bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-structural protein 1 of H3N2 influenza A virus induces nucleolar stress via interaction with nucleolin
Authors: Yan Yinxia , Du Yongming , Wang Gefei , Li Kangsheng 
Published: December 2017

AbstractThe nucleolus is a stress sensor associated with cell cycle progression and a central hub for the replication of pathogenic RNA viruses. However, the role of nucleolus in influenza A virus infection has not been well studied. Here we show that the interaction between NS1 protein of influenza A/Shantou/602/06 (H3N2) and nucleolin, a ubiquitous protein of nucleolus repressed RNA Pol I-dependent transcription via establishing hyper-methylation in the UCE of rRNA gene promoter. NS1 expressed cells showed significant association of ribosomal proteins with MDM2, and p53 accumulation, suggesting induced nucleolar stress. Disruption of the interaction of NS1 with nucleolin or overexpression of nucleolin in NS1 expressed cells revived RNA Pol I-dependent transcription, indicating nucleolin could be one target for NS1 to repress rRNA synthesis of host cells. Our present study suggests that NS1 protein of H3N2 could induce nucleolar stress based on epigenetic alteration of rRNA gene promoter via interaction with nucleolin.
Snail collaborates with EGR-1 and SP-1 to directly activate transcription of MMP 9 and ZEB1
Authors: Wu Wen-Sheng , You Ren-In , Cheng Chuan-Chu , Lee Ming-Che , Lin Teng-Yi , Hu Chi-Tan 
Published: December 2017

AbstractThe Snail transcription factor plays as a master regulator of epithelial mesenchymal transition (EMT), one of the steps of tumor metastasis. Snail enhances expressions of a lot of mesenchymal genes including the matrix degradation enzyme matrix metalloproteinases 9 (MMP9) and the EMT transcription factor zinc finger E-box binding homeobox 1 (ZEB1), however, the underlying mechanisms are not clarified. Herein, we investigated how Snail upregulated transcription of ZEB1 and MMP9 induced by the tumor promoter 12-O-tetradecanoyl-phorbol 13-acetate (TPA) in hepatoma cell HepG2. According to deletion mapping and site directed mutagenesis analysis, the TPA-responsive elements on both MMP9 and ZEB1 promoters locate on a putative EGR1 and SP1 overlapping region coupled with an upstream proposed Snail binding motif TCACA. Consistently, chromatin immunoprecipitation (ChIP) assay showed TPA triggered binding of Snail, EGR1 and SP1 on MMP9 and ZEB1 promoters. Double ChIP further indicated TPA induced association of Snail with EGR1 and SP1 on both promoters. Also, electrophoresis mobility shift assay revealed TPA enhanced binding of Snail with a MMP9 promoter fragment. According to shRNA techniques, Snail was essential for gene expression of both ZEB1 and MMP9. In conclusion, Snail transactivates genes involved in tumor progression via direct binding to a specific promoter region.
Analysis of killing of growing cells and dormant and germinated spores of Bacillus species by black silicon nanopillars
Authors: Ghosh Sonali , Niu Shanyuan , Yankova Maya , Mecklenburg Matthew , King Stephen M. , Ravichandran Jayakanth , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya , Setlow Peter 
Published: December 2017

AbstractBlack silicon (bSi) wafers with a high density of high-aspect ratio nanopillars have recently been suggested to have mechanical bactericidal activity. However, it remains unclear whether bSi with the nanopillars can kill only growing bacterial cells or also dormant spores that are harder to kill. We have reexamined the cidal activity of bSi on growing cells, dormant and germinated spores of B. subtilis, and dormant spores of several other Bacillus species by incubation on bSi wafers with and without nanopillars. We found that the bSi wafers with nanopillars were indeed very effective in rupturing and killing the growing bacterial cells, while wafers without nanopillars had no bactericidal effect. However, bSi wafers with or without nanopillars gave no killing or rupture of dormant spores of B. subtilis, Bacillus cereus or Bacillus megaterium, although germinated B. subtilis spores were rapidly killed. This work lays a foundation for novel bactericidal applications of bSi by elucidating the limits of mechanical bactericidal approaches.
A 100,000 Scale Factor Radar Range
Authors: Blanche Pierre-Alexandre , Neifeld Mark , Peyghambarian Nasser 
Published: December 2017

AbstractThe radar cross section of an object is an important electromagnetic property that is often measured in anechoic chambers. However, for very large and complex structures such as ships or sea and land clutters, this common approach is not practical. The use of computer simulations is also not viable since it would take many years of computational time to model and predict the radar characteristics of such large objects. We have now devised a new scaling technique to overcome these difficulties, and make accurate measurements of the radar cross section of large items. In this article we demonstrate that by reducing the scale of the model by a factor 100,000, and using near infrared wavelength, the radar cross section can be determined in a tabletop setup. The accuracy of the method is compared to simulations, and an example of measurement is provided on a 1 mm highly detailed model of a ship. The advantages of this scaling approach is its versatility, and the possibility to perform fast, convenient, and inexpensive measurements.
IFNγ induces PD-L1 overexpression by JAK2/STAT1/IRF-1 signaling in EBV-positive gastric carcinoma
Authors: Moon Ji Wook , Kong Su-Kang , Kim Byung Soo , Kim Hyun Ji , Lim Hyangsoon , Noh Kyeonga , Kim Younghye , Choi Jung-Woo , Lee Ju-Han , Kim Young-Sik 
Published: December 2017

AbstractProgrammed death-ligand 1 (PD-L1) acts as an immune checkpoint inhibitor in various cancers. PD-L1 is known to be more frequently expressed in EBV (+) gastric cancer (GC). However, the mechanisms underlying the regulation of PD-L1 expression in EBV (+) GC remain unclear. We investigated the basal and inducible PD-L1 expressions in GC cells. PD-L1 expression was upregulated upon treatment with IFNγ in both EBV (−) and EBV (+) GC cells. Upon stimulation with the same concentration of IFNγ for 24 h, EBV (+) SNU-719 cells showed dramatically higher PD-L1 expression levels by activating JAK2/STAT1/IRF-1 signaling than those of EBV (−) AGS cells. PD-L1 promoter assays, chromatin immunoprecipitation, and electrophoretic mobility shift assays revealed that IFNγ-inducible PD-L1 overexpression is primarily mediated by the putative IRF-1α site of the PD-L1 promoter in EBV (+) SNU-719 cells. Moreover, EBNA1 knockdown reduced both constitutive and IFNγ-inducible PD-L1 promoter activity by decreasing the transcript and protein levels of JAK2 and subsequently STAT1/IRF-1/PD-L1 signaling. EBNA1 is suggested to be moderately enhance both constitutive and IFNγ-inducible PD-L1 expression in EBV (+) GC cells. Thus, the signaling proteins and EBNA1 that regulate PD-L1 expression are potential therapeutic targets in EBV (+) GC.
Measurement of Nanowire Optical Modes Using Cross-Polarization Microscopy
Authors: Kakko Joona-Pekko , Matikainen Antti , Anttu Nicklas , Kujala Sami , Mäntynen Henrik , Khayrudinov Vladislav , Autere Anton , Sun Zhipei , Lipsanen Harri 
Published: December 2017

AbstractA method to detect optical modes from vertical InGaAs nanowires (NWs) using cross-polarization microscopy is presented. Light scattered from the optical modes in the NWs is detected by filtering out the polarized direct reflection with a crossed polarizer. A spectral peak and a valley were seen to red-shift with increasing NW diameter in the measured spectra. The peak was assigned to scattering from the TE01 optical mode and the valley was an indication of the HE11 mode, based on finite-element and scattering matrix method simulations. The cross-polarization method can be used to experimentally determine the spectral positions of the TE01 and HE11 optical modes. The modes are significantly more visible in comparison to conventional reflectance measurements. The method can be beneficial in the characterization of NW solar cells, light-emitting diodes and lasers where precise mode control is required.
Modelling neuroanatomical variation during childhood and adolescence with neighbourhood-preserving embedding
Authors: Ball Gareth , Adamson Chris , Beare Richard , Seal Marc L. 
Published: December 2017

AbstractBrain development is a dynamic process with tissue-specific alterations that reflect complex and ongoing biological processes taking place during childhood and adolescence. Accurate identification and modelling of these anatomical processes in vivo with MRI may provide clinically useful imaging markers of individual variability in development. In this study, we use manifold learning to build a model of age- and sex-related anatomical variation using multiple magnetic resonance imaging metrics. Using publicly available data from a large paediatric cohort (n = 768), we apply a multi-metric machine learning approach combining measures of tissue volume, cortical area and cortical thickness into a low-dimensional data representation. We find that neuroanatomical variation due to age and sex can be captured by two orthogonal patterns of brain development and we use this model to simultaneously predict age with a mean error of 1.5–1.6 years and sex with an accuracy of 81%. We validate this model in an independent developmental cohort. We present a framework for modelling anatomical development during childhood using manifold embedding. This model accurately predicts age and sex based on image-derived markers of cerebral morphology and generalises well to independent populations.
Screeninginstrumente zur Erfassung von männerspezifischen Symptomen der unipolaren Depression – Ein kritischer Überblick
Authors: Zülke Andrea , Kersting Anette , Dietrich Sandra , Luck Tobias , Riedel-Heller Steffi , Stengler Katarina 
Published: December 2017

Zusammenfassung
Hintergrund Geschlechterunterschiede in der Prävalenz von Depressionen zuungunsten von Frauen sind hinreichend belegt. Dagegen sind wissenschaftliche Publikationen zu diagnostischen Kriterien und Screeninginstrumenten für Geschlechterunterschiede bei Depressionen selten.
Methode Anhand einer systematischen Literatursuche wurden Publikationen recherchiert, die Hinweise für männerspezifische Symptome bei Depressionen bzw. verfügbare Screeninginstrumente geben sollten.
Ergebnisse Von 122 thematisch relevanten Titeln testeten 8 Arbeiten männerspezifische Inventare. Unter Berücksichtigung männertypischer Symptome verringern sich Geschlechterunterschiede in der Prävalenz von Depression.
Diskussion Die Ergebnisse deuten auf einen Bedarf geschlechtersensibler Diagnoseinstrumente für Depressionen hin.
Aktuelle Literaturübersicht zur Therapie der Adipositas bei Kindern und Jugendlichen
Authors: Brauchmann Jana , Weihrauch-Blüher Susann , Ehehalt Stefan , Wiegand Susanna 
Published: December 2017

Zusammenfassung
Hintergrund Adipositas ist durch die mit ihr einhergehende Komorbidität und den Bedarf an langfristiger medizinischer Versorgung als chronische Krankheit zu betrachten. Dabei ist auf jeder Stufe der Pathophysiologie eine therapeutische Intervention möglich. Ziel der Arbeit ist es, den Effekt von multimodalen Lebensstilinterventionen nicht nur bezüglich des BMI/BMI-SDS, sondern auch bezüglich (sekundärer) Outcomes wie Komorbiditäten, Lebensqualität sowie des Ernährungs- und Bewegungsverhalten darzustellen.
Material und Methoden In der Literaturdatenbank PubMed wurde international nach klinischen Studien zu Lebensstilinterventionen bei 0 bis 18-Jährigen mit Übergewicht und Adipositas im Zeitraum vom 01/01/2009 bis 01/01/2016 gesucht.
Ergebnisse Es sind 64 Publikationen mit Daten aus 55 Studien in die Übersichtsarbeit eingeflossen. Durch multimodale Lebensstilinterventionen konnten vielfältige Verbesserungen in den Bereichen Komorbidität, Lebensqualität, Ernährung und Bewegung erzielt werden.
Diskussion Der Nutzen einer Adipositastherapie geht weit über eine Gewichtsreduktion hinaus, weshalb weitere Parameter als Therapieziele regelhaft erfasst werden sollten. So haben die Verbesserung von Komorbiditäten, der Lebensqualität sowie des Bewegungs- und Ernährungsverhaltens für einen langfristig gesunden Lebensstil eine mind. genauso große Bedeutung und reduzieren die Gefahr des Regains nach einer initialen Gewichtsreduktion.
Narrative and History
Authors: Munslow Alun 
Published: December 2017

Narrative history is the practice of writing history in a story-based form. It tends to entail history-writing based on reconstructing series of short-term events, and ever since the influential work of Leopold von Ranke on professionalising history-writing in the nineteenth century has been associated with empiricism. The term narrative history thus overlaps with the term histoire événementielle ('event-history') coined by Fernand Braudel in the early twentieth century, as he promoted forms of history-writing analysing much longer-term trends (what he called the longue durée).
Though history is considered a social science, the story-based nature of history allows for the inclusion of a greater or lesser degree of narration in addition to an analytical or interpretative exposition of historical knowledge. It can be divided into two subgenres: the traditional narrative and the modern narrative.
Traditional narrative focuses on the chronological order of history. It is event driven and tends to center upon individuals, action, and intention. For example, in regard to the French Revolution, an historian who works with the traditional narrative might be more interested in the revolution as a single entity (one revolution), centre it in Paris, and rely heavily upon major figures such as Maximilien Robespierre.
Conversely, modern narrative typically focuses on structures and general trends. A modern narrative would break from rigid chronology if the historian felt it explained the concept better. In terms of the French Revolution, an historian working with the modern narrative might show general traits that were shared by revolutionaries across France but would also illustrate regional variations from those general trends (many confluent revolutions). Also this type of historian might use different sociological factors to show why different types of people supported the general revolution.
Historians who use the modern narrative might say that the traditional narrative focuses too much on what happened and not enough on why and causation. Also, that this form of narrative reduces history into neat boxes and thereby does an injustice to history. J H Hexter characterized such historians as "lumpers". In an essay on Christopher Hill, he remarked that "lumpers do not like accidents: they would prefer them vanish...The lumping historian wants to put all of the past into boxes..and then to tie all the boxes together into one nice shapely bundle."
Historians who use traditional narrative might say that the modern narrative overburdens the reader with trivial data that had no significant effect on the progression of history. They believe that the historian needs to stress what is consequential in history, as otherwise the reader might believe that minor trivial events were more important than they were.
Curatr: a web application for creating, curating and sharing a mass spectral library
Authors: Palmer Andrew , Phapale Prasad , Fay Dominik , Alexandrov Theodore 
Published: December 2017

Abstract

Summary
We have developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries from liquid-chromatography mass spectrometry datasets. Curatr handles datasets from single or multiplexed standards and extracts chromatographic profiles and potential fragmentation spectra for multiple adducts. An intuitive interface helps users to select high quality spectra that are stored along with searchable molecular information, the providence of each standard and experimental metadata. Curatr supports exports to several standard formats for use with third party software or submission to repositories. We demonstrate the use of curatr to generate the EMBL Metabolomics Core Facility spectral library http://curatr.mcf.embl.de.

Availability and implementation
Source code and example data are at http://github.com/alexandrovteam/curatr/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Monitoring Student Immunization, Screening, and Training Records for Clinical Compliance: An Innovative Use of the Institutional Learning Management System
Authors: Elting Julie Kientz 
Published: December 2017

Abstract
Clinical compliance for nursing students is a complex process mandating them to meet facility employee occupational health requirements for immunization, screening, and training prior to patient contact. Nursing programs monitor clinical compliance with in-house management of student records, either paper or electronic, or by contracting with a vendor specializing in online record tracking. Regardless of method, the nursing program remains fully accountable for student preparation and bears the consequences of errors. This article describes how the institution's own learning management system can be used as an accurate, cost-neutral, user-friendly, and Federal Educational Rights Protection Act-compliant clinical compliance system.
Nerve Growth Factor Changes and Corneal Nerve Repair after Keratoplasty
Authors: Pan Yueji , Liu Fang , Qi Xiaofeng , Hu Yuan , Xu Feihong , Jia Hui 
Published: December 2017

SIGNIFICANCE
Measured tear concentration of nerve growth factor is correlated with postoperative corneal reinnervation among patients who undergo keratoplasty. This may be a future therapeutic target for post-keratoplasty corneal nerve regeneration.

PURPOSE
To determine the relationship between changes in the content of nerve growth factor (NGF) in tear fluid and corneal subepithelial nerve regeneration in patients after keratoplasty.

METHODS
In this retrospective study, 30 eyes of 28 patients (15 males, 13 females; mean age 42.8 [range 16–73] years) who underwent primary keratoplasty for the first time were recruited through the clinics of the Department of Ophthalmology, Jilin University affiliated First Hospital, between May and December 2015. All patients underwent a complete ophthalmic examination preoperatively. Tear fluid samples were collected to detect the content of NFG at different time points in the follow-up period (day 1 preoperatively and days 1, 7, 30, and 90 postoperatively) and analyzed correlations between NFG content and age, infective factors, and variables of the surgical procedure as well as with subepithelial nerve repair at 30 and 90 days postoperatively.

RESULTS
The NFG content in tear fluid on day 1 postoperatively was lower than that on the day preceding surgery; however, it was higher than the preoperative value on postoperative days 7, 30, and 90 (F = 5.046, P < 0.05). Further, the NFG content of tear fluid at 30 days postoperatively correlated with the surgical procedure (coefficient = −2.775, P = 0.010); however, no significant correlation was found on postoperative day 1 (coefficient = −1.315, P
> 0.05). At all study time points, the NFG content of tear fluid had no correlation with infective factors or age (P
> 0.05). Postoperatively, at day 30, small nerve buds were observed in the periphery of the corneal graft in 13 eyes (43.3% of cases) but not in 17 eyes (56.7% of cases), which showed a significant correlation with the NFG content of tear fluid (coefficient = −3.370, P = 0.010). By postoperative day 90, small nerve buds were observed in the periphery of the corneal graft in 24 eyes (80.0% of cases) and showed a significant correlation with the NFG content of tear fluid (coefficient = −2.750, P = 0.006).

CONCLUSIONS
The NFG content in tear fluid increases with the increasing ratio of small nerve buds indicating corneal nerve regeneration. NFG promotes subepithelial nerve regeneration in patients after keratoplasty.
The Validity of Training Endoscopic Sinus and Skull Base Surgery Techniques on the Experimental Head Model
Authors: Mladina Ranko , Skitarelić Neven , Cingi Cemal , Chen Lei , Bayar Muluk Nuray 
Published: December 2017

Objectives:
The aim of this study was to better understand the usual learning curve in acquiring endonasal endoscopic sinus and skull base surgery (ESSBS) techniques during the novice training on the lamb's head model.

Methods:
Ten novices were asked to perform 10 bilateral dissections on the particular lamb's head each. The dissections were uniform, consisted of 10 well-defined steps, beginning from the simple removal of the inferior turbinate, and ending with more complicated procedures like cerebrospinal fluid leak repair, Draf 3 procedure for the frontal sinus and elevation of the nasal septal flap. The dissections have been supervised by experienced surgeons. A set of standard ESSBS instruments and 0° and 45° endoscopes have been used under the navigational system. The time required to complete each step has been measured in minutes.

Results:
In general and quite expectedly, time rates have been obviously lowering as the number of the dissections performed has been growing in each of the participants.

Conclusion:
Training of the endonasal ESSBS techniques on the lamb's head proved to be useful for novices in getting basic surgical skills in the field. Because of the high degree of anatomic similarity and high level of the anatomic dimensions congruency between the lamb's head and human head (sheep's head has bigger dimensions!) it proved to be an essential preparation for the human cadaveric dissection. The median values of the time rates having been needed to complete the particular of the 10 steps in the last novices’ dissections could be accepted as an orientation, just suggesting that once the time needed to complete 1 of the 10 steps has been and achieved by the particular novice, this could be an approximate sign of the maturity for the exercises on human cadaver head.
Pathway enrichment analysis of -omics data
Authors: Reimand Jüri , Isserlin Ruth , Voisin Veronique , Kucera Mike , Tannus-Lopes Christian , Rostamianfar Asha , Wadi Lina , Meyer Mona , Wong Jeff , Xu Changjiang , Merico Daniele , Bader Gary D. 
Published: December 2017

ABSTRACTPathway enrichment analysis helps gain mechanistic insight into large gene lists typically resulting from genome scale (–omics) experiments. It identifies biological pathways that are enriched in the gene list more than expected by chance. We explain pathway enrichment analysis and present a practical step-by-step guide to help interpret gene lists resulting from RNA-seq and genome sequencing experiments. The protocol comprises three major steps: define a gene list from genome scale data, determine statistically enriched pathways, and visualize and interpret the results. We focus on differentially expressed genes and mutated cancer genes, however the described principles can be applied to diverse –omics data. The protocol is designed for biologists with no prior bioinformatics training and uses freely available software including g:Profiler, GSEA, Cytoscape and Enrichment Map.