bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanofabrication of Conductive Metallic Structures on Elastomeric Materials
Authors: Tan Edward K. W. , Rughoobur Girish , Rubio-Lara Juan , Tiwale Nikhil , Xiao Zhuocong , Davidson Colin A. B. , Lowe Christopher R. , Occhipinti Luigi G. 
Published: April 2018

AbstractExisting techniques for patterning metallic structures on elastomers are limited in terms of resolution, yield and scalability. The primary constraint is the incompatibility of their physical properties with conventional cleanroom techniques. We demonstrate a reliable fabrication strategy to transfer high resolution metallic structures of <500 nm in dimension on elastomers. The proposed method consists of producing a metallic pattern using conventional lithographic techniques on silicon coated with a thin sacrificial aluminium layer. Subsequent wet etching of the sacrificial layer releases the elastomer with the embedded metallic pattern. Using this method, a nano-resistor with minimum feature size of 400 nm is fabricated on polydimethylsiloxane (PDMS) and applied in gas sensing. Adsorption of solvents in the PDMS causes swelling and increases the device resistance, which therefore enables the detection of volatile organic compounds (VOCs). Sensitivity to chloroform and toluene vapor with a rapid response (~30 s) and recovery (~200 s) is demonstrated using this PDMS nano-resistor at room temperature.
Internalization of CD239 highly expressed in breast cancer cells: a potential antigen for antibody-drug conjugates
Authors: Kikkawa Yamato , Enomoto-Okawa Yurie , Fujiyama Aiko , Fukuhara Takeshi , Harashima Nozomi , Sugawara Yumika , Negishi Yoichi , Katagiri Fumihiko , Hozumi Kentaro , Nomizu Motoyoshi , Ito Yuji 
Published: April 2018

AbstractAntibody–drug conjugates (ADCs) are attractive in cancer therapy because they can directly bind to cancer cells and provide anticancer activity. To kill cancer cells with ADCs, the target antigens are required not only to be highly and/or selectively expressed on cancer cells but also internalized by the cells. CD239, also known as the Lutheran blood group glycoprotein (Lu) or basal cell adhesion molecule (B-CAM), is a specific receptor for laminin α5, a major component of basement membranes. Here, we show that CD239 is strongly expressed in a subset of breast cancer cells and internalized into the cells. We also produced a human single-chain variable fragment (scFv) specific to CD239 fused with human IgG1 Fc, called C7-Fc. The binding affinity of the C7-Fc antibody is similar to that of mouse monoclonal antibodies. Although the C7-Fc antibody alone does not influence cellular functions, when conjugated with a fragment of diphtheria toxin lacking the receptor-binding domain (fDT), it can selectively kill breast cancer cells. Interestingly, fDT-bound C7-Fc shows anticancer activity in CD239-highly positive SKBR3 cells, but not in weakly positive cells. Our results show that CD239 is a promising antigen for ADC-based breast cancer therapy.
Diversity, structure and sources of bacterial communities in earthworm cocoons
Authors: Aira Manuel , Pérez-Losada Marcos , Domínguez Jorge 
Published: April 2018

AbstractAnimals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthwormsEisenia andreiandE. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts,Microbacteriaceae,VerminephrobacterandCa. Nephrothrix, which accounted for 88% and 66% of the sequences respectively.VerminephrobacterandCa. Nephrothrix showed a high rate of sequence variation, suggesting that they could be biparentally acquired during mating. The other bacterial species inhabiting the cocoons came from the bedding, where they accounted for a small fraction of the diversity (27% and 7% of bacterial species forE. andreiandE. fetidabedding). Hence, earthworm cocoon microbiome includes a large fraction of the vertically-transmitted symbionts and a minor fraction, but more diverse, horizontally and non-randomly acquired from the environment. These data suggest that horizontally-transmitted bacteria to cocoons may play an important role in the adaptation of earthworms to new environments or diets.
Light-activated cell identification and sorting (LACIS) for selection of edited clones on a nanofluidic device
Authors: Mocciaro Annamaria , Roth Theodore L. , Bennett Hayley M. , Soumillon Magali , Shah Abhik , Hiatt Joseph , Chapman Kevin , Marson Alexander , Lavieu Gregory 
Published: April 2018

AbstractDespite improvements in the CRISPR molecular toolbox, identifying and purifying properly edited clones remains slow, laborious, and low-yield. Here, we establish a method to enable clonal isolation, selection, and expansion of properly edited cells, using OptoElectroPositioning technology for single-cell manipulation on a nanofluidic device. Briefly, after electroporation of primary T cells with CXCR4-targeting Cas9 ribonucleoproteins, single T cells are isolated on a chip and expanded into colonies. Phenotypic consequences of editing are rapidly assessed on-chip with cell-surface staining for CXCR4. Furthermore, individual colonies are identified based on their specific genotype. Each colony is split and sequentially exported for on-target sequencing and further off-chip clonal expansion of the validated clones. Using this method, single-clone editing efficiencies, including the rate of mono- and bi-allelic indels or precise nucleotide replacements, can be assessed within 10 days from Cas9 ribonucleoprotein introduction in cells.
Integrating ultra‐fast charging stations within the power grids of smart cities: a review
Authors: Meyer Danielle , Wang Jiankang 
Published: April 2018

Plug‐in electric vehicles (PEVs) have become a key factor driving towards smart cities, which allow for higher energy efficiency and lower environmental impact across urban sectors. Industry vision for future PEV includes the ability to recharge a vehicle at a speed comparable to traditional gas refuelling, i.e. <3 min. per vehicle. Such a technology, referred to as ultra‐fast charging (UFC), has drawn much interest from research and industry. However, UFC poses unprecedented challenges to existing electricity supply infrastructure due to its large power density, impulsive, and stochastic load characteristics. Planning the locations and electric capacities of UFC stations is critical to preventing detrimental impacts. In particular, efforts must be made of mitigate grid asset depreciation, grid instabilities, and deteriorated power quality. The authors first review planning methods for conventional charging stations. Next, they discuss outlooks for UFC planning solutions by drawing an analogy with renewable energy (RE) source planning. This analogy is based on the similar power density and stochastic characteristics of RE and UFC. While this study mainly focuses on UFC planning from the power grid perspective, other urban aspects, including traffic flow and end‐user behaviour, are examined for feasible UFC integration within smart cities.
Ultraluminous X-ray sources: new distance indicators?
Authors: Różańska A. , Bresler K. , Bełdycki B. , Madej J. , Adhikari T. P. 
Published: April 2018

Aims. In this paper we fit the NuSTAR and XMM-Newton data of three sources: NGC 7793 P13, NGC5907 ULX1, and Circinus ULX5.
Methods. Our single model contains emission from a non-spherical system: a neutron star plus an accretion disk directed towards the observer.
Results. We obtained a very good fit with the reduced χ2 per degree of freedom equal to 1.08 for P13, 1.01 for ULX1, and 1.14 for ULX5. The normalization of our model constrains the distance to the source. The resulting distances are D = 3.41−0.10+0.11, 6.55−0.81+0.69, and 2.60−0.03+0.05 Mpc for P13, ULX1, and ULX5 respectively. The distances to P13 and ULX5 are in perfect agreement with previous distance measurements to their host galaxies.
Conclusions. Our results confirm that P13, ULX1, and ULX5 may contain central hot neutron stars. When the outgoing emission is computed by integration over the emitting surface and successfully fitted to the data, then the resulting model normalization is the direct distance indicator.
Offene Ausschaltung des infrarenalen Aortenaneurysmas
Authors: Fellenberg Jana , Wieker Carola 
Published: April 2018

ZusammenfassungDie offene Ausschaltung des infrarenalen Aortenaneurysmas mittels Bifurkations- oder Rohrprothese wird am Universitätsklinikum Heidelberg jährlich zirka sechzig
Mal durchgeführt. Das Operationsprinzip besteht darin, den erkrankten Aortenabschnitt durch eine Polyesterprothese zu ersetzen. Die Exposition der Aorta erfolgt
über einen abdominellen Zugang.
Endemische systemische Mykosen – Besonderheiten bei Reisenden
Authors: Salzer Helmut 
Published: April 2018

ZUSAMMENFASSUNGDie Diagnosestellung einer endemischen Mykose ist häufig schwierig, insbesondere in Nichtendemiegebieten. Eine genaue Reiseanamnese ist entscheidend. Die Histoplasmose ist die häufigste endemische Mykose bei Reisenden. Besichtigungen von Fledermaushöhlen oder Renovierungsarbeiten im Hotel sind mögliche Infektionsquellen. Die Paracoccidioidomykose wurde bei Langzeitreisenden in Südamerika beobachtet, während bei Reisenden nach Südostasien an eine Talaromykose gedacht werden sollte. Abhängig von der Reiseanamnese sind die Coccidioidomykose oder die Blastomykose weitere mögliche endemische Mykosen bei Reisenden. Der kulturelle oder histologische Nachweis ist die Methode der Wahl zur Diagnosesicherung für die meisten endemischen Mykosen. Im Mittelpunkt der antimykotischen Therapie steht Itraconazol bei milden bis mittelschweren und Amphotericin B bei schweren Verlaufsformen.
Bin ich anfällig für Höhenkrankheiten?
Authors: Bärtsch Peter , Dehnert Christoph 
Published: April 2018

ZusammenfassungAbsolute Höhe, Vorakklimatisation, Aufstiegsgeschwindigkeit und individuelle Anfälligkeit sind die wichtigsten Prädiktoren der akuten Bergkrankheit (ABK), des Höhenhirnödems (HHÖ) und des Höhenlungenödems (HLÖ). Die Anfälligkeit für akute Höhenkrankheiten lässt sich am besten durch anamnestische Angaben abschätzen. Messungen der Sauerstoffsättigung und der Ventilation in akuter Hypoxie zur Beurteilung der Anfälligkeit für ABK sind aufgrund der ungenügenden Trennschärfe nicht sinnvoll. Obwohl der überschießende pulmonal-arterielle Druckanstieg in Hypoxie ein entscheidender pathophysiologischer Faktor des HLÖ ist, kann er nicht zur Identifizierung von HLÖ-Anfälligkeit im Tiefland herangezogen werden, weil noch weitere (unbekannte) Faktoren in der Pathogenese dieser Krankheit eine Rolle spielen. Ob Tests in Hypoxie bei fehlender Höhenanamnese eine Verbesserung der Vorhersage bringen und zu einer größeren Reduktion von Höhenkrankheiten führen als Beratungen ohne Hypoxietests wurde bisher nicht untersucht. Deshalb können Hypoxietests außerhalb von kontrollierten Studien nicht empfohlen werden. Die Bestimmung genetischer Polymorphismen zur Erfassung der individuellen Anfälligkeit ist wegen fehlender Aussagekraft nicht sinnvoll. Eine gute aerobe Leistungsfähigkeit schützt nicht vor ABK und HLÖ, ist aber eine wichtige Voraussetzung für das Bergsteigen in großen Höhen (> 4000 m). Aus Berganamnese, geplanter Präakklimatisation und Aufstiegsprofil können das individuelle Risiko abgeschätzt und entsprechende Empfehlungen ausgesprochen werden.
Im besten Alter
Authors: Welk Ina 
Published: April 2018

ZusammenfassungDamit die Leistungsfähigkeit und Motivation der Mitarbeiter bis zur Rente erhalten bleibt, muss ein alter(n)sgerechtes Arbeitsumfeld geschaffen werden. Warum das
vor allem im Hinblick auf knappe Personalressourcen wichtig ist, welche Chancen und Potenziale ältere Pflegende haben und wie ihre Kompetenzen optimal ins Team
integriert werden können, beschreibt unsere Autorin.
Eins für alle – alle mit einem
Authors: Sauer Traute 
Published: April 2018

ZusammenfassungTraute SauerUm dem Personalmangel im OP vorzubeugen, werden immer häufiger Mitarbeiter aus unterschiedlichen Gesundheitsfachbereichen eingesetzt. Damit dennoch
eine gleichbleibende Qualität in der Patientenversorgung gesichert ist, wurde von der UKSH Akademie am Universitätsklinikum Schleswig-Holstein ein
Bildungskonzept entwickelt, das allen Berufsgruppen eine vergleichbare Qualifikation ermöglicht.
Frühzeitig wärmen
Authors: Gamon Eike 
Published: April 2018

ZusammenfassungPerioperative Veränderung der Körperkerntemperatur während der intraoperativen Nutzung eines konvektiven Luftwärmesystems anhand einer retrospektiven
Untersuchung an 552 Patienten – Bekanntermaßen hat das perioperative Wärmemanagement einen großen Stellenwert hinsichtlich eines möglichen Wärmeverlustes des
Patienten und den daraus resultierenden multifaktoriellen Problemen. Ziel dieser Arbeit war es, anhand einer Auswertung von perioperativen
Temperaturaufzeichnungen der Anästhesiepflege festzustellen, wie gut das von uns angewendete Wärmekonzept unter Nutzung eines Systems zur konvektiven
Lufterwärmung den Wärmeerhalt beim operativen Patienten sichern kann.
Characterization of CoPK02, a Ca2+/calmodulin-dependent protein kinase in mushroomCoprinopsis cinerea
Authors: Yamashita Masashi , Sueyoshi Noriyuki , Yamada Hiroki , Katayama Syouichi , Senga Yukako , Takenaka Yasuhiro , Ishida Atsuhiko , Kameshita Isamu , Shigeri Yasushi 
Published: April 2018

ABSTRACTWe surveyed genome sequences from the basidiomycetous mushroom Coprinopsis cinerea and isolated a cDNA homologous to CMKA, a calmodulin-dependent protein kinase (CaMK) in Aspergillus nidulans. We designated this sequence, encoding 580 amino acids with a molecular weight of 63,987, as CoPK02. CoPK02 possessed twelve subdomains specific to protein kinases and exhibited 43, 35, 40% identity with rat CaMKI, CaMKII, CaMKIV, respectively, and 40% identity with CoPK12, one of the CaMK orthologs in C. cinerea. CoPK02 showed significant autophosphorylation activity and phosphorylated exogenous proteins in the presence of Ca2+/CaM. By the CaM-overlay assay we confirmed that the C-terminal sequence (Trp346-Arg358) was the calmodulin-binding site, and that the binding of Ca2+/CaM to CoPK02 was reduced by the autophosphorylation of CoPK02. Since CoPK02 evolved in a different clade from CoPK12, and showed different gene expression compared to that of CoPK32, which is homologous to mitogen-activated protein kinase-activated protein kinase, CoPK02 and CoPK12 might cooperatively regulate Ca2+-signaling in C. cinerea.
The Utilization of VCO (Virgin Coconut Oil) in Manufacturing of Solid Soap with Red Betel Leaf Extract Addition (Paper Crotum Ruiz &Pav)
Authors: Sari M 
Published: April 2018

Abstract
Soap is a compound of sodium or potassium with fatty acids from vegetable oils or solid animal fats, soft or liquid, and foamy. Considering the potential of VCO as the raw material for making soap and supported by the benefits of red betel leaves, then this research is done by making solid bath soap from VCO which is supplemented with Red betel leaf extract. The purpose of this research is to make solid soap from VCO with an extract of red betel leaf based on SNINo.06-3532199. Analyzing VCO oil, which is used for the manufacture of soap, consists of analysis of saponification figures, Iodine number and peroxide number. Has made solid soap from VCO oil with Red betel leaf extract. From the five quality standards established under SNI 06-3532-1994 only two quality standards that can be done that is water quality and the amount of acidity. The percent of water quality obtained is 10% meanwhile the amount of acidity obtained is 9,32%. According to the data, it can be concluded that the solid soap made was not fulfill SNI 06-3532-1994.
NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks
Authors: Abdellah Marwan , Hernando Juan , Eilemann Stefan , Lapere Samuel , Antille Nicolas , Markram Henry , Schürmann Felix 
Published: April 2018

Abstract

Motivation
From image stacks to computational models, processing digital representations of neuronal morphologies is essential to neuroscientific research. Workflows involve various techniques and tools, leading in certain cases to convoluted and fragmented pipelines. The existence of an integrated, extensible and free framework for processing, analysis and visualization of those morphologies is a challenge that is still largely unfulfilled.

Results
We present NeuroMorphoVis, an interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks. Our framework is capable of detecting and repairing tracing artifacts, allowing the generation of high fidelity surface meshes and high resolution volumetric models for simulation and in silico imaging studies. The applicability of NeuroMorphoVis is demonstrated with two case studies. The first simulates the construction of three-dimensional profiles of neuronal somata and the other highlights how the framework is leveraged to create volumetric models of neuronal circuits for simulating different types of in vitro imaging experiments.

Availability and implementation
The source code and documentation are freely available on https://github.com/BlueBrain/NeuroMorphoVis under the GNU public license. The morphological analysis, visualization and surface meshing are implemented as an extensible Python API (Application Programming Interface) based on Blender, and the volume reconstruction and analysis code is written in C++ and parallelized using OpenMP. The framework features are accessible from a user-friendly GUI (Graphical User Interface) and a rich CLI (Command Line Interface).

Supplementary information
Supplementary data are available at Bioinformatics online.
Automatic selection of verification tools for efficient analysis of biochemical models
Authors: Bakir Mehmet Emin , Konur Savas , Gheorghe Marian , Krasnogor Natalio , Stannett Mike 
Published: April 2018

Abstract

Motivation
Formal verification is a computational approach that checks system correctness (in relation to a desired functionality). It has been widely used in engineering applications to verify that systems work correctly. Model checking, an algorithmic approach to verification, looks at whether a system model satisfies its requirements specification. This approach has been applied to a large number of models in systems and synthetic biology as well as in systems medicine. Model checking is, however, computationally very expensive, and is not scalable to large models and systems. Consequently, statistical model checking (SMC), which relaxes some of the constraints of model checking, has been introduced to address this drawback. Several SMC tools have been developed; however, the performance of each tool significantly varies according to the system model in question and the type of requirements being verified. This makes it hard to know, a priori, which one to use for a given model and requirement, as choosing the most efficient tool for any biological application requires a significant degree of computational expertise, not usually available in biology labs. The objective of this article is to introduce a method and provide a tool leading to the automatic selection of the most appropriate model checker for the system of interest.

Results
We provide a system that can automatically predict the fastest model checking tool for a given biological model. Our results show that one can make predictions of high confidence, with over 90% accuracy. This implies significant performance gain in verification time and substantially reduces the ‘usability barrier’ enabling biologists to have access to this powerful computational technology.

Availability and implementation
SMC Predictor tool is available at http://www.smcpredictor.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bayesian negative binomial regression for differential expression with confounding factors
Authors: Dadaneh Siamak Zamani , Zhou Mingyuan , Qian Xiaoning 
Published: April 2018

AbstractMotivationRapid adoption of high-throughput sequencing technologies has enabled better understanding of genome-wide molecular profile changes associated with phenotypic differences in biomedical studies. Often, these changes are due to multiple interacting factors. Existing methods are mostly considering differential expression across two conditions studying one main factor without considering other confounding factors. In addition, they are often coupled with essential sophisticated ad-hoc pre-processing steps such as normalization, restricting their adaptability to general experimental setups. Complex multi-factor experimental design to accurately decipher genotype-phenotype relationships signifies the need for developing effective statistical tools for genome-scale sequencing data profiled under multi-factor conditions.ResultsWe have developed a novel Bayesian negative binomial regression (BNB-R) method for the analysis of RNA sequencing (RNA-seq) count data. In particular, the natural model parameterization removes the needs for the normalization step, while the method is capable of tackling complex experimental design involving multi-variate dependence structures. Efficient Bayesian inference of model parameters is obtained by exploiting conditional conjugacy via novel data augmentation techniques. Comprehensive studies on both synthetic and real-world RNA-seq data demonstrate the superior performance of BNB-R in terms of the areas under both the receiver operating characteristic and precision-recall curves.Availability and implementationBNB-R is implemented in R language and is available at https://github.com/siamakz/BNBR.Supplementary informationSupplementary data are available at Bioinformatics online.
Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya
Authors: Cehovin Ana , Harrison Odile B , Lewis Steven B , Ward Philip N , Ngetsa Caroline , Graham Susan M , Sanders Eduard J , Maiden Martin C J , Tang Christoph M 
Published: April 2018

AbstractBackgroundAfrica has the highest incidence of gonorrhea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR).MethodsWhole-genome sequence data were analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have sex with men, from coastal Kenya. We annotated loci, defined the core genome, defined mechanisms of AMR, and performed phylogenetic analysis. For patients with multiple episodes of gonorrhea, we determined whether infections occurred with related strains.ResultsWe identified 3 clusters of isolates that are phylogenetically distinct from isolates found elsewhere. Plasmids were virtually ubiquitous: pTetM and pblaTEM were found in 97%, and 55% of isolates, respectively. This was associated with high doxycycline use for undiagnosed sexually transmitted infections. Twenty-three percent of multiple episodes of gonorrhea in the same individual were caused by a related strain, suggesting inadequate treatment or reinfection.ConclusionsThe prevalence of plasmid-mediated AMR in Kenyan gonococci contrasts with that in wealthy countries, where AMR is largely chromosomally mediated. Antimicrobials have a profound effect on the maintenance of lineages harboring plasmids. Doxycycline can select for tetracycline and penicillin resistance, through plasmid cooperation. Understanding the mechanisms of AMR in high-risk groups is required to inform treatment strategies.