bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-specific autoimmunity controlled by Aire in thymic and peripheral tolerance mechanisms
Authors: Matsumoto Minoru , Tsuneyama Koichi , Morimoto Junko , Hosomichi Kazuyoshi , Matsumoto Mitsuru , Nishijima Hitoshi 
Published: October 2019

Abstract
Tissue-specific autoimmune diseases are assumed to arise through malfunction of two checkpoints for immune tolerance: defective elimination of autoreactive T cells in the thymus and activation of these T cells by corresponding autoantigens in the periphery. However, evidence for this model and the outcome of such alterations in each or both of the tolerance mechanisms have not been sufficiently investigated. We studied these issues by expressing human AIRE (huAIRE) as a modifier of tolerance function in NOD mice wherein the defects of thymic and peripheral tolerance together cause type I diabetes (T1D). Additive huAIRE expression in the thymic stroma had no major impact on the production of diabetogenic T cells in the thymus. In contrast, huAIRE expression in peripheral antigen-presenting cells (APCs) rendered the mice resistant to T1D, while maintaining other tissue-specific autoimmune responses and antibody production against an exogenous protein antigen, because of the loss of Xcr1+ dendritic cells, an essential component for activating diabetogenic T cells in the periphery. These results contrast with our recent demonstration that huAIRE expression in both the thymic stroma and peripheral APCs resulted in the paradoxical development of muscle-specific autoimmunity. Our results reveal that tissue-specific autoimmunity is differentially controlled by a combination of thymic function and peripheral tolerance, which can be manipulated by expression of huAIRE/Aire in each or both of the tolerance mechanisms.
Occurrence of intI1-associated VIM-5 carbapenemase and co-existence of all four classes of β-lactamase in carbapenem-resistant clinical Pseudomonas aeruginosa DMC-27b
Authors: Jahan M Ishrat , Rahaman M Mizanur , Hossain M Anwar , Sultana Munawar 
Published: October 2019

Abstract

Objectives
Emergence of carbapenem-resistant Pseudomonas aeruginosa is limiting current treatment options. Carbapenemases and their association with integrons can cause rapid dissemination of resistance traits. We report here the co-existence and chromosomal inheritance of all four classes of β-lactamase and the presence of a unique class 1 integron (intI1) harbouring blaVIM-5 within a single isolate of P. aeruginosa, DMC-27b.

Methods
DMC-27b, isolated from urine, was characterized for carbapenem resistance both phenotypically and genotypically. The orientation of gene cassette structures of class 1 integrons was determined using referenced and designed overlapping primers and complete genome sequence (CGS) data. The antimicrobial resistance profile, porin protein mutations and the presence of active efflux activity were studied from the CGS.

Results
P. aeruginosa DMC-27b was resistant to a total of 20 antibiotics, with imipenem and meropenem MIC90s of >512 mg/L. The isolate harboured all four classes of β-lactamase: VEB-1 (class A), VIM-5 (class B), PDC-35 (class C) and OXA-2 and OXA-50 (both class D). Chromosomal harbouring of blaVIM-5 was associated with the intI1 gene cassette as the sole gene, a unique cassette so far reported. A total of 11 mutations, among them some mutations causing extra folds and changes in binding sites, in porin protein OprD might also affect its functionality regarding the transportation of antibiotics.

Conclusions
This is one of the earliest reports of its kind on the co-existence of all four β-lactamase classes in P. aeruginosa DMC-27b. Acquisition of multiple resistance determinants is paving the way for the development of MDR. This superbug is a model for rapid dissemination of resistance traits both horizontally and vertically.
Do Managers Matter? A Natural Experiment from 42 R&D Labs in India
Authors: Choudhury Prithwiraj , Khanna Tarun , Makridis Christos A 
Published: October 2019

Abstract
We exploit plausibly exogenous variation in the staggered entry of new managers into India’s 42 public R&D labs between 1994 and 2006 to study how alignment between the CEO and middle-level managers affects research productivity. We show that the introduction of new lab managers aligned with the national R&D reforms raised patenting and multinational licensing revenues by 58% and 75%, respectively, and scientist research productivity, including: a 16%, 10%, 11%, and 22% increase in h-indices, number of coauthors, publications, and citations per scientist, respectively. Using natural language processing techniques on the set of research abstracts produced among these scientists, we also find that overall mood and sentiment increased by 8.5% following the first managerial change. (JEL L22, L23, O32, O33)
Time since fire is an over-simplified measure of habitat suitability for the New Holland mouse
Authors: Burns Phoebe A , Phillips Ben L 
Published: October 2019

AbstractFire has shaped much of the Australian landscape, and alterations to natural or historical fire regimes are implicated in the decline of many native mammal species. Time since fire (TSF) is a common metric used to understand vegetation and faunal responses to fire but is unlikely to capture the complexity of successional changes following fire. The New Holland mouse (Pseudomys novaehollandiae), a threatened and declining rodent species native to southeastern Australia, is traditionally considered an early post-fire successional species. Here, we use a 48-year dataset to test whether this posited association with early TSF is upheld, and whether the species’ occurrence and abundance are governed by TSF. We find support for a minimal influence of TSF on the species’ occurrence, and that while abundance of P. novaehollandiae is partly explained by TSF, considerable uncertainty and variation among fire events and locations limit the usefulness of TSF in informing conservation management strategies. We suggest that it is not helpful to consider the species as early successional and that fire planning for P. novaehollandiae conservation is best considered at a local scale. Additionally, we provide guidelines for maximizing individual survival and persistence during and after planned burns.
Neovaginoplasty for radiation-induced vaginal stenosis using Nile Tilapia Fish Skin as a biological graft
Authors: Dias Maria Tereza Pinto Medeiros , Bilhar Andreisa Paiva Monteiro , Rios Livia Cunha , Costa Bruno Almeida , Duete Úlima Rates , Lima Júnior Edmar Maciel , Alves Ana Paula Negreiros Nunes , Bruno Zenilda Vieira , Moraes Filho Manoel Odorico de , Bezerra Leonardo Robson Pinheiro Sobreira 
Published: October 2019

Abstract
Tilapia skin showed good results when used as a biological graft for surgical management of Mayer–Rokitansky–Küster–Hauser syndrome. Thus, our researchers considered the use of this biomaterial for neovaginoplasty in radiation-induced vaginal stenosis. We report the case of a 41-year-old female patient with a total occlusion of the vaginal canal after radiotherapy for vaginal cancer. McIndoe neovaginoplasty using tilapia skin as a scaffold for proliferation of new vaginal epithelium was performed. Initially, laparoscopic dissection of the rectovaginal septum and vesicovaginal space spaces was conducted. In the vaginal surgical time, a transverse transmural incision was made in the scarred vaginal reminiscent followed by blunt dissection and insertion of an acrylic mold covered with tilapia skin. Good anatomical and functional outcomes were noted. Vaginal reconstruction with tilapia skin seems to be an excellent option for patients with radiation-induced vaginal stenosis due to its wide availability, easy application and high effectiveness.
Endourologic treatment for a fibroepithelial ureteral polyp protruding from the urethra
Authors: Abdessater Maher , Kanbar Anthony , Khoury Joey El , Hachem Charbel El , Halabi Rami , Boustany Johnny , Khoury Raghid El 
Published: October 2019

Abstract
Fibroepithelial polyps (FP) of the ureter are rare and benign mesodermal tumors frequently mistaken for transitional cell carcinoma. We hereby report a rare case of a 19-year-old patient with two FPs, originating from the distal left ureter that were successfully treated with ureteroscopy. One of these polyps was completely protruding outside the bladder through the urethra, which makes this case unique in the literature. Ureteroscopy is currently the best method available for identification, histologic diagnosis and treatment of these polyps.
Self-gravitating planetary envelopes and the core-nucleated instability
Authors: Béthune William 
Published: October 2019

Abstract
Planet formation scenarios can be constrained by the ratio of the gaseous envelope mass relative to the solid core mass in the observed exoplanet populations. One-dimensional calculations find a critical (maximal) core mass for quasi-static envelopes to exist, suggesting that envelopes around more massive cores should collapse due to a ‘core-nucleated’ instability. We study self-gravitating planetary envelopes via hydrodynamic simulations, progressively increasing the dimensionality of the problem. We characterize the core-nucleated instability and its non-linear evolution into runaway gas accretion in one-dimensional spherical envelopes. We show that rotationally supported envelopes can enter a runaway accretion regime via polar shocks in a two-dimensional axisymmetric model. This picture remains valid for high-mass cores in three dimensions, where the gas gravity mainly adds up to the core gravity and enhances the mass accretion rate of the planet in time. We relate the core-nucleated instability to the absence of equilibrium connecting the planet to its parent disc and discuss its relevance for massive planet formation.
Ensembl Genomes 2020—enabling non-vertebrate genomic research
Authors: Howe Kevin L , Contreras-Moreira Bruno , De Silva Nishadi , Maslen Gareth , Akanni Wasiu , Allen James , Alvarez-Jarreta Jorge , Barba Matthieu , Bolser Dan M , Cambell Lahcen , Carbajo Manuel , Chakiachvili Marc , Christensen Mikkel , Cummins Carla , Cuzick Alayne , Davis Paul , Fexova Silvie , Gall Astrid , George Nancy , Gil Laurent , Gupta Parul , Hammond-Kosack Kim E , Haskell Erin , Hunt Sarah E , Jaiswal Pankaj , Janacek Sophie H , Kersey Paul J , Langridge Nick , Maheswari Uma , Maurel Thomas , McDowall Mark D , Moore Ben , Muffato Matthieu , Naamati Guy , Naithani Sushma , Olson Andrew , Papatheodorou Irene , Patricio Mateus , Paulini Michael , Pedro Helder , Perry Emily , Preece Justin , Rosello Marc , Russell Matthew , Sitnik Vasily , Staines Daniel M , Stein Joshua , Tello-Ruiz Marcela K , Trevanion Stephen J , Urban Martin , Wei Sharon , Ware Doreen , Williams Gary , Yates Andrew D , Flicek Paul 
Published: October 2019

Abstract
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
Lamin A/C promotes DNA base excision repair
Authors: Maynard Scott , Keijzers Guido , Akbari Mansour , Ezra Michael Ben , Hall Arnaldur , Morevati Marya , Scheibye-Knudsen Morten , Gonzalo Susana , Bartek Jiri , Bohr Vilhelm A 
Published: October 2019

AbstractThe A-type lamins (lamin A/C), encoded by the LMNA gene, are important structural components of the nuclear lamina. LMNA mutations lead to degenerative disorders known as laminopathies, including the premature aging disease Hutchinson-Gilford progeria syndrome. In addition, altered lamin A/C expression is found in various cancers. Reports indicate that lamin A/C plays a role in DNA double strand break repair, but a role in DNA base excision repair (BER) has not been described. We provide evidence for reduced BER efficiency in lamin A/C-depleted cells (Lmna null MEFs and lamin A/C-knockdown U2OS). The mechanism involves impairment of the APE1 and POLβ BER activities, partly effectuated by associated reduction in poly-ADP-ribose chain formation. Also, Lmna null MEFs displayed reduced expression of several core BER enzymes (PARP1, LIG3 and POLβ). Absence of Lmna led to accumulation of 8-oxoguanine (8-oxoG) lesions, and to an increased frequency of substitution mutations induced by chronic oxidative stress including GC>TA transversions (a fingerprint of 8-oxoG:A mismatches). Collectively, our results provide novel insights into the functional interplay between the nuclear lamina and cellular defenses against oxidative DNA damage, with implications for cancer and aging.
Major adverse renal events (MARE): a proposal to unify renal endpoints
Authors: Prischl Friedrich C , Rossing Peter , Bakris George , Mayer Gert , Wanner Christoph 
Published: October 2019

AbstractBackgroundIn renal studies, various outcome endpoints are used with variable definitions, making it nearly impossible to perform meta-analyses and deduce meaningful conclusions. Increasing attention is directed towards standardization of renal outcome reporting.MethodsA working group was formed to produce a unifying definition of renal outcomes that can be used by all investigators. We propose major adverse renal events (MARE) as the term for a standardized composite of hard renal outcomes. We discuss the components for inclusion in MARE from existing evidence.ResultsMARE could include three to five items, considered relevant to patients and regulators. New onset of kidney injury, that is persistent albuminuria/proteinuria and/or decreasing glomerular filtration rate (GFR) &lt;60 ml/min/1.73 m2, persistent signs of worsening kidney disease, development of end-stage kidney disease with estimated GFR &lt;15 ml/min/1.73 m2 without or with initiation of kidney replacement therapy, and death from renal cause are core items of MARE. Additionally, patient reported outcomes should be reported in parallel to MARE as a standard set of primary (or secondary) endpoints in studies on kidney disease of diabetic, hypertensive-vascular, or other origin.ConclusionsMARE as a reporting standard will enhance the ability to compare studies and thus, facilitate meaningful meta-analyses. This will result in standardized endpoints that should result in guideline improvement to better individualize care of patients with kidney disease.
Lumbar Arthroplasty: Past, Present, and Future
Authors: Sandhu Faheem A , Dowlati Ehsan , Garica Rolando 
Published: October 2019

Abstract
Lumbar degenerative disc disease is a pathologic process that affects a large portion of our aging population. In the recent past, surgical treatment has involved fusion procedures. However, lumbar disc arthroplasty and replacement provides an alternative for carefully selected patients. It provides the major advantage of motion preservation and thus keeps adjacent segments from significantly progressive degeneration. The history of lumbar disc replacement has roots that start in the 1960s with the implantation of stainless-steel balls. Decades later, multiple implants with different material design and biomechanical properties were introduced to the market. New third-generation implants have made great strides in improved biomechanics and clinical outcomes. Although there is room for further advancement and studies are warranted to assess the long-term durability and sustainability of lumbar disc arthroplasty, it has certainly proven to be a very acceptable alternative within the surgical armamentarium that should be offered to patients who meet indications. In this review we present an overview of lumbar disc arthroplasty including its history, indications, biomechanics, challenges, and future directions.
Networks in economic development
Authors: Breza Emily , Chandrasekhar Arun , Golub Benjamin , Parvathaneni Aneesha 
Published: October 2019

AbstractThis chapter surveys the implications of some studies in network economics research for economic development. We focus on information flow and risk-sharing—two topics where work in theory, empirics, and policy analysis have been especially intensive and complementary. In analysing information, we distinguish models of information diffusion and aggregation, highlight how different models imply very different guidance regarding the right way to seed information. In discussing risk-sharing, we look at the key frictions that impede efficient informal insurance, and some potential unintended consequences when policymakers intervene to help. Throughout, we stress practical insights that can be used with limited measurement of the details of networks.
Oxygenic Phototrophs Need ζ-Carotene Isomerase (Z-ISO) for Carotene Synthesis: Functional Analysis in Arthrospira and Euglena
Authors: Sugiyama Kenjiro , Takahashi Koh , Nakazawa Keisuke , Yamada Masaharu , Kato Shota , Shinomura Tomoko , Nagashima Yoshiki , Suzuki Hideyuki , Ara Takeshi , Harada Jiro , Takaichi Shinichi 
Published: October 2019

Abstract
For carotenogenesis, two biosynthetic pathways from phytoene to lycopene are known. Most bacteria and fungi require only phytoene desaturase (PDS, CrtI), whereas land plants require four enzymes: PDS (CrtP), ζ-carotene desaturase (ZDS, CrtQ), ζ-carotene isomerase (Z-ISO) and cis-carotene isomerase (CrtISO, CrtH). The gene encoding Z-ISO has been functionally identified in only two species, Arabidopsis thaliana and Zea mays, and has been little studied in other organisms. In this study, we found that the deduced amino acid sequences of Arthrospira Z-ISO and Euglena Z-ISO have 58% and 62% identity, respectively, with functional Z-ISO from Arabidopsis. We studied the function of Z-ISO genes from the cyanobacterium Arthrospira platensis and eukaryotic microalga Euglena gracilis. The Z-ISO genes of Arthrospira and Euglena were transformed into Escherichia coli strains that produced mainly 9,15,9′-tri-cis-ζ-carotene in darkness. In the resulting E. coli transformants cultured under darkness, 9,9′-di-cis-ζ-carotene was accumulated predominantly as Z-ISO in Arabidopsis. This indicates that the Z-ISO genes were involved in the isomerization of 9,15,9′-tri-cis-ζ-carotene to 9,9′-di-cis-ζ-carotene in darkness. This is the first functional analysis of Z-ISO as a ζ-carotene isomerase in cyanobacteria and eukaryotic microalgae. Green sulfur bacteria and Chloracidobacterium also use CrtP, CrtQ and CrtH for lycopene synthesis as cyanobacteria, but their genomes did not comprise Z-ISO genes. Consequently, Z-ISO is needed in oxygenic phototrophs, whereas it is not found in anoxygenic species.
Do Individual Differences Matter in the Way People View Police Legitimacy? A Partial Replication and Extension of Invariance Thesis
Authors: Zahnow Renee , Mazerolle Lorraine , Pang Alicia 
Published: October 2019

Abstract
The invariance thesis of police legitimacy argues that, regardless of individual differences, the more citizens perceive police as procedurally just and effective, the more they will see the police as a legitimate authority. Research primarily undertaken in the USA shows support for the invariance thesis with some nuanced findings for victims and those with prior police contact. This study conducts a partial replication and extension of the Wolfe et al.’s study (Wolfe, S., Nix, J., Kaminski, R., and Rojek, J. (2016). ‘Is the Effect of Procedural Justice on Police Legitimacy Invariant? Testing the Generality of Procedural Justice and Competing Antecedents of Legitimacy.’ Journal of Quantitative Criminology 32(2): 253–282) testing the invariance thesis, comparing the effects of citizen perceptions of procedural justice (PJ) and police effectiveness (PE) on perceptions of police legitimacy across individual characteristics in Australia. Using a survey of 4,167 residents across 148 communities, we find the effects of PJ perceptions on police legitimacy are largely invariant across individual differences. Yet contrary to previous research, our study finds that the impact of PE perceptions is not invariant and particularly matter for people with visible minority status.
‘What sport do you prefer to do?’ Improving knowledge of adolescents’ preferred sports within the sport participation decline framework
Authors: Gatouillat C , Luiggi M , Griffet J , Travert M 
Published: October 2019

Abstract

Background
Sport participation is declining in some European countries. Previous findings recommended considering territorial specificities to adapt local sports promotion programs. However, in France, little is known about adolescents’ preferences and their changes across time. This study aimed to measure preferred sports and their changes among a representative sample of adolescents of the third biggest French département.

Methods
Data were extracted from a previous cross-sectional study that used a quota sampling design to respect the proportions of advantaged and disadvantaged schools. The present study involved 744 and 938 participants, in 2001 and 2015, respectively. Adolescent preferences were calculated by sex and socioeconomic status (SES). Multiple binary logistic regressions were performed to measure changes between 2001 and 2015 by sex and SES.

Results
Sports preferences and their evolution differed by sex and SES. Three cases were observed: no significant change in sports preferences (low-SES boys), a sharp loss of interest for some sports (low-SES girls and high-SES boys) and a sharp loss of interest for some sports whilst others gained significant interest (high-SES girls).

Conclusions
This knowledge may help the development of sport promotion programs. Future sport policies could choose to develop sports that are preferred and increasingly appreciated by adolescents.