bluuebunny/crossref_metadata_2025_split huggingface dataset:
RMalign: an RNA structural alignment tool based on a size independent scoring function
Authors: Zheng Jinfang , Xie Juan , Hong Xu , Liu Shiyong 
Published: January 2018

ABSTRACTRNA-protein 3D complex structure prediction is still challenging. Recently, a template-based approach PRIME is proposed in our team to build RNA-protein complex 3D structure models with a higher success rate than computational docking software. However, scoring function of RNA alignment algorithm SARA in PRIME is size-dependent, which limits its ability to detect templates in some cases. Herein, we developed a novel RNA 3D structural alignment approach RMalign, which is based on a size-independent scoring function RMscore. The parameter in RMscore is then optimized in randomly selected RNA pairs and phase transition points (from dissimilar to similar) are determined in another randomly selected RNA pairs. In tRNA benchmarking, the precision of RMscore is higher than that of SARAscore (0.8771 and 0.7766, respectively) with phase transition points. In balance-FSCOR benchmarking, RMalign performed as good as ESA-RNA with a non-normalized score measuring RNA structure similarity. In balance-x-FSCOR benchmarking, RMalign achieves much better than a state-of-the-art RNA 3D structural alignment approach SARA due to a size-independent scoring function. Taking the advantage of RMalign, we update our RNA-protein modeling approach PRIME to version 2.0. The PRIME2.0 significantly improves about 10% success rate than PRIME.Author summaryRNA structures are important for RNA functions. With the increasing of RNA structures in PDB, RNA 3D structure alignment approaches have been developed. However, the scoring function which is used for measuring RNA structural similarity is still length dependent. This shortcoming limits its ability to detect RNA structure templates in modeling RNA structure or RNA-protein 3D complex structure. Thus, we developed a length independent scoring function RMscore to enhance the ability to detect RNA structure homologs. The benchmarking data shows that RMscore can distinct the similar and dissimilar RNA structure effectively. RMscore should be a useful scoring function in modeling RNA structures for the biological community. Based on RMscore, we develop an RNA 3D structure alignment RMalign. In both RNA structure and function classification benchmarking, RMalign obtains as good as or even better performance than the state-of-the-art approaches. With a length independent scoring function RMscore, RMalign should be useful for the modeling RNA structures. Based on above results, we update PRIME to PRIME2.0. We provide a more accurate RNA-protein 3D complex structure modeling tool PRIME2.0 which should be useful for the biological community.
HCMV glycoprotein B subunit vaccine efficacy was mediated by non-neutralizing antibody effector functions
Authors: Nelson Cody S. , Huffman Tori , de la Rosa Eduardo Cisneros , Xie Guanhua , Vandergrift Nathan , Pass Robert F. , Pollara Justin , Permar Sallie R. 
Published: January 2018

AbstractHuman cytomegalovirus (HCMV) is the most common congenital infection worldwide, frequently causing hearing loss and brain damage in afflicted infants. A vaccine to prevent maternal acquisition of HCMV during pregnancy is necessary to reduce the incidence of infant disease. The glycoprotein B (gB) + MF59 adjuvant subunit vaccine platform is the most successful HCMV vaccine tested to-date, demonstrating approximately 50% efficacy in preventing HCMV acquisition in phase II trials. However, the mechanism of vaccine protection remains unknown. Plasma from 33 gB/MF59 vaccinees at peak immunogenicity was tested for gB epitope specificity as well as neutralizing and non-neutralizing anti-HCMV effector functions, and compared to an HCMV-seropositive cohort. gB/MF59 vaccination elicited IgG responses with gB-binding magnitude and avidity comparable to natural infection. Additionally, IgG subclass distribution was similar with predominant IgG1 and IgG3 responses induced by gB vaccination and HCMV infection. However, vaccine-elicited antibodies exhibited limited neutralization of the autologous virus, negligible neutralization of multiple heterologous strains, and limited binding responses against gB structural motifs targeted by neutralizing antibodies including AD-1, AD-2, and Domain I. Interestingly, vaccinees had high-magnitude IgG responses against AD-3 linear epitopes, demonstrating immunodominance against this non-neutralizing, cytosolic region. Finally, vaccine-elicited IgG robustly bound trimeric, membrane-associated gB on the surface of transfected or HCMV-infected cells and mediated virion phagocytosis, though were poor mediators of NK cell activation. Altogether, these data suggest that non-neutralizing antibody functions, including virion phagocytosis, likely played a role in the observed 50% vaccine-mediated protection against HCMV acquisition.SignificanceThe CDC estimates that every hour, a child is born in the United States with permanent neurologic disability resulting from human cytomegalovirus (HCMV) infection – more than is caused by Down syndrome, fetal alcohol syndrome, and neural tube defects combined. A maternal vaccine to block transmission of HCMV to the developing fetus is a necessary intervention to prevent these adverse outcomes. The gB/MF59 vaccine is the most successful tested clinically to-date, achieving 50% reduction in HCMV acquisition. This manuscript establishes the function and epitope specificity of the humoral response stimulated by this vaccine that may explain the partial vaccine efficacy. Understanding the mechanism of gB/MF59-elicited protective immune responses will guide rational design and evaluation of the next generation of HCMV vaccines.
Implementing the sustainable development goals at University level
Authors: Albareda-Tiana Silvia , Vidal-Raméntol Salvador , Fernández-Morilla Mónica 
Published: January 2018

Purpose
The purpose of this case study is to explore the principles and practices of sustainable development (SD) in the university curriculum.

Design/methodology/approach
To explore the principles linked with the sustainable development goals (SDGs) and the learning and teaching practices in sustainability at the International University of Catalonia (Universitat Internacional de Catalunya, UIC, in Catalan), an empirical study was carried out by using a mixed methodology for data collection. Indicators related to SDGs found in the University curriculum (quantitative analysis) were measured using Excel, combined with in-depth semi-structured interviews to the deans of different faculties (qualitative study), which were analysed using Atlas.ti.

Findings
Several visions, difficulties and challenges were identified in this mixed-method study around the concept of sustainability, which allowed the authors to describe and portray a specific starting position in relation to the SDGs at the UIC.

Research limitations/implications
The presence of dimensions linked to the SDGs in the University curriculum were analysed by means of a quantitative study. However, global competences related to education for sustainable development were not studied.

Practical implications
Special emphasis was given to the challenges and opportunities for training future graduates and the whole University community in SD.

Originality/value
This paper shows a methodological exploration of the principles related to the SDGs and the learning and teaching practices in sustainability in higher education.
Delivering warmth by hand: customer responses to different formats of written communication
Authors: Ren Xingyao , Xia Lan , Du Jiangang 
Published: January 2018

Purpose
The effect of different formats of message delivery has received little theoretical and empirical examination. This research focuses on the effect of written relational communication formats used by service providers. This study aims to answer three questions: Do different formats of written communications (i.e. handwriting and print) influence customer perceptions (i.e. feelings of warmth) of service firms? What are the mediators of these influences (i.e. perceived effort and psychological closeness)? And under what conditions do they occur (i.e. what is the contextual factor)?

Design/methodology/approach
One field study and three laboratory studies were conducted to provide a comprehensive understanding of the role of format in written communication.

Findings
Handwritten messages are more effective than print messages in building relationships in a service context because they elicit stronger feelings of warmth because of both the perception of greater effort and feelings of greater psychological closeness to the service provider. However, the presence of handwriting fails to deliver feelings of warmth when the quality of core services is low.

Practical implications
Service providers can effectively use handwritten communication to signal effort and create psychological closeness for relationship building with their key customers only when the quality of core services meets customer expectations.

Originality/value
First, the research differentiates the formats of written relational communication (handwritten vs print), and links communication formats with feelings of warmth, which is an important factor for impression and relationship formation in the practice of services marketing. Second, based on cognitive-experiential self-theory, this research demonstrates the dual mediators underlying the effect of handwriting (vs print) on warmth: perceived effort and psychological closeness. Third, it identifies the quality of core service as a boundary condition for the effect of handwritten communication.
Cassava flour slurry as a low‐cost alternative to commercially available gel for obstetrical ultrasound: a blinded non‐inferiority trial comparison of image quality
Authors: Aziz A , Dar P , Hughes F , Solorzano C , Muller MM , Salmon C , Salmon M , Benfield N 
Published: January 2018

ObjectiveTo evaluate the quality of ultrasound images obtained with cassava flour slurry (CFS) compared with conventional gel in order to determine objectively whether CFS could be a true low‐cost alternative.DesignBlinded non‐inferiority trial.SettingObstetrical ultrasound unit in an academic medical centre.Population or SampleWomen with a singleton pregnancy, undergoing anatomy ultrasounds.MethodsThirty pregnant women had standard biometry measures obtained with CFS and conventional gel. Images were compared side‐by‐side in random order by two blinded sonologists and rated for image resolution, detail and total image quality using a 10‐cm visual analogue scale. Ratings were compared using paired t‐tests. Participant and sonographer experience was measured using five‐point Likert scales.Main outcome measuresImage resolution, detail, and total image quality. Participant experience of gel regarding irritation, messiness, and ease of removal.ResultsWe found no significant difference between perceived image quality obtained with CFS (mean = 6.2, SD = 1.2) and commercial gel (mean = 6.4, SD = 1.2) [t (28) = −1.1; P = 0.3]. Images were not rated significantly differently for either reviewer in any measure, any standardized image or any view of a specific anatomic structure. All five sonographers rated CFS as easy to obtain clear images and easy for patient and machine cleanup. Only one participant reported itching with CFS.ConclusionsCFS produces comparable image quality to commercial ultrasound gel. The dissemination of these results and the simple CFS recipe could significantly increase access to ultrasound for screening, monitoring and diagnostic purposes in resource‐limited settings.FundingThis study was internally funded by our department.Tweetable abstractLow‐cost homemade cassava flour slurry creates images equal to commercial ultrasound gel, improving access.
Respiratory complications of anaesthesia
Authors: Mills G. H. 
Published: January 2018

SummaryPostoperative pulmonary complications are a major determinant of outcome for patients and consume huge resources within hospital, particularly in critical care. Prediction and anticipation of postoperative pulmonary complications are vital for patient selection and, in some cases, for informed patient consent. Being able to assess the likelihood of postoperative pulmonary complications also allows research into methods to reduce them by allowing allocation of patients to the appropriate arms of research trials. Some patients have pre‐operative characteristics or belong to patient groups such as those with chronic obstructive pulmonary disease or obstructive sleep apnoea, where techniques and evidence‐based guidance to avoid or reduce complications are becoming established. Intra‐operative ventilation and the use of lung‐protective ventilation may be helpful during major surgery, but studies looking at reduced tidal volumes, recruitment and levels of positive end‐expiratory pressure, have this far only led to a degree of consensus in terms of tidal volume, although parameters that predispose to postoperative pulmonary complications are becoming clearer. Optimal postoperative care in terms of analgesia, positioning, physiotherapy and mobilisation is another developing area. Techniques such as continuous positive airways pressure, non‐invasive ventilation and high‐flow nasal humidified oxygen appear to show some benefit, but the exact roles, pressures and timings of each are currently being explored. Much remains to be researched and developed into evidence‐based practice.
Peripheral nerve injury arising in anaesthesia practice
Authors: Hewson D. W. , Bedforth N. M. , Hardman J. G. 
Published: January 2018

SummaryIn this article, we will discuss the pathophysiology of peripheral nerve injury in anaesthetic practice, including factors which increase the susceptibility of nerves to damage. We will describe a practical and evidence‐based approach to the management of suspected peripheral nerve injury and will go on to discuss major nerve injury patterns relating to intra‐operative positioning and to peripheral nerve blockade. We will review the evidence surrounding particular strategies to reduce the incidence of peripheral nerve injury during nerve blockade, including nerve localisation methods, timing of blocks, needle techniques and design, injection pressure‐monitoring and local anaesthetic and adjunct choice.
What to do when complications occur
Authors: Cruikshanks A. , Bryden D. C. 
Published: January 2018

SummaryAdverse events and complications, even if minor, can result in considerable negative effects on patients, including loss of life. They can also have an impact on the healthcare workers involved. Offering an apology to a patient who has suffered a complication is necessary, and is not an admission of fault. In England and Wales, there are also statutory obligations of candour in cases of more severe notifiable events. Local and national systems exist for incident reporting, with a strong emphasis on learning from events and sharing of best practice. Complaints may arise from poor management of a patient's complications, and in situations where there is a clear breach of a professional duty that has resulted in patient harm, negligence may be deemed to have occurred. National Health Service Resolution focuses on learning from events to help reduce the growth in litigation and emphasises that discussions should be timely, include appropriate explanation and information, and provide ongoing support and, if necessary, continuity of care.
EAST GERMAN WRITERS, THE PUBLIC SPHERE, AND THE 1956 WRITERS' CONGRESS
Authors: Brockmann Stephen 
Published: January 2018

ABSTRACTThis article examines the debates surrounding the 1956 Writers' Congress in East Germany as part of a complex and conflicted process of negotiation and contestation between writers, institutions, the East German government, and the Socialist Unity Party (SED) in a year that witnessed, initially, widespread efforts at liberalisation in much of the socialist world (the USSR, Poland, and Hungary, as well as the GDR) and, subsequently, a crackdown on dissent (especially in Hungary and the GDR). The article shows that there was considerable dispute in the run‐up to the congress, as well as during the congress itself and in its aftermath. The goal is to demonstrate that the 1956 Writers' Congress was more contested than is sometimes believed, and that, on a larger scale, East German literary life in the 1950s was less conformist than its critics have sometimes claimed.
GÜNTER WALLRAFF'S BUNDESWEHR DIARIES AND THE MAKING OF A CONTROVERSIAL FIGURE
Authors: Plowman Andrew 
Published: January 2018

ABSTRACTGünter Wallraff's diaries of his conscription to the Bundeswehr and his belated conscientious objection (1964) were his first publication. He republished them several times in revised form throughout a controversial career extending from industrial reportage in Wir brauchen dich (1966) to his impersonation of a Turkish ‘guest worker’ in Ganz unten (1985). This article examines how successive versions of Wallraff's text engaged with evolving debates about conscription and conscientious objection in the FRG for different readers; and it explores how Wallraff drew upon his diaries as a narrative about the origins of his methods at the same time as he revised them in line with current concerns. A first version in the magazine twen in 1964 provided future conscripts with information about conscription and objection following scandal around the abuse of conscripts. Against the background of 1968, his ‘Protokoll aus der Bundeswehr’ (1970) encouraged serving conscripts to emulate his refusal and constructed Wallraff as a ‘participant observer’ after controversy around his methods. His diaries also supported a shift towards satirical impersonation in his work, and in 1992 Mein Tagebuch aus der Bundeswehr offered a definitive version with a view to the text's literary status and legacy. Wallraff's Bundeswehr diaries are a fascinating historical and literary document of controversies around the Bundeswehr in Germany and central to the process in which he fashioned himself as a critical figure.
LANGUAGE AS A FORCE FOR GOOD IN THE WORK OF HERTA MÜLLER*
Authors: Shopin Pavlo 
Published: January 2018

ABSTRACTHerta Müller creates sophisticated metaphors to convey her vision of language and its relationship to suffering and subjugation. With reference to both her fiction and non‐fiction, this essay explores how she uses the idea of forceful language. It delineates how the trope of force illuminates the power of language. I analyse the metaphorical conceptualisation of forceful language that makes survival possible through resistance to social oppression. Language is understood as a force that provides support and protection to the author and her characters. The metaphorical image of force enables Müller to represent language as a means by which to lighten the burden of oppression, to put up resistance, and to help the victims of persecution cope with their suffering and survive.
DEUTSCHE SEELENZUSTÄNDE: MITTENDRIN UND DOCH NICHT DABEI? INTERVIEW MIT DEM SCHRIFTSTELLER, HERAUSGEBER UND PUBLIZISTEN ZAFER ŞENOCAK AN DER UNIVERSITY OF TEXAS AT AUSTIN AM 23. APRIL 2015
Authors: Schreiner Daniel 
Published: January 2018

ABSTRACT‘Deutsche Seelenzustände’ is an interview with one of the major Turkish‐German cultural protagonists. The author, essayist, poet, publisher, and translator Zafer Şenocak grew up in Munich and moved to Berlin after the reunification. Şenocak started publishing his first poems and novels in the early 1980s. Since the 1990s he is also in demand as a political commentator on the Turkish‐German experience in the FRG and on Turkish politics. Until today Şenocak remains one of the most important Turkish‐German intellectuals and is known for advocating a Turkish‐German synthesis. In the interview Şenocak discusses his recent books In deinen Worten and Deutschsein, and addresses issues of identity, participation, and acceptance.
miR‐21a negatively modulates tumor suppressor genes PTEN and miR‐200c and further promotes the transformation of M2 macrophages
Authors: Li Ning , Qin Jun‐Fang , Han Xiao , Jin Feng‐Jiao , Zhang Jia‐Hui , Lan Lan , Wang Yue 
Published: January 2018

AbstractmiR‐21a is well‐known to inhibit PTEN expression. We have previously shown that PTEN suppressed the transformation of M2 macrophages in the tumor microenvironment. Therefore, we hypothesized that miR‐21a could influence M2 macrophage transformation by regulating PTEN expression. In this study, we identified how miR‐21a reduced the expression of both PTEN mRNA and protein in murine macrophage cell lines and primary macrophages. Moreover, opposite effects were identified upon the use of a miR‐21a inhibitor. Using a cytokine array, we identified the cytokines closely associated with miR‐21a‐mediated macrophage transformation to the M2 phenotype. miR‐21a mimics could also enhance the migratory ability of murine breast cancer 4T1 cells, the growth of breast cancer in vivo and CD206 intratumor expression. In addition, quantitative PCR (qPCR) and methylation‐specific PCR analysis showed that miR‐21a enhanced miR‐200c methylation and then decreased miR‐200c and PTEN expression. These effects could be reversed by treatment with 5′‐Aza, a DNA‐demethylating agent. MiR‐200c was predicted to target the PTEN 3′UTR, but qPCR illustrated the miR‐200c mimic that increased PTEN expression, and 5′‐Aza could enhance its effect. The above results indicate that miR‐21a negatively modulates two tumor suppressor genes, miR‐200c and PTEN, thereby promoting M2 macrophage transformation. This demonstrates that miR‐21a represents a novel target for improving the overall tumor microenvironment.
Targeted deletion of c‐Met in thymic epithelial cells leads to an autoimmune phenotype
Authors: Su Min , Hu Rong , Song Yinhong , Liu Yalan , Lai Laijun 
Published: January 2018

AbstractHepatocyte growth factor (HGF) and its receptor c‐Met signaling have been implicated in regulating various types of cells including epithelial cells. We have previously reported that c‐Met is expressed by thymic epithelial cells (TECs), and that in vivo administration of hybrid cytokines containing IL‐7 and the beta‐ or alpha‐chain of HGF significantly increase the number of TECs. In order to study the role of c‐Met signaling in TECs, we generated conditional knockout (cKO) mice in which c‐Met was specifically deleted in TECs using a Foxn1‐Cre transgene. We show here that c‐Met deficiency in TECs results in age‐progressive reduction in TEC number and reduced number of regulatory T cells. Consequently, c‐Met TEC cKO mice displayed an autoimmune phenotype. Thus, c‐Met signaling in TECs is important for the maintenance of TECs and immune self‐tolerance.