bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution
Authors: Perumal Sampath , Waminal Nomar Espinosa , Lee Jonghoon , Lee Junki , Choi Beom-Soon , Kim Hyun Hee , Grandbastien Marie-Angèle , Yang Tae-Jin 
Published: December 2017

AbstractDecoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences ofBrassica rapa(A genome),B.oleracea(C) andB.napus(AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in theB.rapaandB.oleraceagenomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates ourinsilicoanalysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the threeBrassicaspecies. Overall, our work elucidates hidden portions of threeBrassicagenomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes.
Immunotoxicological impact and biodistribution assessment of bismuth selenide (Bi2Se3) nanoparticles following intratracheal instillation in mice
Authors: Mishra Vani , Baranwal Vikas , Mishra Rohit K. , Sharma Shivesh , Paul Bholanath , Pandey Avinash C. 
Published: December 2017

AbstractVariously synthesized and fabricated Bi2Se3 nanoparticles (NPs) have recently been explored for their theranostic properties. Herein, we investigated the long term in-vivo biodistribution of Bi2Se3 NPs and systematically screened its immune-toxic potential over lungs and other secondary organs post intratracheal instillation. X-Ray CT scan and ICP MS results revealed significant particle localization and retention in lungs monitored for 1 h and 6 months time period respectively. Subsequent particle trafficking was observed in liver, the major reticuloendothelial organ followed by gradual but incomplete renal clearance. Pulmonary cytotoxicity was also found to be associated with persistent neutrophilic and ROS generation at all time points following NP exposure. The inflammatory markers along with ROS generation further promoted oxidative stress and exaggerated additional inflammatory pathways leading to cell death. The present study, therefore, raises serious concern about the hazardous effects of Bi2Se3 NPs and calls for further toxicity assessments through different administration routes and doses as well.
Design, fabrication and characterization of Computer Generated Holograms for anti-counterfeiting applications using OAM beams as light decoders
Authors: Ruffato Gianluca , Rossi Roberto , Massari Michele , Mafakheri Erfan , Capaldo Pietro , Romanato Filippo 
Published: December 2017

AbstractIn this paper, we present the design, fabrication and optical characterization of computer-generated holograms (CGH) encoding information for light beams carrying orbital angular momentum (OAM). Through the use of a numerical code, based on an iterative Fourier transform algorithm, a phase-only diffractive optical element (PO-DOE) specifically designed for OAM illumination has been computed, fabricated and tested. In order to shape the incident beam into a helicoidal phase profile and generate light carrying phase singularities, a method based on transmission through high-order spiral phase plates (SPPs) has been used. The phase pattern of the designed holographic DOEs has been fabricated using high-resolution Electron-Beam Lithography (EBL) over glass substrates coated with a positive photoresist layer (polymethylmethacrylate). To the best of our knowledge, the present study is the first attempt, in a comprehensive work, to design, fabricate and characterize computer-generated holograms encoding information for structured light carrying OAM and phase singularities. These optical devices appear promising as high-security optical elements for anti-counterfeiting applications.
The expression of AURKA is androgen regulated in castration-resistant prostate cancer
Authors: Kivinummi Kati , Urbanucci Alfonso , Leinonen Katri , Tammela Teuvo L. J. , Annala Matti , Isaacs William B. , Bova G. Steven , Nykter Matti , Visakorpi Tapio 
Published: December 2017

AbstractAlthough second generation endocrine therapies have significantly improved survival, castration-resistant prostate cancer (CRPC) cells are eventually able to escape available hormonal treatments due to reactivation of androgen receptor (AR) signaling. Identification of novel, non-classical and druggable AR-target genes may provide new approaches to treat CRPC. Our previous analyses suggested that Aurora kinase A (AURKA) is regulated by androgens in prostate cancer cells that express high levels of AR. Here, we provide further evidence that AURKA is significantly overexpressed in AR-positive CRPC samples carrying amplification of AR gene and/or expressing AR in high levels. We also demonstrate androgen-induced AR binding in the intronic region of AURKA. The expression of AURKA is increased upon androgen stimulation in LNCaP-ARhi cells that express high levels of AR. The growth of the cells was also significantly inhibited by an AURKA specific inhibitor, alisertib (MLN8237). Together, these findings suggest that the expression of AURKA is regulated by androgen in prostate cancer cells that highly express AR, emphasizing its potential as a therapeutic target in patients with CRPC.
The Effect of Time, Roasting Temperature, and Grind Size on Caffeine and Chlorogenic Acid Concentrations in Cold Brew Coffee
Authors: Fuller Megan , Rao Niny Z. 
Published: December 2017

AbstractThe extraction kinetics and equilibrium concentrations of caffeine and 3-chlorogenic acid (3-CGA) in cold brew coffee were investigated by brewing four coffee samples (dark roast/medium grind, dark roast/coarse grind, medium roast/medium grind, medium roast/coarse grind) using cold and hot methods. 3-CGA and caffeine were found at higher concentrations in cold brew coffee made with medium roast coffees, rather than dark roast. The grind size did not impact 3-CGA and caffeine concentrations of cold brew samples significantly, indicating that the rate determining step in extraction for these compounds did not depend on surface area. Caffeine concentrations in cold brew coarse grind samples were substantially higher than their hot brew counterparts. 3-CGA concentrations and pH were comparable between cold and hot brews. This work suggests that the difference in acidity of cold brew coffee is likely not due to 3-CGA or caffeine concentrations considering that most acids in coffee are highly soluble and extract quickly. It was determined that caffeine and 3-CGA concentrations reached equilibrium according to first order kinetics between 6 and 7 hours in all cold brew samples instead of 10 to 24 hours outlined in typical cold brew methods.
Three-Dimensional Evaluation of Posterior Pole and Optic Nerve Head in Myopes with Glaucoma
Authors: Kim Yong Chan , Jung Kyoung In , Park Hae-Young Lopilly , Park Chan Kee 
Published: December 2017

AbstractThe degree of myopia is represented by a global index, such as refractive error or axial length. However, the progression of myopia mainly develops in the posterior eyeball. Therefore, it is reasonable to assume that the evaluation of myopia should be confined to the posterior segment, where most of the growth and lengthening occurs. Swept source optical coherence tomography software can reconstruct the scans to the coronal view of the posterior pole, which provides additional anterior-posterior depth (z axis in the Cartesian coordinates) that is not provided with the common fundus photograph. We deduced that the parameter of deepest point of the eyeball (DPE) as a surrogate for posterior pole configuration. Between myopes with and without normal tension glaucoma (NTG) with similar axial length, myopes with NTG had deeper and more distant location of the DPE from the optic disc. The difference of the DPE position between the myopes with and without NTG may have implications for the larger optic disc tilt and torsion characteristic of myopes with NTG. Furthermore, these data suggest that myopes with NTG go through excessive posterior scleral remodeling, which may result in vulnerable optic nerve head.
Functional characterization of a novel non-coding mutation “Ghent +49A > G” in the iron-responsive element of L-ferritin causing hereditary hyperferritinaemia-cataract syndrome
Authors: Van de Sompele Stijn , Pécheux Lucie , Couso Jorge , Meunier Audrey , Sanchez Mayka , De Baere Elfride 
Published: December 2017

AbstractHereditary hyperferritinaemia-cataract syndrome (HHCS) is a rare disorder usually caused by heterozygous mutations in the iron-responsive element (IRE) in the 5′ untranslated region (5′UTR) of the L-ferritin gene (FTL), disturbing the binding of iron regulatory proteins (IRPs) and the post-transcriptional regulation of ferritin expression. Here, the proband of a consanguineous family displayed moderate bilateral cataracts and elevated serum ferritin in the absence of iron overload. The parents and siblings showed variable degrees of mild bilateral cataracts combined with elevated levels of circulating ferritin. Sequencing of FTL identified a novel 5′UTR mutation c.-151A > G, also named “Ghent +49A > G”. The zygosity of the mutation, occurring in homozygous and heterozygous state in the proband and other affected family members respectively, correlated well with severity of ophthalmological and hematological manifestations. The substitution is expected to impair the secondary structure of the upper IRE stem. Functional characterization of +49A > G by electrophoretic mobility shift assays demonstrated a reduced binding affinity for IRP1 compared to the wild-type IRE of FTL. Overall, we have expanded the repertoire of deleterious biallelic FTL IRE mutations in HHCS with this novel +49A > G mutation, the zygosity of which correlated well with the disease expression.
Amino acids as modulators of the European seabass, Dicentrarchus labrax, innate immune response: an in vitro approach
Authors: Azeredo Rita , Serra Cláudia R. , Oliva-Teles Aires , Costas Benjamín 
Published: December 2017

AbstractTeleost innate immune system is a most developed and powerful system in which fish highly rely throughout their lives. Conditions in aquaculture farms are particularly prone to disease, thus, health and welfare ensuring strategies are an urgent call to which nutrition is gradually becoming a most regarded achievement tool. This study intended to evaluate different amino acids’ effect on immune-related mechanisms as well as their potential as enhancers of European seabass, Dicentrarchus labrax, leucocyte functioning. To achieve these goals, primary cultures of head-kidney leucocytes were established and kept in amino acid (glutamine, arginine, tryptophan or methionine) supplemented culture media in two doses. The effects of amino acids treatments were then evaluated after stimulation with either Vibrio anguillarum or Vibrio anguillarum lipopolysaccharides by measuring nitric oxide production, extracellular respiratory burst, ATP and arginase activities, and expression of immune-related genes. Glutamine, arginine and tryptophan showed to be particularly relevant regarding cell energy dynamics; arginine and tryptophan supplementation also resulted in down-regulation of important immune-related genes. Immune responses in cells treated with methionine were generally enhanced but further studies, particularly those of enzymes activity, are essential to complement gene expression results and to better understand this nutrient’s immune role in fish.
Nanopore DNA Sequencing and Genome Assembly on the International Space Station
Authors: Castro-Wallace Sarah L. , Chiu Charles Y. , John Kristen K. , Stahl Sarah E. , Rubins Kathleen H. , McIntyre Alexa B. R. , Dworkin Jason P. , Lupisella Mark L. , Smith David J. , Botkin Douglas J. , Stephenson Timothy A. , Juul Sissel , Turner Daniel J. , Izquierdo Fernando , Federman Scot , Stryke Doug , Somasekar Sneha , Alexander Noah , Yu Guixia , Mason Christopher E. , Burton Aaron S. 
Published: December 2017

AbstractWe evaluated the performance of the MinION DNA sequencer in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). Nine sequencing runs were performed aboard the ISS over a 6-month period, yielding a total of 276,882 reads with no apparent decrease in performance over time. From sequence data collected aboard the ISS, we constructed directed assemblies of the ~4.6 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% consensus pairwise identity, respectively; de novo assembly of the E. coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. Simulated real-time analyses of in-flight sequence data using an automated bioinformatic pipeline and laptop-based genomic assembly demonstrated the feasibility of sequencing analysis and microbial identification aboard the ISS. These findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.
Using newborn screening analytes to identify cases of neonatal sepsis
Authors: Fell Deshayne B. , Hawken Steven , Wong Coralie A. , Wilson Lindsay A. , Murphy Malia S. Q. , Chakraborty Pranesh , Lacaze-Masmonteil Thierry , Potter Beth K. , Wilson Kumanan 
Published: December 2017

AbstractNeonatal sepsis is associated with high mortality and morbidity, yet challenges with available diagnostic approaches can lead to delays in therapy. Our study assessed whether newborn screening analytes could be utilized to identify associations with neonatal sepsis. We linked a newborn screening registry with health databases to identify cases of sepsis among infants born in Ontario from 2010–2015. Correlations between sepsis and screening analytes were examined within three gestational age groups (early preterm: <34 weeks; late preterm: 34–36 weeks; term: ≥37 weeks), using multivariable logistic regression models. We started with a model containing only clinical factors, then added groups of screening analytes. Among 793,128 infants, 4,794 were diagnosed with sepsis during the neonatal period. Clinical variables alone or in combination with hemoglobin values were not strongly predictive of neonatal sepsis among infants born at term or late preterm. However, model fit improved considerably after adding markers of thyroid and adrenal function, acyl-carnitines, and amino acids. Among infants born at early preterm gestation, neither clinical variables alone nor models incorporating screening analytes adequately predicted neonatal sepsis. The combination of clinical variables and newborn screening analytes may have utility in identifying term or late preterm infants at risk for neonatal sepsis.
Electron-blocking by the potential barrier originated from the asymmetrical local density of state in the oxide semiconductor
Authors: Lee Hyeon-Jun , Abe Katsumi , Kim Jun Seo , Lee Myoung-Jae 
Published: December 2017

AbstractDefect generation in oxide semiconductor thin-film transistors under high-voltage driving has not been studied in depth despite being a crucial bottleneck in the making of the integrated circuit utilized in an oxide semiconductor. Here we report on the origin of the asymmetrical transport characteristics caused by the degradation in the oxide semiconductor during integrated circuit driving. The variation of the current profiles based on test conditions is related to the generation of local defect states in the oxide material; this generation could be caused by the structural change of the material. The numerical calculations show that the flow of the electron is blocked by the “electrical pocket” formed by the electric-field distortion due to the local defect states near the edge of the electrode.
Prohibitin: a potential therapeutic target in tyrosine kinase signaling
Authors: Ande Sudharsana Rao , Xu Yang Xin Zi , Mishra Suresh 
Published: December 2017

AbstractProhibitin is a pleiotropic protein that has roles in fundamental cellular processes, such as cellular proliferation and mitochondrial housekeeping, and in cell- or tissue-specific functions, such as adipogenesis and immune cell functions. The different functions of prohibitin are mediated by its cell compartment-specific attributes, which include acting as an adaptor molecule in membrane signaling, a scaffolding protein in mitochondria, and a transcriptional co-regulator in the nucleus. However, the precise relationship between its distinct cellular localization and diverse functions remain largely unknown. Accumulating evidence suggests that the phosphorylation of prohibitin plays a role in a number of cell signaling pathways and in intracellular trafficking. Herein, we discuss the known and potential importance of the site-specific phosphorylation of prohibitin in regulating these features. We will discuss this in the context of new evidence from tissue-specific transgenic mouse models of prohibitin, including a mutant prohibitin lacking a crucial tyrosine phosphorylation site. We conclude with the opinion that prohibitin can be used as a potential target for tyrosine kinase signal transduction-targeting therapy, including in insulin, growth factors, and immune signaling pathways.
Spannende Vielfalt
Authors: Henrich Hans-Günther 
Published: December 2017

Zusammenfassung
OP-Management OP-Manager gestalten und steuern einen der komplexesten Bereiche eines Krankenhauses. Um hier etwas bewirken zu können,
stehen vielfältige Instrumente zur Verfügung, deren Auswahl sich an den Bedürfnissen der verschiedenen Anspruchsgruppen orientieren sollte.
Ein Patentrezept für wirksames OP-Management kann unser Autor zwar nicht liefern. Dafür beleuchtet er einige ausgewählte Schwerpunkte und
vermittelt, was OP-Management tatsächlich ist – oder zumindest sein könnte.
Teil des Teams
Authors: Schäfer Simon 
Published: December 2017

Zusammenfassung
Mitarbeiter mit Behinderung im OP Können Schwerbehinderte im OP arbeiten? Welche Rechte und Pflichten hat dabei der Arbeitgeber? Unser
Autor – der von Geburt an sogenannte „Schaufelhände“ hat – beschreibt in seinem sehr persönlichen Bericht, wie er sich in das OP-Team
integriert hat und welche unkonventionellen Lösungen ihm bei der Arbeit am Tisch helfen.
Die Mineralsalze in der ärztlichen Praxis
Authors: Emmrich Peter 
Published: December 2017

ZusammenfassungWeltweit finden Schüßler-Salze sowohl bei akuten als auch bei chronischen Leiden Anwendung. Seit über 145 Jahren haben sich die potenzierten
Mineralsalze, die auch in der Schwangerschaft und Stillzeit erfolgreich angewendet werden können, als zuverlässiger Partner in der
Naturheilkunde erwiesen. In Europa sind Schüßler-Salze ein fester Bestandteil in fast jeder Apotheke auch als Add-on-Therapie. Das
angezeigte Mineralsalz lässt sich anhand von Modalitäten, dem Zungenbefund und den vorhandenen Symptomen eines Patienten leicht
auswählen.
Verbesserung der Lebensqualität von Endometriosepatientinnen durch naturheilkundliche und komplementärmedizinische
Behandlungsverfahren
Authors: Grzanna Noëlle 
Published: December 2017

ZusammenfassungEndometriose ist eine benigne, proliferative, chronische Erkrankung, für die das Auftreten von endometriumartigen Zellverbänden außerhalb
ihrer eutopen Lokalisation im Cavum uteri charakteristisch ist. Die Erkrankung äußert sich mit sekundärer Dysmenorrhö, zyklischen,
azyklischen oder chronischen Unterbauchschmerzen und Dyspareunie. Aufgrund der unklaren Ätiologie stehen nur kausale, endokrine und
operative Therapieansätze zur Verfügung, die häufig von starken Nebenwirkungen begleitet werden. Die vorliegende Befragungsstudie ergab,
dass die Patientinnen durch naturheilkundliche und komplementärmedizinische Behandlungsverfahren, besonders von TCM und ihr verwandten
Verfahren, Homöopathie und Osteopathie, profitieren.
Menstruationsstörungen und der Einfluss der Hormone
Authors: Krug Marianne 
Published: December 2017

ZusammenfassungDer Artikel gibt einen Überblick über das weibliche Zyklusgeschehen, Menstruationsgeschehen und die verschiedenen Störungen, die damit
verbunden sind. Es werden die Einwirkungen der Hormone aus den drei Ebenen Hypothalamus, Hypophyse und Ovar erläutert. Zusätzlich wird in
Tempo- und Typusanomalien unterschieden. Die Schilddrüse hat ebenfalls einen bedeutenden Einfluss auf den Menstruationsrhythmus. Ebenso
können erhöhte Ausschüttungen von Prolaktin die Menstruation in Art und Rhythmus verändern. Therapeutisch kommen Phytotherapeutika (z. B.
Vitex agnus-castus) in Frage und der Ersatz von fehlenden oder unzureichend gebildeten Hormonen. Dies geschieht durch die Gabe von
bioidentischen Hormonen unter besonderer Berücksichtigung der Balance zwischen den verschiedenen Hormonen.
Gene Expression Analyses in Early Breast Carcinoma — Quo Vadis?
Authors: Almstedt Katrin , Denkert Carsten , Schmidt Marcus 
Published: December 2017

AbstractIn order to establish whether adjuvant therapy should be administered in patients with breast carcinoma, it is decisive to have as precise as possible an assessment of the risk of recurrence. In this context, gene expression — and thus gene expression signatures as well — have become a focus of attention as prognostic factors. For practical application, it is important to be able to analyze gene expression signatures in formalin-fixed, paraffin-embedded tumor tissue. Careful analytic and clinical validations and a high level of evidence (LoE) are required in order to avoid imprecise risk classification and thus potential overtreatment or undertreatment of the patients. Among the commercially available gene expression signatures, the Working Group on Gynecological Oncology (Arbeitsgemeinschaft Gynäkologische Onkologie, AGO) currently grades MammaPrint® and Oncotype DX® as having LoE IA, with prospective study results; and Endopredict® and Prosigna® as having LoE IB. The panel members at this year’s St. Gallen consensus conference also voted by a majority in favor of the possible usage of Oncotype DX®, MammaPrint®, Prosigna®, EndoPredict®, and Breast Cancer Index®. These multigene tests can be used in selected patients with hormone receptor–positive and HER2-negative findings if none of the other criteria allow a treatment decision to be made.