bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transplantation tolerance and its outcome during infections and inflammation
Authors: Chong Anita S. , Alegre Maria‐Luisa 
Published: February 2014

SummaryMuch progress has been made toward understanding the mechanistic basis of transplantation tolerance in experimental models, which implicates clonal deletion of alloreactive T and B cells, induction of cell‐intrinsic hyporesponsiveness, and dominant regulatory cells mediating infectious tolerance and linked suppression. Despite encouraging success in the laboratory, achieving tolerance in the clinic remains challenging, although the basis for these challenges is beginning to be understood. Heterologous memory alloreactive T cells generated by infections prior to transplantation have been shown to be a critical barrier to tolerance induction. Furthermore, infections at the time of transplantation and tolerance induction provide a pro‐inflammatory milieu that alters the stability and function of regulatory T cells as well as the activation requirements and differentiation of effector T cells. Thus, infections can result in enhanced alloreactivity, resistance to tolerance induction, and destabilization of the established tolerance state. We speculate that these experimental findings have relevance to the clinic, where infections have been associated with allograft rejection and may be a causal event precipitating the loss of grafts after long periods of stable operational tolerance. Understanding the mechanisms by which infections prevent and destabilize tolerance can lead to therapies that promote stable life‐long tolerance in transplant recipients.
Tissue‐resident T cells, in situ immunity and transplantation
Authors: Turner Damian L. , Gordon Claire L. , Farber Donna L. 
Published: February 2014

SummaryT cells coordinate rejection of transplanted allografts and are key targets for depletion, immunosuppression, and tolerance induction to promote long‐term graft survival. Studies in mouse models and humans generally focus on circulating T cells or those from lymphoid sites; however, vast numbers of T cells reside in multiple peripheral tissue sites including lungs, intestines, liver, and skin as non‐circulating, tissue‐resident memory T cells (Trm cells). In this review, we define the basic properties of Trm cells, the emerging evidence of their importance for protective immunity, and the potential role of resident versus circulating T cells in transplant rejection and in providing protection to prevalent infections posttransplantation. We also discuss potential susceptibilities and/or resistance of protective Trm to immunosuppression therapies, and how consideration of Trm, their compartmentalization, and specificity can enable improved therapies for targeted inhibition of pathogenic and preservation of protective T‐cell subsets.
Innate allorecognition
Authors: Oberbarnscheidt Martin H. , Lakkis Fadi G. 
Published: February 2014

SummaryVertebrates mount strong adaptive immune responses to transplanted organs (allografts), but the mechanisms by which the innate immune system initiates this response are not completely understood. In anti‐microbial immunity, non‐self molecules associated with pathogens but not present in the host induce the maturation of innate antigen‐presenting cells (APCs) by binding to germ‐line‐encoded receptors. Mature APCs then initiate the adaptive immune response by presenting microbial antigen and providing costimulatory signals to T cells. How allografts activate APCs, however, is less clear, because allografts are presumably sterile. A widely accepted view is that inflammatory or ‘danger’ molecules released by dying graft cells at the time of transplantation trigger APC maturation and the T‐cell response that follows. Alternatively, it has been proposed that the introduction of microbial products during the surgical procedure could also alert the innate immune system to the presence of the transplanted organ. Here, we review why these hypotheses fail to fully explain how the alloimmune response is initiated after transplantation and summarize evidence that recognition of allogeneic non‐self by monocytes is a key event in triggering alloimmunity and graft rejection.
The biology of NK cells and their receptors affects clinical outcomes after hematopoietic cell transplantation (HCT)
Authors: Foley Bree , Felices Martin , Cichocki Frank , Cooley Sarah , Verneris Michael R. , Miller Jeffrey S. 
Published: February 2014

SummaryNatural killer (NK) cells were first identified for their capacity to reject bone marrow allografts in lethally irradiated mice without prior sensitization. Subsequently, human NK cells were detected and defined by their non‐major histocompatibility complex (MHC)‐restricted cytotoxicity toward transformed or virally infected target cells. Karre et al. later proposed ‘the missing self hypothesis’ to explain the mechanism by which self‐tolerant cells could kill targets that had lost self MHC class I. Subsequently, the receptors that recognize MHC class I to mediate tolerance in the host were identified on NK cells. These class I‐recognizing receptors contribute to the acquisition of function by a dynamic process known as NK cell education or licensing. In the past, NK cells were assumed to be short lived, but more recently NK cells have been shown to mediate immunologic memory to secondary exposures to cytomegalovirus infection. Because of their ability to lyse tumors with aberrant MHC class I expression and to produce cytokines and chemokines upon activation, NK cells may be primed by many stimuli, including viruses and inflammation, to contribute to a graft‐versus‐tumor effect. In addition, interactions with other immune cells support the therapeutic potential of NK cells to eradicate tumor and to enhance outcomes after hematopoietic cell transplantation.
Urinary cell mRNA profiles predictive of human kidney allograft status
Authors: Lee John R. , Muthukumar Thangamani , Dadhania Darshana , Ding Ruchuang , Sharma Vijay K. , Schwartz Joseph E. , Suthanthiran Manikkam 
Published: February 2014

SummaryKidney allograft status is currently characterized using the invasive percutaneous needle core biopsy procedure. The procedure has become safer over the years, but challenges and complications still exist including sampling error, interobserver variability, bleeding, arteriovenous fistula, graft loss, and even death. Because the most common type of acute rejection is distinguished by inflammatory cells exiting the intravascular compartment and gaining access to the renal tubular space, we reasoned that a kidney allograft may function as an in vivo flow cytometer and sort cells involved in rejection into urine. To test this idea, we developed quantitative polymerase chain reaction (PCR) assays for absolute quantification of mRNA and pre‐amplification protocols to overcome the low RNA yield from urine. Here, we review our single center urinary cell mRNA profiling studies that led to the multicenter Clinical Trials in Organ Transplantation (CTOT‐04) study and the discovery and validation of a 3‐gene signature of 18S rRNA‐normalized measures of CD3ε mRNA and IP‐10 mRNA and 18S rRNA that is diagnostic and predictive of acute cellular rejection in the kidney allograft. We also review our development of a 4‐gene signature of mRNAs for vimentin, NKCC2, E‐cadherin, and 18S rRNA diagnostic of interstitial fibrosis/tubular atrophy (IF/TA).
Palauans who chew betel nut: social impact of oral disease
Authors: Quinn Griffin M.T. , Mott M. , Burrell P.M. , Fitzpatrick J.J. 
Published: February 2014

BackgroundChewing betel nut is a tradition extending fromSoutheastAsia to thePacific. Globally, betel nut is the fourth main psychotropic substance containing a stimulant, arecoline, that has a similar effect to nicotine. InPalau, there is broad acceptance of betel nut chewing. One of the largest immigrant groups inHawaii is thePalauans. Chewing betel nut has significant social implications that make it difficult for those who engage in this practice to separate potential oral disease from the social importance. However, little is known about the social impact of oral disease from chewing betel nut onPalauans inHawaii.AimThe study aimed to describe the perceptions of betel‐chewingPalauans inHawaii regarding betel nut and to determine the social impact of oral disease among these individuals.MethodsDescriptive study conducted on the island ofOahu,Hawaii with 30 adultPalauans. Data were collected using theOralHealthImpactProfile‐14 to measure perceptions of social impact of oral disease on well‐being. Demographic and general health information was collected.ResultsParticipants perceived little negative social impact of oral disease on well‐being.DiscussionFamilies, peers and society exert a strong influence on the decision to chew betel nut, a known carcinogen. Participants in this study showed little concern on the impact of betel nut chewing on their oral health. They continue the habit in spite of the awareness of potential for oral disease.Implications for nursing and health policyNurses face challenges in educatingPalauans about the negative aspects of bethel nut, particularly those related to oral health especially when they do not perceive problems. Nurses must be involved in the development of health policies to design and implement strategies to promote behavioural change, and to ensure clinical services that are culturally sensitive to bethel nut chewers.
Session 1: Big Data/Ethnography or Big Data Ethnography
Authors: DE PAULA ROGERIO ABREU 
Published: February 2014

The first session explores the many ways and forms Data shape our lives. What are new roles, forms of research, methodologies and practices that contribute to the on‐going exploration of boundaries between “big data” and ethnography.“Is Data the new oil?” This has become a proverbial question that many organizations and research institutions have been asking themselves when they face the ever increasing proliferation of data (and data discourses, thereof). This is an enticing postulate, but not one without controversies. But, if data is the new oil, what does it mean for our ethnographic praxis? What roles will ethnography play? What forms of research methods and practices will spring up? In fact, what do we mean by data? These are some of the questions that lie at the heart of EPIC's on‐going methodological and practical pursuits. All papers in this session thus contribute to this on‐going debate by exploring the boundaries (epistemological, methodological, and practical) between “big data” and ethnography. From describing the use of mixed‐methods for investigating mobile money to exploring the emergence of analytic technology tools to help ethnographers collect and explore data to investigating the ‘meanings’ of data in data‐intensive social settings, such as, health and wellness communities, this session will offer a broad perspective on the subject, asking us to reflect not only on our own research practices but on the future of our field.
Session 4: (Co)creation and (co)participation: multiple actors in the research
Authors: ORTLIEB MARTIN 
Published: February 2014

The fourth session questions how ethnography is produced through multiple voices. Coming from different disciplinary backgrounds including Design, Business and Software Engineering, researchers report on co‐creating and co‐participating in the formation of ideas, practices and outcomes.Once upon a time, ethnographic reports were stereotypically produced in the Malinowskian manner: a single outside researcher enters the location to subsequently reproduce and represent his vision of the reality in that place. In 2013, and probably for the majority of the attendees of EPIC, this is no longer the case. Ethnography no longer has just a single voice: There are multiple stakeholders, often directly involved in the research, even though they may hail from different disciplinary backgrounds ranging from Design, Business to Software Engineering. Moreover, these days we often have multiple researchers reporting several perspectives for the same project. Finally, often the ‘subjects’ of the research are becoming involved in data reporting, data analysis, and/or implementation of insights as well as consumers/recipients of and through ethnography. In this session we hear from 4 different groups on such co‐creative, and co‐participatory endeavours that cut across all the above developments in various situated projects, ranging from post‐disaster community rebuilding to intra‐company international employee relationships and from post‐operation cancer care to capturing the intangible of successful individuals in specific company roles.
Co‐opetition as the new path to innovation? Negotiating strategic change through user‐centred design approaches:
Authors: Peinado Alice , Jarvin Magdalena , Jouanny Corinne 
Published: February 2014

This essay analyses how consensus was reached in a co‐opetitive setting by looking at two, consecutive but related projects spanning from 14 to 18 months in length. The projects took place in Paris, France, between 2009 and 2013, and involved key players from the banking and insurance industry. FiDJi, short for Finance, Design et Joie d'Innover, was meant to test a new innovation method based on a design thinking approach. FAIR, short for Finance, Assurance & Innovation Responsable, was conceived as a sequel to FiDJi but had the more ambitious goal to develop a new methodology that, while using a design thinking approach as a starting mode, would provide an independent set of guidelines with respect to sustainable, responsible innovation. Consequently, the dynamic of each project varied, as did the end goals. Both projects took design thinking as a starting point but while FiDJi produced a new innovation methodology based on a user‐centred design approach, FAIR had the more ambitious goal to develop a set of guidelines and a method for responsible innovation specific to the banking and insurance industry.The essay builds on a previous essay that analysed the dynamics proper to the FiDJi project in order to explore how anthropologists and designers are increasingly called upon to enable change (Peinado et al. 2011). It seeks to further expand on the role of anthropologists and designers as not merely enablers but enactors of change in multi‐disciplinary, team based, co‐opetitive contexts. Moving beyond an understanding of anthropologists and designers as providing discipline specific knowledge and skills to an understanding of their role as consultants, this essay will argue that as professionals anthropologists and designers need to be able to both contextualise their role and translate it so as to create value for their clients, users and themselves. This is consonant with repeated calls within the EPIC community to move beyond discipline specific definitions in order to understand the role we currently play and we could play in the future within industry‐based contexts. We will argue that both anthropologists and designers are particularly apt at this since they can understand organisational contexts and provide insights into the nature of transformation.
Alcohol abuse in deceased liver donors: impact on post‐transplant outcomes
Authors: Mangus Richard S , Kubal Chandrashekhar A , Fridell Jonathan A , Pena Jose M , Frost Evan M , Joseph Tector A. 
Published: February 2014

AbstractBackgroundMany deceased liver donors with a history of alcohol abuse are excluded based upon medical history alone. This paper summarizes the transplant outcomes for a large number of deceased liver donors with a documented history of alcohol abuse.MethodsThe records for 1478 consecutive deceased liver donors were reviewed (2001–2012). As per the United Network for Organ Sharing criteria, heavy alcohol use by an organ donor is defined as chronic intake of two or more drinks per day. Donors with a documented history of alcohol abuse were divided into three groups according to duration of abuse (<10 years, 10–24 years and 25 + years). Reperfusion biopsies are reported. Outcomes include biopsy appearance, early graft function and early and late graft survival.ResultsThere were 161 donors with alcohol abuse: <10 years (29%); 10–24 years (42%); and ≥25 years (29%). Risk of 90‐day graft loss for these three groups was: 0%, 3% and 2%, compared to 3% for all other donors (P = 0.62). Graft survival at 1 year for donor grafts with and without alcohol abuse was 89% and 87% (P = 0.52). There was no difference in early graft function. Cox proportional hazards modelling for graft survival demonstrates no statistically significant difference in survival up to 10 years post‐transplant.ConclusionsThis study demonstrates successful transplantation of a large number of deceased donor liver grafts from donors with a documented history of alcohol abuse (n = 161; 11% of all grafts). These extended criteria donor allografts may, therefore, be utilized successfully with similar outcomes.
Identification and characterization of the ‘missing’ terminal enzyme for siroheme biosynthesis in α‐proteobacteria
Authors: Bali Shilpa , Rollauer Sarah , Roversi Pietro , Raux‐Deery Evelyne , Lea Susan M. , Warren Martin J. , Ferguson Stuart J. 
Published: February 2014

SummaryIt has recently been shown that the biosynthetic route for both the d1‐haem cofactor of dissimilatory cd1 nitrite reductases and haem, via the novel alternative‐haem‐synthesis pathway, involves siroheme as an intermediate, which was previously thought to occur only as a cofactor in assimilatory sulphite/nitrite reductases. In many denitrifiers (which require d1‐haem), the pathway to make siroheme remained to be identified. Here we identify and characterize a sirohydrochlorin–ferrochelatase from Paracoccus pantotrophus that catalyses the last step of siroheme synthesis. It is encoded by a gene annotated as cbiX that was previously assumed to be encoding a cobaltochelatase, acting on sirohydrochlorin. Expressing this chelatase from a plasmid restored the wild‐type phenotype of an Escherichia coli mutant‐strain lacking sirohydrochlorin–ferrochelatase activity, showing that this chelatase can act in the in vivo siroheme synthesis. A ΔcbiX mutant in P. denitrificans was unable to respire anaerobically on nitrate, proving the role of siroheme as a precursor to another cofactor. We report the 1.9 Å crystal structure of this ferrochelatase. In vivo analysis of single amino acid variants of this chelatase suggests that two histidines, His127 and His187, are essential for siroheme synthesis. This CbiX can generally be identified in α‐proteobacteria as the terminal enzyme of siroheme biosynthesis.
Tacrolimus does not alter the production of several cytokines and antimicrobial peptide in Malassezia furfur‐infected‐keratinocytes
Authors: Balato Anna , Paoletti Iole , De Gregorio Vincenza , Cantelli Mariateresa , Ayala Fabio , Donnarumma Giovanna 
Published: February 2014

SummaryTopical immunosuppressant therapy is widely used in the treatment of inflammatory skin diseases, such as atopic dermatitis and psoriasis. Besides its beneficial therapeutic effects, application of topical anti‐inflammatory drugs may render the epidermis more vulnerable to invading pathogens by suppressing innate immune responses in keratinocytes (KCs). Cytokines, chemokines and antimicrobial peptides (AMPs) produced by epithelial cells enable them to participate in innate and acquired immune responses. The aim of the present work was to study the influence of tacrolimus (FK506) on KCs infected with Malassezia furfur (M. furfur), evaluating the expression of pro‐inflammatory cytokines IL‐1α and IL‐6, chemokine IL‐8, anti‐inflammatory cytokines transforming growth factor beta1 (TGF‐β1) and IL‐10 and AMP β‐defensin‐2. Human KCs were obtained from surgical specimens of normal adult skin. The expression of mRNAs in KCs: FK506‐treated, FK506‐treated and M. furfur‐infected as well as only M. furfur‐infected was quantified by real‐time quantitative polymerase chain reaction. Next, the production of the AMP β‐defensin‐2 and of the above‐mentioned pro‐inflammatory and anti‐inflammatory cytokines was evaluated using enzyme‐linked immunosorbent assay. In this study, FK506 did not alter cytokine and AMP production by KCs; this led us to hypothesise that it may not enhance the risk of mycotic skin infections.
Influence of the Lubrication Model on the Dynamic Response of Mechanical Systems
Authors: Flores Paulo 
Published: February 2014

The main objective of this work is to present a study on the use of different hydrodynamic force models on the dynamic response of mechanical systems with lubricated revolute joints. For this purpose, the fundamental issues related to the classical theory of lubrication for dynamically loaded journal-bearings are revised, which is used to evaluate the Reynolds’ equation for dynamic regime. The hydrodynamic forces that develop at the lubricated revolute joints are determined and included into the dynamic equations of motion.
In this study, three different approaches are considered to evaluate the hydrodynamic forces, namely the Pinkus and Sternlicht approach for long journal-bearings and the Frêne et al. models for both long and short journal-bearings. Results for a mechanical system with a lubricated revolute joint are presented and used to discuss the main assumptions and procedures adopted in this work. From the computational simulations performed, it can be observed that the hydrodynamic force model play a crucial role in predicting the dynamic behavior of mechanical systems and originate some uncertainties in their dynamic responses.
Utilizing Emergent Levels to Facilitate Complex Systems Design: Demonstrated in a Synthetic Biology Domain
Authors: Egan Paul F. , Cagan Jonathan , Schunn Christian , LeDuc Philip R. 
Published: February 2014

Designing complex systems often requires consideration of many components interacting across vast scales of space and time, thus producing highly challenging design spaces to search. In particular, nano-based technologies may require considerations of how nanoscale (10−9) embodiments affect macroscale (∼100) systems and typically have multiple layers of emergent behavior. It is frequently cited that counter-intuitive properties of emergence complicates design tasks; however, we investigate whether some multiscale emergent systems have organizational levels that may inform more effective design methods and searches.
Investigations are conducted by extending an agent-based simulation that predicts the emergent interactions of myosin motors interacting with a motile actin filament. Both the behaviors of individual motors and an ensemble of motors are stochastic, therefore analytical methods are often unable to form accurate design evaluations and computationally intensive simulations are required for investigation. Our modification of the simulation enables the prediction of the duration of time that motors will carry an actin filament before system dissociation (termed its processive life-time), which is a vital performance metric for future nanotechnology designs such as molecular sorters.
Virtual experiments were conducted that determines how perturbations of synthetic myosin design configurations, and the number of myosins present, affects emergent ensemble performance with respect to run-length and energy usage. It is found that all systems have nearly identical average processive life-times for a given input energy regardless of how much energy individual myosins utilize. Such a finding reduces the total information that a designer must consider, since it is a fundamental relationship that holds regardless of lower level component configurations. Such relationships may occur in complex systems in additional domains, and knowledge of these emergent relationships could greatly facilitate the efficiencies of design methods and automated searches for future technologies.