bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum Dot Optomechanics in Suspended Nanophononic Strings
Authors: Vogele Anja , Sonner Maximilian M. , Mayer Benjamin , Yuan Xueyong , Weiß Matthias , Nysten Emeline D. S. , Covre da Silva Saimon F. , Rastelli Armando , Krenner Hubert J. 
Published: November 2019

AbstractThe optomechanical coupling of quantum dots and flexural mechanical modes is studied in suspended nanophononic strings. The investigated devices are designed and monolithically fabricated on an (Al)GaAs heterostructure. Radio frequency elastic waves with frequencies ranging between and 400 MHz are generated as Rayleigh surface acoustic waves on the unpatterned substrate and injected as Lamb waves in the nanophononic string. Quantum dots inside the nanophononic string exhibit a 15‐fold enhanced optomechanical modulation compared to those dynamically strained by the Rayleigh surface acoustic wave. Detailed finite element simulations of the phononic mode spectrum of the nanophononic string confirm that the observed modulation arises from valence band deformation potential coupling via shear strain. The corresponding optomechanical coupling parameter is quantified to . This value exceeds that reported for vibrating nanorods by approximately one order of magnitude at 100 times higher frequencies. Using this value, a derived vertical displacement in the range of 10 nm is deduced from the experimentally observed modulation. The results represent an important step toward the creation of large scale optomechanical circuits interfacing single optically active quantum dots with optical and mechanical waves.
Injectable and Radiopaque Liquid Metal/Calcium Alginate Hydrogels for Endovascular Embolization and Tumor Embolotherapy
Authors: Fan Linlin , Duan Minghui , Xie Zhongchen , Pan Keqin , Wang Xuelin , Sun Xuyang , Wang Qian , Rao Wei , Liu Jing 
Published: November 2019

AbstractImproved endovascular embolization can contribute to assistant treatment for patients. However, many traditional embolic materials, such as metal microcoils or liquid embolic agents, are associated with limitations of coil migration or recanalization. Herein, as the first trial, an injectable and radiopaque liquid metal/calcium alginate (LM/CA) hydrogel is introduced and fabricated as a candidate for endovascular embolization and tumor embolotherapy through developing LM droplets as radiopaque units into biocompatible calcium alginate cross‐linked network. The adoption of LM droplets makes hydrogels radiopaque under X‐ray and CT scan, which significantly facilitates the tracking of material location during surgical vascular operation. In addition, in vitro and in vivo experiments prove that such smart hydrogel could convert from liquid to solid rapidly via cross‐linking, showing pretty flexible and controllable functions. Benefiting from these properties, the hydrogel can be performed in blood vessels through injection via syringes and then served as an embolic material for endovascular embolization procedures. In vivo experiments demonstrate that such hydrogels can occlude arteries and block blood flow until they ultimately lead to ischemic necrosis of tumors and partial healthy tissues. Overall, the present LM/CA hydrogels are promising to be developed as new generation embolic materials for future tumor embolotherapy.
Universal Nanocarrier Ink Platform for Biomaterials Additive Manufacturing
Authors: Guzzi Elia A. , Bovone Giovanni , Tibbitt Mark W. 
Published: November 2019

AbstractInk engineering is a fundamental area of research within additive manufacturing (AM) that designs next‐generation biomaterials tailored for additive processes. During the design of new inks, specific requirements must be considered, such as flowability, postfabrication stability, biointegration, and controlled release of therapeutic molecules. To date, many (bio)inks have been developed; however, few are sufficiently versatile to address a broad range of applications. In this work, a universal nanocarrier ink platform is presented that provides tailored rheology for extrusion‐based AM and facilitates the formulation of biofunctional inks. The universal nanocarrier ink (UNI) leverages reversible polymer–nanoparticle interactions to form a transient physical network with shear‐thinning and self‐healing properties engineered for direct ink writing (DIW). The unique advantage of the material is that a range of functional secondary polymers can be combined with the UNI to enable stabilization of printed constructs via secondary cross‐linking as well as customized biofunctionality for tissue engineering and drug delivery applications. Specific UNI formulations are used for bioprinting of living tissue constructs and DIW of controlled release devices. The robust and versatile nature of the UNI platform enables rapid formulation of a broad range of functional inks for AM of advanced biomaterials.
Design and validation of a C++ code generator from Abstract State Machines specifications
Authors: Bonfanti Silvia , Gargantini Angelo , Mashkoor Atif 
Published: November 2019

AbstractAccording to best practices of model‐driven engineering, the implementation of a system should be obtained from its model through a systematic model‐to‐code transformation. We present in this paper a methodology supported by the Asm2C++ tool, which allows the users to generate C++ code from abstract state machine models. Thanks to Asm2C++, the implementation is generated in a seamless manner with an assurance of potential bug freeness of the generated code. Following the same approach, model‐based testing suggests deriving also (unit) tests from abstract models. We extend the Asm2C++ tool such that it can automatically produce unit tests for the generated code. Abstract test sequences, either generated randomly or through model checking, are translated to concrete C++ unit tests using the Boost library. In a similar manner, also, scenarios are generated in a behavior‐driven development (BDD) approach. To guarantee the correctness of the transformation process, we define a mechanism to test the correctness of the model‐to‐code transformation with respect to two main criteria: syntactical correctness and semantic correctness, which is based on the definition of conformance between the specification and the code. Using this approach, we have devised a process able to test the generated code by reusing unit tests. The process has been used to validate our model‐to‐code transformations.
Computational methods for ribosome profiling data analysis
Authors: Kiniry Stephen J. , Michel Audrey M. , Baranov Pavel V. 
Published: November 2019

AbstractSince the introduction of the ribosome profiling technique in 2009 its popularity has greatly increased. It is widely used for the comprehensive assessment of gene expression and for studying the mechanisms of regulation at the translational level. As the number of ribosome profiling datasets being produced continues to grow, so too does the need for reliable software that can provide answers to the biological questions it can address. This review describes the computational methods and tools that have been developed to analyze ribosome profiling data at the different stages of the process. It starts with initial routine processing of raw data and follows with more specific tasks such as the identification of translated open reading frames, differential gene expression analysis, or evaluation of local or global codon decoding rates. The review pinpoints challenges associated with each step and explains the ways in which they are currently addressed. In addition it provides a comprehensive, albeit incomplete, list of publicly available software applicable to each step, which may be a beneficial starting point to those unexposed to ribosome profiling analysis. The outline of current challenges in ribosome profiling data analysis may inspire computational biologists to search for novel, potentially superior, solutions that will improve and expand the bioinformatician's toolbox for ribosome profiling data analysis.This article is characterized under:

Translation > Ribosome Structure/Function
RNA Evolution and Genomics > Computational Analyses of RNA
Translation > Translation Mechanisms
Translation > Translation Regulation
Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs
Authors: Cruz Cristina , Houseley Jonathan 
Published: November 2019

AbstractOver the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights into ncRNA distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex RNA populations but are rarely employed outside specialist RNA research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated RNA on agarose gels and heat denatured RNA on polyacrylamide–urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncRNAs of interest.
The Bridge: Redux—The Breakdown of Normative Conviviality
Authors: Ristilammi Per-Markku 
Published: November 2019

AbstractIn this chapter the concept of conviviality is used as an analytic concept around which recent developments concerning the changing role of state borders in Europe are discussed. It aims at highlighting a specific kind of normative state-driven conviviality through the example of the transnational Öresund Bridge, between Sweden and Denmark, thus showing how the concept can be used in an analysis of the changing roles, or even states of the state. The Bridge and the surrounding region was part of a bi-national project of conviviality at its inauguration in 2000, but 15 years later the border controls that were put in place in response to the so called refugee-crisis, which signaled a breakdown of this specific form of conviviality. The chapter shows how this breakdown of state conviviality opens up for a new form of biopolitical regime at the border.
Charting a Convivial Continuum in British Post-war Popular Music 1948–2018
Authors: Boothby Hugo 
Published: November 2019

AbstractThis chapter seeks to chart a convivial continuum within Caribbean influenced British post-war popular music. Conviviality is understood here to find expression in social formations where essentialised racial identifications and their associated hierarchies breakdown. Popular music is an important site at which to trace convivial formation and its relationship with migration within the UK because it offers a productive site at which vibrant intermixture and combination have taken place. In this chapter, these processes of intermixture and combination are understood in terms of creolisation. Calypso, reggae, post-punk, jungle, two-step garage, dubstep and grime are explored as sites of signifying-practice and corporeal affect with potential to articulate identity positions and experiences that are anti-essential and capable of disrupting racial hierarchies.
Creolisation as a Recipe for Conviviality
Authors: Eriksen Thomas Hylland 
Published: November 2019

AbstractThis chapter argues that the historical and contemporary experiences of the Creole world have created a set of possible social and cultural configurations which encompass cosmopolitanism, create conditions for conviviality and expand the project of living together by engaging the arts and music, language and food, as well as transgressing social boundaries. The miracle of creolisation can be described as an enormous output of cultural creativity growing out of a history of suffering, displacement and oppression. However, the social effects of creolisation are perhaps more important, leading to the emergence of social identities which are unbounded, exogamous as well as endogamous, internally diverse and striking a balance between group and individual which is simultaneously flexible and robust, an inoculation against divisive identity politics.
Creolising Conviviality: Thinking Relational Ontology and Decolonial Ethics Through Ivan Illich and Édouard Glissant
Authors: Gutiérrez Rodríguez Encarnación 
Published: November 2019

AbstractFollowing Ivan Illich and Édouard Glissant, this chapter aims to discuss the conceptual and visionary implications of creolising conviviality. It does so by first providing an account of Illich’s concept of “conviviality” in terms of its material and ethical underpinning. Second, it looks at contemporary empirical research on conviviality in order to understand the complexities that this perspective sets out to study. Third, the chapter establishes that conviviality needs to be placed in relation to Glissant’s creolisation, a visionary outlook of an antagonistic living together. Creolisation as a rhizomatic relational conceptualisation of society departs from the critical understanding of contemporary societies as entrenched in historically produced racialised hierarchies, resulting in economic and social inequalities which impede living together based on equal economic distribution and social justice. The chapter concludes with some thoughts on a decolonial ethics of creolising conviviality.
Sozialer Status, soziale Beziehungen und Gesundheit
Authors: Vonneilich Nico 
Published: November 2019

Zusammenfassung
Das vorliegende Kapitel gibt einen Überblick über die Forschung zu den Zusammenhängen zwischen sozialem Status, sozialen Beziehungen und Gesundheit. Zwei Fragen stehen hierbei im Vordergrund: Können soziale Beziehungen zu einer Erklärung der Zusammenhänge zwischen sozialem Status und Gesundheit beitragen (sog. Hypothese der differenziellen Exposition)? Variiert der Zusammenhang zwischen sozialen Beziehungen und Gesundheit je nach untersuchter sozialer Statusgruppe (sog. Hypothese der differenziellen Vulnerabilität)? Zu beiden Theorien werden die jeweiligen begrifflichen und theoretischen Grundlagen beschrieben und der Stand der Forschung zusammengefasst. Es zeigt sich, dass insbesondere Hinweise zum Erklärungsbeitrag sozialer Beziehungen zu gesundheitlichen Ungleichheiten vorliegen, während die Ergebnisse in Bezug der Hypothese der differenziellen Vulnerabilität insgesamt eher uneindeutig sind.
Netzwerkanalyse – eine methodische Annäherung
Authors: Gamper Markus 
Published: November 2019

Zusammenfassung

Netzwerke bestehen aus Akteuren, die durch Beziehungen miteinander verbunden sind und dessen Verbindungen sich zu unterschiedlichen sozialen Strukturen zusammensetzen.

Man geht davon aus, dass soziale Netzwerke auf die Akteure wirken und Akteure wiederum die Netzwerke beeinflussen.

Es findet sich eine Unterscheidung zwischen Gesamtnetzwerken und egozentrierten Netzwerken. Bei der Gesamtnetzwerkanalyse werden die jeweiligen Akteure und deren Relationen innerhalb vordefinierter Grenzen betrachtet. Bei egozentrierten Netzwerken steht die interpersonale Vernetzung eines bestimmten Akteurs im Zentrum der Analyse.
Multi-scale modeling of drug binding kinetics to predict drug efficacy
Authors: Clarelli Fabrizio , Liang Jingyi , Martinecz Antal , Heiland Ines , Abel zur Wiesch Pia 
Published: November 2019

AbstractOptimizing drug therapies for any disease requires a solid understanding of pharmacokinetics (the drug concentration at a given time point in different body compartments) and pharmacodynamics (the effect a drug has at a given concentration). Mathematical models are frequently used to infer drug concentrations over time based on infrequent sampling and/or in inaccessible body compartments. Models are also used to translate drug action from in vitro to in vivo conditions or from animal models to human patients. Recently, mathematical models that incorporate drug-target binding and subsequent downstream responses have been shown to advance our understanding and increase predictive power of drug efficacy predictions. We here discuss current approaches of modeling drug binding kinetics that aim at improving model-based drug development in the future. This in turn might aid in reducing the large number of failed clinical trials.
Development and optimization of a hybridization technique to type the classical class I and class II B genes of the chicken MHC
Authors: Potts Nicola D. , Bichet Coraline , Merat Laurence , Guitton Edouard , Krupa Andrew P. , Burke Terry A. , Kennedy Lorna J. , Sorci Gabriele , Kaufman Jim 
Published: November 2019

AbstractThe classical class I and class II molecules of the major histocompatibility complex (MHC) play crucial roles in immune responses to infectious pathogens and vaccines as well as being important for autoimmunity, allergy, cancer and reproduction. These classical MHC genes are the most polymorphic known, with roughly 10,000 alleles in humans. In chickens, the MHC (also known as the BF-BL region) determines decisive resistance and susceptibility to infectious pathogens, but relatively few MHC alleles and haplotypes have been described in any detail. We describe a typing protocol for classical chicken class I (BF) and class II B (BLB) genes based on a hybridization method called reference strand-mediated conformational analysis (RSCA). We optimize the various steps, validate the analysis using well-characterized chicken MHC haplotypes, apply the system to type some experimental lines and discover a new chicken class I allele. This work establishes a basis for typing the MHC genes of chickens worldwide and provides an opportunity to correlate with microsatellite and with single nucleotide polymorphism (SNP) typing for approaches involving imputation.
Simulator training and residents’ first laparoscopic hysterectomy: a randomized controlled trial
Authors: Jokinen Ewa , Mikkola Tomi S. , Härkki Päivi 
Published: November 2019

Abstract
Background
Hysterectomy rates are decreasing in many countries, and virtual reality simulators bring new opportunities into residents’ surgical education. The objective of this study was to evaluate the effect of training in laparoscopic hysterectomy module with virtual reality simulator on surgical outcomes among residents performing their first laparoscopic hysterectomy.

Methods
This randomized study was carried out at the Department of Obstetrics and Gynecology in Helsinki University Hospital and Hyvinkää Hospital. We recruited twenty residents and randomly signed half of them to train ten times with the laparoscopic hysterectomy module on a virtual reality simulator, while the rest represented the control group. Their first laparoscopic hysterectomy was video recorded and assessed later by using the Objective Structured Assessment of Technical Skills (OSATS) forms and Visual Analog Scale (VAS). The scores and surgical outcomes were compared between the groups.

Results
The mean OSATS score for the Global Rating Scale (GRS) was 17.0 (SD 3.1) in the intervention group and 11.2 (SD 2.4) in the control group (p = 0.002). The mean procedure-specific OSATS score was 20.0 (SD 3.3) and 16.0 (SD 2.8) (p = 0.012), and the mean VAS score was 55.0 (SD 14.8) and 29.9 (SD 14.9) (p = 0.001). Operative time was 144 min in the intervention group and 165 min in the control group, but the difference did not reach statistical significance (p = 0.205). There were no differences between the groups in blood loss or direct complications.

Conclusion
Residents training with a virtual reality simulator prior to the first laparoscopic hysterectomy seem to perform better in the actual live operation. Thus, a virtual reality simulator hysterectomy module could be considered as a part of laparoscopic training curriculum.
Postoperative rendezvous endoscopic retrograde cholangiopancreaticography as an option in the management of choledocholithiasis
Authors: Syrén Eva-Lena , Sandblom Gabriel , Eriksson Staffan , Eklund Arne , Isaksson Bengt , Enochsson Lars 
Published: November 2019

Abstract
Background
Rendezvous endoscopic retrograde cholangiopancreaticography (ERCP) is a well-established method for treatment of choledocholithiasis. The primary aim of this study was to determine how different techniques for management of common bile duct stone (CBDS) clearance in patients undergoing cholecystectomy have changed over time at tertiary referral hospitals (TRH) and county/community hospitals (CH). The secondary aim was to see if postoperative rendezvous ERCP is a safe, effective and feasible alternative to intraoperative rendezvous ERCP in the management of CBDS.

Methods
Data were retrieved from the Swedish registry for cholecystectomy and ERCP (GallRiks) 2006–2016. All cholecystectomies, where CBDS were found at intraoperative cholangiography, and with complete 30-day follow-up (n = 10,386) were identified. Data concerning intraoperative and postoperative complications, readmission and reoperation within 30 days were retrieved for patients where intraoperative ERCP (n = 2290) and preparation for postoperative ERCP were performed (n = 2283).

Results
Intraoperative ERCP increased (7.5% 2006; 43.1% 2016) whereas preparation for postoperative ERCP decreased (21.2% 2006; 17.2% 2016) during 2006–2016. CBDS management differed between TRHs and CHs. Complications were higher in the postoperative rendezvous ERCP group: Odds Ratio [OR] 1.69 (95% confidence interval [CI] 1.16–2.45) for intraoperative complications and OR 1.50 (CI 1.29–1.75) for postoperative complications. Intraoperative bleeding OR 2.46 (CI 1.17–5.16), postoperative bile leakage OR 1.89 (CI 1.23–2.90) and postoperative infection with abscess OR 1.55 (CI 1.05–2.29) were higher in the postoperative group. Neither post-ERCP pancreatitis, postoperative bleeding, cholangitis, percutaneous drainage, antibiotic treatment, ICU stay, readmission/reoperation within 30 days nor 30-day mortality differed between groups.

Conclusions
Techniques for management of CBDS found at cholecystectomy have changed over time and differ between TRH and CH. Rendezvous ERCP is a safe and effective method. Even though intraoperative rendezvous ERCP is the preferred method, postoperative rendezvous ERCP constitutes an acceptable alternative where ERCP resources are lacking or limited.