bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liver Enzymes and the Development of Posttransplantation Diabetes Mellitus in Renal Transplant Recipients
Authors: Klaassen Gerald , Corpeleijn Eva , Deetman Nicole P.E. , Navis Gerjan J. , Bakker Stephan J.L. , Zelle Dorien M. 
Published: August 2017

Background
Posttransplantation diabetes mellitus (PTDM) is common in renal transplant recipients (RTR), increasing the risk of graft failure, cardiovascular disease, and mortality. Early detection of a high risk for PTDM is warranted. Because liver function and liver fat are involved, we investigated whether serum liver markers are associated with future PTDM in RTR.

Methods
Between 2001 and 2003, 606 RTR with a functioning allograft beyond the first year after transplantation were included of which 500 participants (56% men; age, 50 ± 12 years) were free of diabetes at baseline and had liver enzyme values (1 missing) available. Serum concentrations of alanine aminotransferase (ALT), gamma-glutamyl transferase (GGT), alkaline phosphatase were measured at baseline at 6.0 (6.2-11.5) years posttransplantation. PTDM cases were recorded until April 2012.

Results
During median follow-up for 9.6 years (interquartile range [IQR], 6.2-10.2) beyond baseline, 76 (15.2%) patients developed PTDM. Comparing the highest to the lower tertiles, higher liver enzyme activities were significantly related to incident PTDM for ALT (hazard ratio [HR], 2.22; IQR, 1.42-3.48), for GGT (HR, 2.93; IQR, 1.87-4.61), and for alkaline phosphatase (HR, 1.78; IQR, 1.13-2.80). The associations of ALT and GGT with development of PTDM were independent of potential confounders and risk factors, including age, sex, renal function, medication use, lifestyle factors, adiposity, presence of the metabolic syndrome, fasting glucose, HbA1c, proinsulin, and cytomegalovirus status.

Conclusions
Markers for liver function and liver fat in the subclinical range are potential markers for future PTDM, independent of other known risk factors. This may allow for early detection and management of PTDM development.
Mechanical mapping of spinal cord development and repair in living zebrafish larvae using Brillouin microscopy
Authors: Schlüßler Raimund , Möllmert Stephanie , Abuhattum Shada , Cojoc Gheorghe , Müller Paul , Kim Kyoohyun , Möckel Conrad , Zimmermann Conrad , Czarske Jürgen , Guck Jochen 
Published: August 2017

AbstractThe mechanical properties of biological tissues are increasingly recognized as important factors in developmental and pathological processes. Most existing mechanical measurement techniques either necessitate destruction of the tissue for access or provide insufficient spatial resolution. Here, we show for the first time a systematic application of confocal Brillouin microscopy to quantitatively map the mechanical properties of spinal cord tissues during biologically relevant processes in a contact-free and non-destructive manner. Living zebrafish larvae were mechanically imaged in all anatomical planes, during development and after spinal cord injury. These experiments revealed that Brillouin microscopy is capable of detecting the mechanical properties of distinct anatomical structures without interfering with the animal’s natural development. The Brillouin shift within the spinal cord increased during development and transiently decreased during the repair processes following spinal cord transection. By taking into account the refractive index distribution, we explicitly determined the apparent longitudinal modulus and viscosity of different larval zebrafish tissues. Importantly, mechanical properties differed between tissuesin situand in excised slices. The presented work constitutes the first step towards anin vivoassessment of spinal cord tissue mechanics during regeneration, provides a methodical basis to identify key determinants of mechanical tissue properties and allows to test their relative importance in combination with biochemical and genetic factors during developmental and regenerative processes.
BITE: an R package for biodiversity analyses
Authors: Milanesi Marco , Capomaccio Stefano , Vajana Elia , Bomba Lorenzo , Garcia José Fernando , Ajmone-Marsan Paolo , Colli Licia 
Published: August 2017

AbstractNowadays, molecular data analyses for biodiversity studies often require advanced bioinformatics skills, preventing many life scientists from analyzing their own data autonomously. BITE R package provides complete and user-friendly functions to handle SNP data and third-party software results (i.e. Admixture, TreeMix), facilitating their visualization, interpretation and use. Furthermore, BITE implements additional useful procedures, such as representative sampling and bootstrap for TreeMix, filling the gap in existing biodiversity data analysis tools.Availability:https://github.com/marcomilanesi/BITE
Mitochondrial sirtuinssir-2.2andsir-2.3regulate lifespan in C.elegans
Authors: Chang Sarah M. , McReynolds Melanie R. , Hanna-Rose Wendy 
Published: August 2017

ABSTRACTMitochondrial sirtuins regulate biochemical pathways and are emerging drug targets for metabolic and age-related diseases such as cancer, diabetes, and neurodegeneration. Yet, their functions remain unclear. Here, we uncover a novel physiological role for theC. elegansmitochondrial sirtuins,sir-2.2andsir-2.3,in lifespan regulation. Using a genetic approach, we demonstrate thatsir-2.2andsir-2.3mutants live 28-30% longer than controls when fed the normal lab diet ofE. coliOP50. Interestingly, this effect is diet specific and is not observed when animals are fed the strain HT115, which is typically used for RNAi experiments. While decreased consumption of food is a known mechanism for lifespan extension, this does not account for the increased lifespan in the mitochondrial sirtuin mutants.sir-2.2andsir-2.3mutants display altered expression of genes involved in oxidative stress response, including increased expression of the mitochondrial superoxide dismutasesod-3and decreased levels of catalasesctl-1andctl-2. Like their extended lifespan phenotype, these alterations in oxidative stress gene expression are diet dependent. The mitochondrial sirtuin mutants are more resistant to the lifespan extending effects of low levels of superoxide, suggesting that their increased lifespan involves a hormetic response. Our data suggest thatsir-2.2andsir-2.3are not completely redundant in function and may possess overlapping yet distinct mechanisms for regulating oxidative stress response and lifespan.
Covert Shift of Attention Modulates the Value Encoding in the Orbitofrontal Cortex
Authors: Xie Yang , Nie Chechang , Yang Tianming 
Published: August 2017

AbstractDuring value-based decision making, we often evaluate the value of each option sequentially by shifting our attention, even when the options are presented simultaneously. The orbitofrontal cortex (OFC) has been suggested to encode value during value-based decision making. Yet it is not known how its activity is modulated by attention shifts. We investigated this question by employing a passive viewing task that allowed us to disentangle effects of attention, value, choice and eye movement. We found that the attention modulated OFC activity through a winner-take-all mechanism. When we attracted the monkeys’ attention covertly, the OFC neuronal activity reflected the reward value of the newly attended cue. The shift of attention could be explained by a normalization model. Our results strongly argue for the hypothesis that the OFC neuronal activity represents the value of covertly attended item. They provide important insights toward the neural mechanism of value-based decision making.
Network structure of the human musculoskeletal system shapes neural interactions on multiple timescales
Authors: Kerkman Jennifer N. , Daffertshofer Andreas , Gollo Leonardo L. , Breakspear Michael , Boonstra Tjeerd W. 
Published: August 2017

AbstractHuman motor control requires the coordination of muscle activity under the anatomical constraints imposed by the musculoskeletal system. Interactions within the central nervous system are fundamental to motor coordination, but the principles governing functional integration remain poorly understood. We used network analysis to investigate the relationship between anatomical and functional connectivity amongst 36 muscles. Anatomical networks were defined by the physical connections between muscles and functional networks were based on intermuscular coherence assessed during postural tasks. We found a modular structure of functional networks that was strongly shaped by the anatomical constraints of the musculoskeletal system. Changes in postural tasks were associated with a frequency-dependent reconfiguration of the coupling between functional modules. These findings reveal distinct patterns of functional interactions between muscles involved in flexibly organising muscle activity during postural control. Our network approach to the motor system offers a unique window into the neural circuitry driving the musculoskeletal system.
Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering
Authors: Busk Peter Kamp 
Published: August 2017

AbstractLarge collections of protein sequences with divergent sequences are tedious to analyze for understanding their phylogenetic or structure-function relation. Peptide Pattern Recognition is an algorithm that was developed to facilitate this task but the previous version does only allow a limited number of sequences as input.I implemented Peptide Pattern Recognition as a multithread software designed to handle large numbers of sequences and perform analysis in a reasonable time frame. Benchmarking showed that the new implementation of Peptide Pattern Recognition is twenty times faster than the previous implementation on a small protein collection with 673 MAP kinase sequences. In addition, the new implementation could analyze a large protein collection with 48,570 Glycosyl Transferase family 20 sequences without reaching its upper limit on a desktop computer.Peptide Pattern Recognition is a useful software for providing comprehensive groups of related sequences from large protein sequence collections.
Topology and cooperative stability: the two master regulators of protein half-life in the cell
Authors: Mallik Saurav , Kundu Sudip 
Published: August 2017

AbstractIn a quest for finding additional structural constraints, apart from disordered segments, regulating protein half-life in the cell (and during evolution), here we recognize and assess the influence of native topology of biological proteins and their sequestration into multimeric complexes. Native topology acts as a molecular marker of protein’s mechanical resistance and consequently captures their half-life variations on genome-scale, irrespective of the enormous sequence, structural and functional diversity of the proteins. Cooperative stability (slower degradation upon sequestration into complexes) is a master regulator of oligomeric protein half-life that involves at least three mechanisms. (i) Association with multiple complexes results longer protein half-life; (ii) hierarchy of complex self-assembly involves short-living proteins binding late in the assembly order and (iii) binding with larger buried surface area leads to slower subunit dissociation and thereby longer half-life. Altered half-lives of paralog proteins refer to their structural divergence and oligomerization with non-identical set of complexes.
Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree
Authors: Boeckmann Brigitte , Dylus David , Moretti Sebastien , Altenhoff Adrian , Train Clément-Marie , Kriventseva Evgenia , Bougueleret Lydie , Xenarios Ioannis , Privman Eyal , Gabaldon Toni , Dessimoz Christophe 
Published: August 2017

AbstractMedium to large phylogenetic gene trees constructed from datasets of different species density and taxonomic range are rarely topologically consistent because of missing phylogenetic signal, non-phylogenetic signal and error. In this study, we first use simulations to show that taxon sampling unequally affects nodes in a gene tree, which likely contributes to controversial conclusions from taxon sampling experiments and contradicting species phylogenies such as for the boreoeutherians. Hence, because it is unlikely that a large gene tree can be reconstructed correctly based on a single optimized dataset, we take a two-step approach for the construction of model gene trees. First, stable and unstable clades are identified by comparing phylogenetic trees inferred from multiple datasets and data types (nucleotide, amino acid, codon) from the same gene family. Subsequently, data subsets are optimized for the analysis of individual uncertain clades. Results are summarized in form of a model tree that illustrates the evolutionary relationship of gene loci. A case study shows how a seemingly complex gene phylogeny becomes increasingly consistent with the reference species tree by attentive taxon sampling and subtree analysis. The procedure is progressively introduced to SwissTree (http://swisstree.vital-it.ch), a resource of high confidence model gene (locus) trees. Finally we demonstrate the usefulness of SwissTree for orthology benchmarking.
The impact of persistent bacterial bronchitis on the pulmonary microbiome of children
Authors: Cuthbertson Leah , Craven Vanessa , Bingle Lynne , Cookson William O.C.M. , Everard Mark L. , Moffatt Miriam F. 
Published: August 2017

AbstractPersistent bacterial bronchitis is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of persistent bacterial bronchitis.Blind, protected brushings were obtained from 20 healthy controls and 24 children with persistent bacterial bronchitis, with an additional directed sample obtained from persistent bacterial bronchitis patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing.No significant difference in bacterial diversity or community composition (R2= 0.01,P= 0.36) was observed between paired blind and non-blind brushes, showing that blind brushings are a valid means of accessing the airway microbiota. This has important implications for collecting lower respiratory samples from healthy children. A significant decrease in bacterial diversity (P< 0.001) and change in community composition (R2= 0.08,P= 0.004) was observed between controls and patients. Bacterial communities within patients with PBB were dominated byProteobacteria, and indicator species analysis showed thatHaemophilusandNeisseriawere significantly associated with the patient group. In 15 (52.9%) cases the dominant organism by sequencing was not identified by standard routine clinical culture.The bacteria present in the lungs of patients with persistent bacterial bronchitis were less diverse in terms of richness and evenness. The results validate the clinical diagnosis, and suggest that more attention to bacterial communities in children with chronic cough may lead to more rapid recognition of this condition with earlier treatment and reduction in disease burden.
Single-shot super-resolution total internal reflection fluorescence microscopy
Authors: Guo Min , Chandris Panagiotis , Giannini John Paul , Trexler Adam J. , Fischer Robert , Chen Jiji , Vishwasrao Harshad D. , Rey-Suarez Ivan , Wu Yicong , Waterman Clare M. , Patterson George H. , Upadhyaya Arpita , Taraska Justin , Shroff Hari 
Published: August 2017

AbstractWe demonstrate a simple method for combining instant structured illumination microscopy (SIM) with total internal reflection fluorescence microscopy (TIRF), doubling the spatial resolution of TIRF (down to 115 +/-13 nm) and enabling imaging frame rates up to 100 Hz over hundreds of time points. We apply instant TIRF-SIM to multiple live samples, achieving rapid, high contrast super-resolution imaging in close proximity to the coverslip surface.
Drug discovery to counteract antinociceptive tolerance with mu-opioid receptor endocytosis
Authors: Chao Po-Kuan , Ke Yi-Yu , Chang Hsiao-Fu , Huang Yi-Han , Ou Li-Chin , Chuang Jian-Ying , Lin Yen-Chang , Lee Pin-Tse , Chang Wan-Ting , Chen Shu-Chun , Ueng Shau-Hua , Hsu John Tsu-An , Tao Pao-Luh , Law Ping-Yee , Loh Horace H. , Shih Chuan , Yeh Shiu-Hwa 
Published: August 2017

AbstractMorphine antinociceptive tolerance is highly correlated with its poor ability to promote mu-opioid– receptor (MOR) endocytosis. Our objective was to discover a novel positive allosteric modulator of MOR to enhance morphine-induced MOR endocytosis. We used high-throughput screening to identify several cardiotonic steroids as positive allosteric modulators of morphine-induced MOR endocytosis having high potency and efficacy, independently of Na+/K+-ATPase inhibition. Convallatoxin was found to enhance morphine-induced MOR endocytosis through an adaptor protein 2/clathrin-dependent mechanism without regulating G protein- orβ-arrestin-mediated pathways. Both F243 and I292 residues of MOR were essential to the effect of convallatoxin on MOR endocytosis. Co-treatment with chronic morphine and convallatoxin reduced morphine tolerance in animal models of acute thermal pain and chronic inflammatory pain. Acute convallatoxin administration reversed morphine tolerance in morphine-tolerant mice. These findings suggest that cardiotonic steroids are potentially therapeutic for morphine side effects and open a new avenue for the study of MOR trafficking.
The cultural dividend: a hidden source of economic growth in emerging countries
Authors: Li Shaomin , Park Seung Ho , Selover David Duden 
Published: August 2017

Purpose
The purpose of this paper is to develop the theoretical linkage between culture and economic growth and empirically test the relationship by measuring culture and how it affects labor productivity.

Design/methodology/approach
This study uses a cross-section study of developing countries and regresses economic productivity growth on a set of control variables and cultural factors.

Findings
It is found that three cultural factors, economic attitudes, political attitudes, and attitudes towards the family, affect economic productivity growth.

Originality/value
Many economists ignore culture as a factor in economic growth, either because they discount the value of culture or because they have no simple way to quantify culture, resulting in the role of culture being under-researched. The study is the first to extensively examine the role of culture in productivity growth using large-scale data sources. The authors show that culture plays an important role in productivity gains across countries, contributing to the study of the effects of culture on economic development, and that culture can be empirically measured and linked to an activity that directly affects the economic growth – labor productivity.
Modeling and control of an unbalanced magnetic rotor-bearing system as a bearingless motor
Authors: Chen Shyh-Leh , Lee Pei-Hua , Toh Chow-Shing 
Published: August 2017

Purpose
This paper is concerned with the design and analysis of a bearingless motor.

Design/methodology/approach
The bearingless motor is obtained by a regular three-pole active magnetic bearing with an intentionally attached unbalanced mass on the rotor. It is the unbalanced mass that will generate the rotational torque for the motor function. Modeling and control of the unbalanced mass-type bearingless motor have been considered.

Findings
It is found through simulations that both functions of motor and magnetic bearing can indeed be achieved in this system.

Originality/value
This novel bearingless motor requires no additional windings and permanent magnets. Thus, it can greatly reduce the cost and design of the bearingless motor.
Smart cities
Authors: Öberg Christina , Graham Gary , Hennelly Patrick 
Published: August 2017

Purpose
The smart city idea refers to new ways of organising city functions and urban life, which are believed to move production and consumption from global to local, manufacturing from competitive to collaborative, and business from a shareholder to a multiple-stakeholder point of view. Most previous research has focussed on the societal level of smart cities, while less seems to be known about the management of business as part of smart cities. The purpose of this paper is to present a literature review on the state of the art of management research on smart cities. The following research question is addressed: How has previous research captured the management of organisations in smart cities?

Design/methodology/approach
A literature review using the search term “smart city/cities” in research on business, management, and operational management was conducted for the purpose of capturing previous research. Findings were coded based on main ideas, central concepts, and theories, thematic content of the articles related to the main ideas underpinning smart cities (digitalization, urbanisation, and sustainability as antecedents, and local, collaborative and multiple-stakeholder manufacturing as indicators), and units of analysis.

Findings
The paper points to how most studies on the management of organisations as part of smart cities focus on sustainability and how digitalisation enables new businesses. Collaborative efforts are emphasised and the theoretical framing is fragmented. Issues related to the organising of business is also not problematised and the business network approach could, as discussed in the paper, provide valuable insights related to the collaborative efforts of organisations and the multiple-stakeholder perspective.

Originality/value
The paper is the first to capture and present an overview of previous research on the management of business as part of smart cities. Research on smart cities has focussed on the policy and societal levels, and so far there is a lack of problematisation on how organisations may act, and potentially change their way of acting, should smart cities become a reality.
Business models in business networks – how do they emerge?
Authors: La Rocca Antonella , Snehota Ivan 
Published: August 2017

Purpose
The expanding body of research on business models generally assumes that firms operate in a “transactional” context. Several recent studies suggest that the concept of business models in contexts where relationships matter, such as business markets, involves issues that the transactional microeconomic perspective is ill suited to capture. In the expanding literature on business models, the role of context in how business models emerge and evolve is a topic that appears under researched. The purpose of this paper is to review the findings of these studies and explore how “relational context” affects the emergence and evolution of business models.

Design/methodology/approach
The authors review the literature on business models in business markets where high-involvement relationships with customers and suppliers are common, and report a case to illustrate the critical issues involved.

Findings
The authors find that context where high-involvement relationships are common implies that business models are relationship specific and tend to be different across key relationships of a business; the involvement of others limits the autonomy of a single business in developing its business model; business models are continuously emergent and transient.

Originality/value
This study is among the few that examine the emergence and evolution of business model in business network in a longitudinal perspective. The value of the study also lies in the implications of the relationship-centric business model for management practice and research.