared with normal and benign cells (MCF10A and MCF10AT1). Relevant pathways were then evaluated in vivo for associations with basal-like subtype and were targeted in vitro to evaluate effects on morphogenesis.

Results
Our results show that premalignant MCF10DCIS cells express characteristic gene expression patterns of invasive basal-like microenvironments. Furthermore, while hepatocyte growth factor (HGF) secretion is upregulated (relative to normal, MCF10A levels) when fibroblasts are cocultured with either atypical (MCF10AT1) or premalignant (MCF10DCIS) cells, only MCF10DCIS cells upregulated the HGF receptor MET. In three-dimensional cultures, upregulation of HGF/MET in MCF10DCIS cells induced morphological changes suggestive of invasive potential, and these changes were reversed by antibody-based blocking of HGF signaling. These results are relevant to in vivo progression because high expression of a novel MCF10DCIS-derived HGF signature was correlated with the basal-like subtype, with approximately 86% of basal-like cancers highly expressing the HGF signature, and because high expression of HGF signature was associated with poor survival.

Conclusions
Coordinated and complementary changes in HGF/MET expression occur in epithelium and stroma during progression of pre-invasive basal-like lesions. These results suggest that targeting stroma-derived HGF signaling in early carcinogenesis may block progression of basal-like precursor lesions.
Local and systemic innate immune response to secondary human peritonitis
Authors: Riché Florence , Gayat Etienne , Collet Corinne , Matéo Joaquim , Laisné Marie-Josèphe , Launay Jean-Marie , Valleur Patrice , Payen Didier , Cholley Bernard P 
Published: September 2013

Abstract
Introduction
Our aim was to describe inflammatory cytokines response in the peritoneum and plasma of patients with peritonitis. We also tested the hypothesis that scenarios associated with worse outcome would result in different cytokine release patterns. Therefore, we compared cytokine responses according to the occurrence of septic shock, mortality, type of peritonitis and peritoneal microbiology.

Methods
Peritoneal and plasma cytokines (interleukin (IL) 1, tumor necrosis factor α (TNFα), IL-6, IL-10, and interferon γ (IFNγ)) were measured in 66 patients with secondary peritonitis.

Results
The concentration ratio between peritoneal fluid and plasma cytokines varied from 5 (2 to 21) (IFNγ) to 1310 (145 to 3888) (IL-1). There was no correlation between plasma and peritoneal fluid concentration of any cytokine. In the plasma, TNFα, IL-6, IFNγ and IL-10 were higher in patients with shock versus no shock and in nonsurvivors versus survivors (P ≤0.03). There was no differential plasma release for any cytokine between community-acquired and postoperative peritonitis. The presence of anaerobes or Enterococcus species in peritoneal fluid was associated with higher plasma TNFα: 50 (37 to 106) versus 38 (29 to 66) and 45 (36 to 87) versus 39 (27 to 67) pg/ml, respectively (P = 0.02). In the peritoneal compartment, occurrence of shock did not result in any difference in peritoneal cytokines. Peritoneal IL-10 was higher in patients who survived (1505 (450 to 3130) versus 102 (9 to 710) pg/ml; P = 0.04). The presence of anaerobes and Enterococcus species was associated with higher peritoneal IFNγ: 2 (1 to 6) versus 10 (5 to 28) and 7 (2 to 39) versus 2 (1 to 6), P = 0.01 and 0.05, respectively).

Conclusions
Peritonitis triggers an acute systemic and peritoneal innate immune response with a simultaneous release of pro and anti-inflammatory cytokines. Higher levels of all cytokines were observed in the plasma of patients with the most severe conditions (shock, non-survivors), but this difference was not reflected in their peritoneal fluid. There was always a large gradient in cytokine concentration between peritoneal and plasma compartments highlighting the importance of compartmentalization of innate immune response in peritonitis.
On the design of clone-based haplotyping
Authors: Lo Christine , Liu Rui , Lee Jehyuk , Robasky Kimberly , Byrne Susan , Lucchesi Carolina , Aach John , Church George , Bafna Vineet , Zhang Kun 
Published: September 2013

Abstract
Background
Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable yields due to incompletely understood parameter choices.

Results
We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically the benefits of using larger clones with moderate number of pools and sequencing coverage. In particular, using 140 kb BAC clones, we construct haplotypes for a personal genome and assemble haplotypes with N50 values greater than 2.6 Mb. These assembled haplotypes are longer and at least as accurate as haplotypes of existing clone-based strategies, whether in vivo or in vitro.

Conclusions
Our results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.
Elevated Periimplantation Uterine Natural Killer Cell Density in Human Endometrium Is Associated With Impaired Corticosteroid Signaling in Decidualizing Stromal Cells
Authors: Kuroda Keiji , Venkatakrishnan Radha , James Sean , Šućurović Sandra , Mulac-Jericevic Biserka , Lucas Emma S. , Takeda Satoru , Shmygol Anatoly , Brosens Jan J. , Quenby Siobhan 
Published: September 2013

Background:Decidualizing human endometrial stromal cells (HESCs) profoundly up-regulate 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1), the enzyme that converts inert cortisone to active cortisol. We postulated that the induction of a cortisol gradient upon decidualization of the periimplantation endometrium may impact on the uterine natural killer (uNK) cell population and on local expression of corticosteroid-dependent target genes.Methods:Midluteal endometrial biopsies (n = 55) were processed for uNK cell (CD56) analysis and primary HESC cultures. The cultures remained either untreated or were decidualized for 4 or 8 days. A tissue microarray was constructed from endometria with normal (n = 18) and elevated uNK cell (n = 18) scores. An abnormal uNK cell test was defined as greater than 5% CD56+ cells in the subluminal stroma.Results:Increased uNK cell density was associated with lower endometrial expression of 11βHSD1 and mineralocorticoid receptor (MR) but not glucocorticoid receptor in vivo. Elevated uNK cell density also corresponded to impaired induction of key decidual markers (11βHSD1, prolactin, and insulin-like growth factor binding protein-1) and MR-dependent enzymes (dehydrogenase/reductase member 3 and retinol saturase) in differentiating HESC cultures. Increased uNK cell density in vivo was not associated with increased in vitro expression of either IL-15 or IL-11, two cytokines implicated in uNK cell regulation.Conclusions:Elevated levels of uNK cells in the stroma underlying the surface epithelium are associated with inadequate cortisol biosynthesis by resident decidualizing cells and suboptimal induction of key MR-dependent enzymes involved in lipid biogenesis and the retinoid transport pathway. Our observations suggest that uNK cell testing identifies those women at risk of reproductive failure due to relative uterine cortisol deficiency.
Seizure Outcomes After Corpus Callosotomy for Drop Attacks
Authors: Bower Regina S. , Wirrell Elaine , Nwojo Macaulay , Wetjen Nicholas M. , Marsh W. Richard , Meyer Fredric B. 
Published: September 2013

Abstract

BACKGROUND:
Medically intractable epilepsy involving drop attacks can be difficult to manage and negatively affect quality of life. Most studies investigating the effect of corpus callosotomy (CC) on seizures have been limited, focusing on the pediatric population or drop seizures alone, with little attention to other factors influencing seizure outcome.

OBJECTIVE:
To assess seizure outcomes after CC in adults and children.

METHODS:
Retrospective analysis was performed on all patients who underwent CC (anterior two thirds, 1- or 2-stage complete) at our institution between 1990 and 2011. Change in frequency after CC was assessed for drop seizures and other seizure types. Multiple factors were evaluated for impact on seizure outcome.

RESULTS:
Fifty patients met inclusion criteria. The median age was 1.5 years at seizure onset and 17 years at time of surgery. Anterior two-thirds CC was performed in 28 patients, 1-stage complete in 17, and 2-stage complete in 5. All 3 groups experienced a significant decrease in drop seizures (P &lt; .001, P &lt; .001, and P = .020, respectively), with 40% experiencing complete resolution, and 64% dropping at least 1 frequency category. Other seizure types significantly decreased in anterior two-thirds CC and 1-stage complete (P = .0035, P = .001, respectively). Younger age at surgery correlated with better seizure outcomes (P = .043).

CONCLUSION:
CC for medically refractory generalizing epilepsy is effective for both drop seizures and other seizure types. CC should be considered soon after a patient has been deemed medically refractory because earlier age at surgery results in lower risk and better outcome.
Evaluation of Normalization Strategies Used in Real-time Quantitative PCR Experiments in HepaRG Cell Line Studies
Authors: Ceelen Liesbeth , De Craene Jurgen , De Spiegelaere Ward 
Published: September 2013

Abstract

BACKGROUND
The HepaRG cell line is widely used as an alternative for primary human hepatocytes for numerous applications, including drug screening, and is progressively gaining importance as a human-relevant cell source. Consequently, increasing numbers of experiments are being performed with this cell line, including real-time quantitative PCR (RT-qPCR) experiments for gene expression studies.

CONTENT
When RT-qPCR experiments are performed, results are reliable only when attention is paid to several critical aspects, including a proper normalization strategy. Therefore, in 2011 we determined the most optimal reference genes for gene expression studies in the HepaRG cell system, according to the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines. This study additionally provided clear evidence that the use of a single reference gene [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein S18 (RPS18), or actin, beta (ACTB)] was insufficient for normalization in HepaRG cells. Our screening of relevant studies published after our study suggested that the findings of our study were completely ignored.

SUMMARY
In none of the 24 reviewed studies was a proper normalization method used. Only 1 reference gene was included for normalization in 21 out of the 24 reported studies we screened, with RPS18 and GAPDH used most frequently, followed by hypoxanthine phosphoribosyltransferase 1 (HPRT1), glutathione synthetase (GSS) (hGus), β-2 microglobin (B2M), and acidic ribosomal phosphoprotein P0 (36B4). For 2 studies the use of multiple reference genes (2 and 3) was reported, but these had not been prevalidated for expression stability in HepaRG cells. In 1 study, there was no evidence that any reference gene had been used. Current RT-qPCR gene expression studies in HepaRG cells are being performed without adequate consideration or evaluation of reference genes. Such studies can yield erroneous and biologically irrelevant results.
Sleep disorders in children with developmental delay
Authors: Ahmareen Oneza , Neary Elaine , Sharif Farhana 
Published: September 2013

AbstractDevelopmental disorders in children are common. Associated demanding co-morbidities that include sleep problems are prevalent in this group. In turn, these are linked to daytime performance issues, reduced developmental and academic growth, and considerable familial psychopathology. Behavioral modification measures are and should be the first line approach to management. Medications for sleep disorders have an important role in addition to behavioral modification therapy. This literature review looks into the occurrence and severity of sleep problems in children with developmental disorders. The probable advantages of using medications, mainly focusing on the neurohormone melatonin (a sleep inducer), are also explored.
On the other side: formulaic organizing chunks in spoken and written academic ELF
Authors: Carey Ray 
Published: September 2013

Abstract
An ongoing discussion in ELF research is the ability of ELF speakers to store and retrieve holistic chunks of language, facilitating efficient and fluent production of speech. These questions involve the frequency effects of formulaic chunks of language and their varying degrees of entrenchment for ELF users. In addition, the variable forms in which these chunks may be attested can be treated as approximations of conventional chunks, while serving identical functions. This study addresses these issues by investigating high-frequency organizing chunks in ELF corpora using the Linear Unit Grammar (LUG) framework (Sinclair and Mauranen 2006). Drawing data from the ELFA corpus of spoken academic ELF, the study also considers organizing chunks in written academic ELF from the nascent WrELFA corpus. With ENL comparison data taken from the Michigan Corpus of Academic Spoken English (MICASE), findings are presented on the forms and frequencies of textual and interactive organizing chunks in ELF, with implications for the reality of frequency effects and their connection to distributions of approximated chunks. The lower frequency, organizing chunks showed a higher rate of approximation and number of unique forms, while the higher frequency chunks were primarily attested in conventional forms both in written and spoken ELF.
Non-conformity to ENL norms: a perspective from Chinese English users
Authors: Wang Ying 
Published: September 2013

Abstract
English as a lingua franca (ELF) research poses challenge to mainstream English language teaching (ELT) in terms of its exclusive reference to English as a native language (ENL). On the other hand, some studies have been conducted to show that non-native English speakers (NNESs) have an aspiration for ENL and, in turn, add emphasis to ELT practitioners' effort in helping NNESs to approximate native English speaker (NES) competence. In response to the debate, this paper focuses on Chinese English speakers' perceptions of (non-)conformity to ENL in order to offer insights into the extent to which NNESs are ENL-(in)dependent.
This paper draws on the data contributed by 502 Chinese university students and 267 Chinese professionals through questionnaires and interviews. The questionnaire responses displayed a slightly positive orientation towards instances of non-conformity to ENL norms and revealed the respondents' choice between the formulaic conformity and the functions of non-conformity. The interviews unfolded the tension between exonormative and endonormative orientations to English. The participants' exonormative orientations reflect their belief in the centrality of NESs to norms of English use, their conceptualization of English as a fixed entity, and their aspiration for social advantages that they believe the conformity to ENL norms can bring to them. Their endonormative orientations relate to their acknowledgement of the communicative function of English that diverges from the norms of ENL and their concern for their cultural identity, which they believe conflicts with the conformity to ENL norms. This paper thus demonstrates that the preference for ENL is only one side of NNESs' attitudinal picture. Further, the reasons behind this preference point to the need for change from monolithic English to pluralistic Englishes in mainstream ELT.
Spanish scholars' research article publishing process in English-medium journals: English used as a lingua franca?
Authors: Mur-Dueñas Pilar 
Published: September 2013

Abstract
English has become the language of dissemination of research findings for scholars, especially in certain fields, and this is not an exception for Spanish scholars. They are under increasing pressure to write and publish research articles in international English-medium journals to establish their credentials, get academic promotion and rewards, and also to gain professional recognition. It is the aim of this paper to look at the process of writing research articles by a group of Spanish scholars in the field of finance by exploring the role played by “literacy brokers” (Lillis and Curry 2010): “wordface professionals” (Shashok 2008) (i.e., proofreaders and language consultants, who tend to be external community members) and gatekeepers (i.e., journal editors and reviewers). The study is based on eight text histories which contain the subsequent versions of the authors' manuscripts, the editors' letters, and the referees' reports. Referees and editors frequently point out the non-nativeness of the Spanish scholars' discourse, and encourage them to resort to English native wordface professionals. The analysis reveals the most common type of language revision which their manuscripts go through to comply not only with standard linguistic and discursive uses of the language but also with prevailing Anglo-American rhetorical conventions. Through this analysis an insight is gained into the extent to which English is used as a lingua franca (ELF) in this disciplinary academic community for research publication and dissemination.
Shinjo Matsuri: Community Revitalization through the Construction and Circulation of Decorated Floats
Authors: Kuroishi Izumi 
Published: September 2013

Abstract Shinjo Matsuri in Yamagata prefecture is a 250-year old summer festival recognized as one of the nationally designated Important Folk and Cultural Properties. Besides the procession of a mikoshi from Tenman shrine, 20 decorated floats circulate through the city for two days, by collaboration between the people in the town and farm areas. Characteristically, as the local lord Tozawa allowed people to design the float as they liked at the beginning of the festival, groups of young people in each area still design, finance and construct the float by themselves without any institution’s nor profession’s help. This paper aims to explain how the construction and the spatial assignment of the float work to sustain the community bond between generations and define its local identity in the whole city. Especially, I would like to discuss how people interpret the idea of furyu in enhancing their well-being in the community by creating the extraordinary socio-symbolical space, and by accommodating the festival to the social change.
Transnational Ecstasy and Japanese Ganbarism: Cultural Patterns in the Pedagogy of Outward Bound Japan
Authors: Mattig Ruprecht 
Published: September 2013

Abstract Contemporary cross-cultural happiness research commonly defines the concept of culture in regard to nation states. This paper takes up anthropological criticisms of this traditional culture concept arguing that the view on national cultures needs to be complemented by a view on transnational cultural movements. These theoretical reflections are applied to a qualitative case study that examines the transnational “Outward Bound Schools” in Japan and Germany. Based on document reviews, interviews, and observations two cultural patterns in Outward Bound Japan are reconstructed. The first one refers to an emphasis on ecstatic happiness. As this emphasis is found in Outward Bound Japan as well as in Outward Bound Germany it is analyzed as a transnational cultural pattern. The second pattern refers to an emphasis on what is often called “ganbarism” in Japan, i.e., the virtue of endurance. The analysis shows that this emphasis is unique in Outward Bound Japan and that it can be linked to the broader Japanese cultural context. With this empirical study the paper thus draws the attention to the complexity of cultural patterns in regard to cross-cultural happiness research.
Berührungslose optische Vermessung von Spannbetonfertigteilen / Contact-Free Optical Measurement of Precast Prestressed Concrete Parts
Authors: Grote Alexander , Schwab Erwin 
Published: September 2013

Zusammenfassung
In diesem Beitrag wird ein 3D Visionsystem zur Vermessung von Spannbetonfertigteilen beschrieben, das eine Vollprüfung im Fertigungsprozess ermöglicht. Mit Hilfe von Lasertriangulationsensoren werden die zu untersuchenden Merkmale erfasst und als Punktewolke der Bildverarbeitung zugänglich gemacht. Insbesondere wird dargestellt, wie die Vermessung des Objektes mittels zweier Sensoren, realisiert wurde.
Estimating Individual Admixture Proportions from Next Generation Sequencing Data
Authors: Skotte Line , Korneliussen Thorfinn Sand , Albrechtsen Anders 
Published: September 2013

Abstract
Inference of population structure and individual ancestry is important both for population genetics and for association studies. With next generation sequencing technologies it is possible to obtain genetic data for all accessible genetic variations in the genome. Existing methods for admixture analysis rely on known genotypes. However, individual genotypes cannot be inferred from low-depth sequencing data without introducing errors. This article presents a new method for inferring an individual’s ancestry that takes the uncertainty introduced in next generation sequencing data into account. This is achieved by working directly with genotype likelihoods that contain all relevant information of the unobserved genotypes. Using simulations as well as publicly available sequencing data, we demonstrate that the presented method has great accuracy even for very low-depth data. At the same time, we demonstrate that applying existing methods to genotypes called from the same data can introduce severe biases. The presented method is implemented in the NGSadmix software available at http://www.popgen.dk/software.