bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twisting of DNA Origami from Intercalators
Authors: Zadegan Reza M. , Lindau Elias G. , Klein William P. , Green Christopher , Graugnard Elton , Yurke Bernard , Kuang Wan , Hughes William L. 
Published: August 2017

AbstractDNA nanostructures represent the confluence of materials science, computer science, biology, and engineering. As functional assemblies, they are capable of performing mechanical and chemical work. In this study, we demonstrate global twisting of DNA nanorails made from two DNA origami six-helix bundles. Twisting was controlled using ethidium bromide or SYBR Green I as model intercalators. Our findings demonstrate that DNA nanorails: (i) twist when subjected to intercalators and the amount of twisting is concentration dependent, and (ii) twisting saturates at elevated concentrations. This study provides insight into how complex DNA structures undergo conformational changes when exposed to intercalators and may be of relevance when exploring how intercalating drugs interact with condensed biological structures such as chromatin and chromosomes, as well as chromatin analogous gene expression devices.
Early involvement of cellular stress and inflammatory signals in the pathogenesis of tubulointerstitial kidney disease due to UMOD mutations
Authors: Trudu Matteo , Schaeffer Celine , Riba Michela , Ikehata Masami , Brambilla Paola , Messa Piergiorgio , Martinelli-Boneschi Filippo , Rastaldi Maria Pia , Rampoldi Luca 
Published: August 2017

AbstractAutosomal dominant tubulointerstitial kidney disease (ADTKD) is an inherited disorder that causes progressive kidney damage and renal failure. Mutations in the UMOD gene, encoding uromodulin, lead to ADTKD-UMOD related. Uromodulin is a GPI-anchored protein exclusively produced by epithelial cells of the thick ascending limb of Henle’s loop. It is released in the tubular lumen after proteolytic cleavage and represents the most abundant protein in human urine in physiological condition. We previously generated and characterized a transgenic mouse model expressing mutant uromodulin (Tg
UmodC147W) that recapitulates the main features of ATDKD-UMOD. While several studies clearly demonstrated that mutated uromodulin accumulates in endoplasmic reticulum, the mechanisms that lead to renal damage are not fully understood. In our work, we used kidney transcriptional profiling to identify early events of pathogenesis in the kidneys of Tg
UmodC147W mice. Our results demonstrate up-regulation of inflammation and fibrosis and down-regulation of lipid metabolism in young Tg
UmodC147W mice, before any functional or histological evidence of kidney damage. We also show that pro-inflammatory signals precede fibrosis onset and are already present in the first week after birth. Early induction of inflammation is likely relevant for ADTKD-UMOD pathogenesis and related pathways can be envisaged as possible novel targets for therapeutic intervention.
Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries
Authors: Ong Swee Hoe , Li Yilong , Koike-Yusa Hiroko , Yusa Kosuke 
Published: August 2017

AbstractGenome-wide CRISPR-based knockout (CRISPR-KO) screening is an emerging technique which enables systematic genetic analysis of a cellular or molecular phenotype in question. Continuous improvements, such as modifications to the guide RNA (gRNA) scaffold and the development of gRNA on-target prediction algorithms, have since been made to increase their screening performance. We compared the performance of three available second-generation human genome-wide CRISPR-KO libraries that included at least one of the improvements, and examined the effect of gRNA scaffold, number of gRNAs per gene and number of replicates on screen performance. We identified duplicated screens using a library with 6 gRNAs per gene as providing the best trade-off. Despite the improvements, we found that each improved library still has library-specific false negatives and, for the first time, estimated the false negative rates of CRISPR-KO screens, which are between 10% and 20%. Our newly-defined optimal screening parameters would be helpful in designing screens and constructing bespoke gRNA libraries.
Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species
Authors: Kindler Carolin , Chèvre Maxime , Ursenbacher Sylvain , Böhme Wolfgang , Hille Axel , Jablonski Daniel , Vamberger Melita , Fritz Uwe 
Published: August 2017

AbstractRecent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspeciesNatrix natrix helveticaand the eastern subspeciesN. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified withN. n. natrixandN. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and thatNatrix helveticashould be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.
Graphene Enhanced Secondary Ion Mass Spectrometry (GESIMS)
Authors: Michałowski Paweł Piotr , Kaszub Wawrzyniec , Pasternak Iwona , Strupiński Włodek 
Published: August 2017

AbstractThe following invention - Graphene Enhanced Secondary Ion Mass Spectrometry - (pending European patent application no. EP 16461554.4) is related to a method of analysing a solid substrate by means of Secondary Ion Mass Spectrometry (SIMS). It comprises the steps of providing a graphene layer over the substrate surface and analysing ejected secondary anions through mass spectrometry analysis. The graphene layer acts as a kind of filament that emits a lot of secondary electrons during the experiment which significantly increases the negative ionization probability and thus the intensity of the SIMS signal can be more than two orders of magnitude higher than that of a similar sample without graphene. The method is particularly useful for the analysis of surfaces, 2D materials and ultra-thin films. The intensity of dopants and contamination signals can be enhanced up to 35 times, which approaches the detection limit of ~1015atoms/cm3, otherwise unreachable in a standard static SIMS analysis.
Short-term treatment with eicosapentaenoic acid improves inflammation and affects colonic differentiation markers and microbiota in patients with ulcerative colitis
Authors: Prossomariti Anna , Scaioli Eleonora , Piazzi Giulia , Fazio Chiara , Bellanova Matteo , Biagi Elena , Candela Marco , Brigidi Patrizia , Consolandi Clarissa , Balbi Tiziana , Chieco Pasquale , Munarini Alessandra , Pariali Milena , Minguzzi Manuela , Bazzoli Franco , Belluzzi Andrea , Ricciardiello Luigi 
Published: August 2017

AbstractPatients with long-standing ulcerative colitis (UC) have an increased colorectal cancer (CRC) risk. In this pilot study we evaluated the effect of Eicosapentaenoic acid as free fatty acid (EPA-FFA) supplementation on mucosal disease activity, colonic differentiation markers and microbiota composition in UC patients. Twenty long-standing UC patients in stable clinical remission and with fecal calprotectin (FC) > 150 µg/g were enrolled (T0) and supplemented with EPA-FFA 2 g/daily for 90 days (T3). Endoscopic and histologic disease activities were measured by Mayo and Geboes scores, respectively. HES1, KLF4, STAT3, IL-10 and SOCS3 levels were determined using western blotting and qRT-PCR, while phospho-STAT3 levels were assessed by western blotting. Goblet cells were stained by Alcian blue. Microbiota analyses were performed on both fecal and colonic samples. Nineteen patients completed the study; seventeen (89.5%) were compliant. EPA-FFA treatment reduced FC levels at T3. Patients with FC > 150 µg/g at T3 (n = 2) were assumed as non-responders. EPA-FFA improved endoscopic and histological inflammation and induced IL-10, SOCS3, HES1 and KLF4 in compliant and responder patients. Importantly, long-term UC-driven microbiota composition was partially redressed by EPA-FFA. In conclusion, EPA-FFA supplementation reduced mucosal inflammation, promoted goblet cells differentiation and modulated intestinal microbiota composition in long-standing UC patients.
Facial appearance reveals immunity in African men
Authors: Phalane Khutso G. , Tribe Catherine , Steel Helen C. , Cholo Moloko C. , Coetzee Vinet 
Published: August 2017

AbstractFacial appearance is thought to indicate immunity in humans, but very few studies have tested this relationship directly. The aim of this study was to test the relationship between direct measures of immunity, perceived facial health and attractiveness, and facial cues in African men. We show that men with a stronger cytokine response are considered significantly more attractive and healthy. Men with more masculine, heavier facial features (i.e. muscular appearance) have a significantly higher cytokine response and appear significantly healthier and more attractive, while men with a yellower, lighter, “carotenoid” skin colour, have a marginally higher immune response and are also considered significantly more healthy and attractive. In contrast, more symmetrical, skinnier looking men appeared more attractive and healthier, but did not have a stronger cytokine response. These findings also shed new light on the “androgen-mediated” traits proposed by the immunocompetence handicap hypothesis (ICHH) and we propose that facial muscularity serves as a better estimate of an “androgen-mediated” trait than facial masculinity. Finally, we build on previous evidence to show that men’s facial features do indeed reveal aspects of immunity, even better than more traditional measures of health, such as body mass index (BMI).
An improved database of coastal flooding in the United Kingdom from 1915 to 2016
Authors: Haigh Ivan D. , Ozsoy Ozgun , Wadey Matthew P. , Nicholls Robert J. , Gallop Shari L. , Wahl Thomas , Brown Jennifer M. 
Published: August 2017

AbstractCoastal flooding caused by extreme sea levels can produce devastating and wide-ranging consequences. The ‘SurgeWatch’ v1.0 database systematically documents and assesses the consequences of historical coastal flood events around the UK. The original database was inevitably biased due to the inconsistent spatial and temporal coverage of sea-level observations utilised. Therefore, we present an improved version integrating a variety of ‘soft’ data such as journal papers, newspapers, weather reports, and social media. SurgeWatch2.0 identifies 329 coastal flooding events from 1915 to 2016, a more than fivefold increase compared to the 59 events in v1.0. Moreover, each flood event is now ranked using a multi-level categorisation based on inundation, transport disruption, costs, and fatalities: from 1 (Nuisance) to 6 (Disaster). For the 53 most severe events ranked Category 3 and above, an accompanying event description based upon the Source-Pathway-Receptor-Consequence framework was produced. Thus, SurgeWatch v2.0 provides the most comprehensive and coherent historical record of UK coastal flooding. It is designed to be a resource for research, planning, management and education.
Morphology of Dbx1 respiratory neurons in the preBötzinger complex and reticular formation of neonatal mice
Authors: Akins Victoria T. , Weragalaarachchi Krishanthi , Picardo Maria Cristina D. , Revill Ann L. , Del Negro Christopher A. 
Published: August 2017

AbstractThe relationship between neuron morphology and function is a perennial issue in neuroscience. Information about synaptic integration, network connectivity, and the specific roles of neuronal subpopulations can be obtained through morphological analysis of key neurons within a microcircuit. Here we present morphologies of two classes of brainstem respiratory neurons. First, interneurons derived from Dbx1-expressing precursors (Dbx1 neurons) in the preBötzinger complex (preBötC) of the ventral medulla that generate the rhythm for inspiratory breathing movements. Second, Dbx1 neurons of the intermediate reticular formation that influence the motor pattern of pharyngeal and lingual movements during the inspiratory phase of the breathing cycle. We describe the image acquisition and subsequent digitization of morphologies of respiratory Dbx1 neurons from the preBötC and the intermediate reticular formation that were first recorded in vitro. These data can be analyzed comparatively to examine how morphology influences the roles of Dbx1 preBötC and Dbx1 reticular interneurons in respiration and can also be utilized to create morphologically accurate compartmental models for simulation and modeling of respiratory circuits.
Data processing pipeline for Herschel HIFI
Authors: Shipman R. F. , Beaulieu S. F. , Teyssier D. , Morris P. , Rengel M. , McCoey C. , Edwards K. , Kester D. , Lorenzani A. , Coeur-Joly O. , Melchior M. , Xie J. , Sanchez E. , Zaal P. , Avruch I. , Borys C. , Braine J. , Comito C. , Delforge B. , Herpin F. , Hoac A. , Kwon W. , Lord S. D. , Marston A. , Mueller M. , Olberg M. , Ossenkopf V. , Puga E. , Akyilmaz-Yabaci M. 
Published: August 2017

Context. The HIFI instrument on the Herschel Space Observatory performed over 9100 astronomical observations, almost 900 of which were calibration observations in the course of the nearly four-year Herschel mission. The data from each observation had to be converted from raw telemetry into calibrated products and were included in the Herschel Science Archive.
Aims. The HIFI pipeline was designed to provide robust conversion from raw telemetry into calibrated data throughout all phases of the HIFI missions. Pre-launch laboratory testing was supported as were routine mission operations.
Methods. A modular software design allowed components to be easily added, removed, amended and/or extended as the understanding of the HIFI data developed during and after mission operations.
Results. The HIFI pipeline processed data from all HIFI observing modes within the Herschel automated processing environment as well as within an interactive environment. The same software can be used by the general astronomical community to reprocess any standard HIFI observation. The pipeline also recorded the consistency of processing results and provided automated quality reports. Many pipeline modules were in use since the HIFI pre-launch instrument level testing.
Conclusions. Processing in steps facilitated data analysis to discover and address instrument artefacts and uncertainties. The availability of the same pipeline components from pre-launch throughout the mission made for well-understood, tested, and stable processing. A smooth transition from one phase to the next significantly enhanced processing reliability and robustness.
Cluster Preface: Catalytic Aerobic Oxidations
Authors: Stahl Shannon , Rovis Tomislav 
Published: August 2017

Shannon S. Stahl was an undergraduate at the University of Illinois at Urbana-Champaign, and a graduate student at Caltech (PhD, 1997), where he worked with Professor John Bercaw. He was an NSF postdoctoral fellow with Professor Stephen Lippard at Massachusetts Institute of Technology from 1997–1999. He is currently a Professor of Chemistry at the University of Wisconsin–Madison, where he began his independent career in 1999. His research group specializes in catalysis, with an emphasis on aerobic oxidation reactions and oxygen chemistry related to energy conversion.
Tomislav Rovis was born in Zagreb in former Yugoslavia but was largely raised in southern Ontario, Canada. He earned his PhD degree at the University of Toronto (Canada) in 1998 under the direction of Professor Mark Lautens. From 1998–2000, he was an NSERC Postdoctoral Fellow at Harvard University (USA) with Professor David A. Evans. In 2000, he began his independent career at Colorado State University and was promoted in 2005 to Associate Professor and in 2008 to Professor. His group’s accomplishments have been recognized by a number of awards including an Arthur C. Cope Scholar, an NSF CAREER Award, a Fellow of the American Association for the Advancement of Science and a ­Katritzky Young Investigator in Heterocyclic Chemistry. In 2016, he moved to Columbia University where he is currently Professor of Chemistry.
The Osteocutaneous Fibular Flap for Mandibular Replacement—Which Factors Influence Long-Term Success?
Authors: Kolk Andreas , Haidari S. , Wolff K.-D. , Fichter A. , Kehl V. , Götz C. , Kesting M. , Weitz J. 
Published: August 2017

Background The free fibular flap (FFF) is established for mandibular reconstruction. Some complications, such as non-union, fistulas, and complete graft loss, are sometimes unavoidable. There are no clinically relevant data regarding the optimum selection of osteosynthesis and risk analysis prior to reconstruction.
Methods Eighty-three FFFs with up to four osteotomies were analyzed for possible complications during the course of a longitudinal analysis. Forty-one patients underwent simultaneous mandibular reconstruction after tumor resection, and another 42 subjects received FFFs due to infected osteoradionecrosis (ORN). Patients who experienced transplant losses due to vascular occlusion in the grafts were excluded from the study.
Results The most common complications were fistulas, bony non-union, and failure of osteosynthesis material. Major contributing risk factors were radiotherapy (p = 0.004), number of osteosynthesis plates >6 (p = 0.002), length of the harvested fibula (p = 0.027), the size of the skin island (p = 0.002), and the number of osteotomies (p = 0.001).
Conclusion For the success of FFF, there are many influencing factors. If the mentioned risk factors are considered, the number of osteotomies, size of the skin paddle, and fibula are as small as possible, and a suitable osteosynthesis material is chosen, the FFF is a safe solution for mandibular reconstruction.
Die körperdysmorphe Störung in der Plastischen Chirurgie – Eine systematische Übersicht der Screening
Methoden
Authors: Houschyar K. S. , Philipps H. M. , Duscher D. , Rein S. , Weissenberg K. , Nietzschmann I. , Maan Z. N. , Pyles M. N. , Siemers F. 
Published: August 2017

Zusammenfassung
Hintergrund Die körperdysmorphe Störung, englisch „body dysmorphic disorder“ (BDD), gilt als Unterform der somatoformen Störungen. BDD
kann sich in wahnhaftem Erleben, einer übermäßigen Bewertung und Beschäftigung des äußeren Erscheinungsbildes, insbesondere dem Gesicht
äußern. Vorläufige Ergebnisse legen nahe, dass Personen mit BDD nicht von plastisch-chirurgischen Behandlungen profitieren, so dass durch
ästhetische operative Eingriffe häufig sogar eine Aggravation ihrer Symptome resultiert. Somit ist die Identifikation von Anzeichen für ein
BDD entscheidend, ob ein Patient plastisch-ästhetisch operiert werden sollte. Diese Übersichtsarbeit erläutert die oft schwierige Diagnostik
der BDD, indem sie die aktuelle Literatur zu dessen Screening zusammenfasst.
Studiendesign Systematische Übersichtsarbeit
Methoden Es wurde eine elektronische Suche in der deutsch- und englischsprachigen Literatur durchgeführt, um alle
Screening-Instrumente für die BDD zu identifizieren. Es werden die spezifischen Entwicklungs- und Validierungsprozesse beurteilt, ob die
Screening-Instrumente einen positiven prädiktiven Wert für die BDD haben.
Ergebnisse Sechs verschiedene Screening-Instrumente wurden für die BDD identifiziert. Davon wurden nur zwei in einem kosmetischen
Rahmen evaluiert: der „Body Dysmorphic Disorder Questionnaire–Dermatology Version“ (BDDQ-DV) und der „Dysmorphic Concern Questionnaire“
(DCQ). Der Einfluss auf die subjektiven Ergebnisse nach einem plastisch-ästhetischen Eingriff wurde nur für den DCQ gemessen.
Schlussfolgerung Die begrenzte Verfügbarkeit von validierten Screening-Instrumenten für die BDD in der plastischen Chirurgie steht in
bemerkenswerten Gegensatz zu der vermeintlich hohen Prävalenz der Erkrankung von 2,4 %. Unter den derzeit verwendeten Screening-Tools
scheinen die BDDQ-DV und der DCQ am besten geeignet zu sein. Weitere Forschungsbemühungen zur Etablierung besserer Screeningmethoden für die
BDD in der plastischen chirurgischen Patientenpopulation und zur Untersuchung der Auswirkungen von BDD auf Behandlungsergebnisse sind
notwendig.
Mastopexie nach massivem Gewichtsverlust – Erweiterte Ribeiro-Technik und Einsatz der lateralen
Interkostalarterien-Perforatorlappenplastik (LICAP-Flap) zur Autoaugmentation
Authors: Wolter Andreas , Scholz Till , Pluto Naja , Diedrichson Jens , Arens-Landwehr Andreas , Liebau Jutta 
Published: August 2017

Zusammenfassung
Hintergrund Eine Mastopexie nach massivem Gewichtsverlust stellt eine besondere Herausforderung in der Mammachirurgie dar. Der
Brusthügel ist oft stark abgeflacht mit reduzierter Hautqualität. Die chirurgische Vorgehensweise basiert in erster Linie auf einer
Umformung des Drüsengewebes statt auf einer Straffung des Hautmantels. Publizierte Techniken beinhalten eine Plikation, Suspension und
Autoaugmentation. Das vorhandene ortsständige Gewebe (Brustdrüse, Fettgewebe, Dermofettlappen) wird vollumfänglich verwendet mit dem Ziel,
eine Brust mit stabiler Projektion nachhaltig zu formen. Die Entwicklung einer solchen Technik wird präsentiert.
Patienten und Methoden Es handelt sich um eine retrospektive Analyse von 68 Patientinnen (136 Brüste), bei denen eine modifizierte
Ribeiro-Technik mit superomedialer Mamillenstielung durch eine Suspension mit einem inferioren dermoglandulären Lappen durchgeführt wurde.
Darüberhinaus beinhaltet die vorgestellte Technik eine Einbeziehung der lateralen Interkostalarterien-Perforatorlappenplastik (LICAP flap)
sowie des medialen Brustpfeilers als zusätzliche Volumengewinnung zum Ribeiro-Lappen. Dies trägt wesentlich zur Autoaugmentation des oberen
Brustpols bei, führt zur Verschmälerung der verbreiterten Brust, bildet einen internen BH und redefiniert die Inframammärfalte. Die
Ergebnisse zur Komplikationsrate, Patientenzufriedenheit, Brustwarzensensibilität und Korrekturrate wurden überprüft.
Ergebnisse Von 01/2011–12/2016 führten wir 136 Auto-Augmentationsmastopexien durch. Das Durchschnittsalter betrug 41,2 Jahre, der
durchschnittliche Body-Mass-Index (BMI) war 27,1 kg/m2, der durchschnittliche Gewichtsverlust war 54,3 kg, der durchschnittliche
Mamillen-Jugulum-Abstand war 32,3 cm, die durchschnittliche OP-Dauer betrug 109 Minuten. Bei 12 Brüsten erfolgte eine freie
Brustwarzentransplantation. Die Komplikationsrate lag bei insgesamt 5,1 %, die Korrekturrate bei 17,6 %. 95 % der Patientinnen waren „sehr
zufrieden“ bis „zufrieden“ mit dem ästhetischen Ergebnis bei in 85 % „sehr gut“ bis „gut“ erhaltener Brustwarzensensibilität.
Fazit Die Modifikation der Ribeiro-Technik mit zusätzlicher Anwendung der medialen und lateralen Brustanteile (LICAP flap) erlaubt
eine Autoaugmentation des oberen Brustpols bei Patientinnen nach massivem Gewichtsverlust. Die Brustumformung durch Raffung und Suspension
des residualen Brustgewebes soll die Langzeitformstabilität der Brust verbessern und die Inzidenz einer erneuten Ptosis verringern. Die
präsentierte Vorgehensweise stellt eine reproduzierbare, verlässliche Methode mit geringer Komplikationsrate dar.