bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can artificial intelligence replace manual search for systematic literature? Review on cutaneous manifestations in primary Sjögren’s syndrome
Authors: Orgeolet Laure , Foulquier Nathan , Misery Laurent , Redou Pascal , Pers Jacques-Olivier , Devauchelle-Pensec Valérie , Saraux Alain 
Published: July 2019

AbstractObjectivesManual systematic literature reviews are becoming increasingly challenging due to the sharp rise in publications. The primary objective of this literature review was to compare manual and computer software using artificial intelligence retrieval of publications on the cutaneous manifestations of primary SS, but we also evaluated the prevalence of cutaneous manifestations in primary SS.MethodsWe compared manual searching and searching with the in-house computer software BIbliography BOT (BIBOT) designed for article retrieval and analysis. Both methods were used for a systematic literature review on a complex topic, i.e. the cutaneous manifestations of primary SS. Reproducibility was estimated by computing Cohen’s κ coefficients and was interpreted as follows: slight, 0–0.20; fair, 0.21–0.40; moderate, 0.41–0.60; substantial, 0.61–0.80; and almost perfect, 0.81–1.ResultsThe manual search retrieved 855 articles and BIBOT 1042 articles. In all, 202 articles were then selected by applying exclusion criteria. Among them, 155 were retrieved by both methods, 33 by manual search only, and 14 by BIBOT only. Reliability (κ = 0.84) was almost perfect. Further selection was performed by reading the 202 articles. Cohort sizes and the nature and prevalence of cutaneous manifestations varied across publications. In all, we found 52 cutaneous manifestations reported in primary SS patients. The most described ones were cutaneous vasculitis (561 patients), xerosis (651 patients) and annular erythema (215 patients).ConclusionAmong the final selection of 202 articles, 155/202 (77%) were found by the two methods but BIBOT was faster and automatically classified the articles in a chart. Combining the two methods retrieved the largest number of publications.
Trade Less and Exit Overcrowded Markets: Lessons from International Mutual Funds*
Authors: Dyakov Teodor , Jiang Hao , Verbeek Marno 
Published: July 2019

Abstract
We study active investment skills in relation to returns to scale in the active mutual fund industry. Using a sample of 13,807 funds from sixteen domicile countries investing in forty-two equity markets from 2001 to 2014, we find that they achieve negative trading performance on average, driven mainly by particularly low returns to their trades in US equities. Exploring their investment environment, we find convincing evidence of decreasing returns to scale around the world, especially for the US market. Based on theory of optimal fund size, we estimate the optimal size of the active mutual fund industry. We find that the active mutual fund industry in USA has exceeded the optimal level, whereas in the international markets, there may still be room for further expansion. Consistent with this view, we find that mutual fund managers have been gradually reallocating their assets away from the USA and more into international equity markets.
Iron Cage or Paper Cage? The Interplay of Worker Characteristics and Organizational Policy in Shaping Unequal Responses to a Standardized Decision-Making Tool
Authors: Bosk Emily A 
Published: July 2019

AbstractStudies are largely optimistic about the ability of standardized procedures to constrain decision-makers’ biases and produce more equitable results across fields. However, work that embraces standardization as an equalizing force stands in contrast to research on standardization and street-level bureaucrats, which asserts that standardized procedures are not self-actuating and cannot be understood apart from the environments in which they are used. I examine how frontline workers vary in their approach to an actuarial-based tool intended to standardize judgments. In a highly controlled decision-making environment, child welfare workers whose racial and sex characteristics afford them higher status report subverting the tool; conversely, workers in the same position whose ascriptive characteristics yield them lower status in terms of race and sex describe following the rules. In an environment where the same tool is adopted only ceremonially, all workers experience decision-making as unconstrained, regardless of their ascriptive characteristics. This work fills gaps in knowledge about how social status and organizational context intersect to affect rule abidance. Examining these dynamic relationships advances understanding of how organizations reproduce inequality and the limits and potential for standardization to transform social hierarchies.
Carriage duration of carbapenemase-producing Enterobacteriaceae in a hospital cohort - implications for infection control measures
Authors: Mo Yin , Hernandez-Koutoucheva Anastasia , Musicha Patrick , Bertrand Denis , Lye David , Tek Ng Oon , Fenlon Shannon N. , Chen Swaine L. , Lin Ling Moi , Tang Wen Ying , Barkham Timothy , Nagarajan Niranjan , Cooper Ben S , Marimuthu Kalisvar 
Published: July 2019

AbstractCarriage duration of carbapenemase-producing Enterobacteriaceae (CPE) is uncertain. We followed 21 CPE carriers over one year. Mean carriage duration was 86 (95%CrI= [60, 122]) days, with 98.5% (95%CrI= [95.0, 99.8]) probability of decolonization in one year. Antibiotic consumption was associated with prolonged carriage. CPE-carriers’ status should be reviewed yearly.
TANGLED1 mediates interactions between microtubules that may promote spindle organization and phragmoplast guidance to the division site in maize
Authors: Martinez Pablo , Dixit Ram , Balkunde Rachappa S. , O’Leary Seán E. , Brakke Kenneth A. , Rasmussen Carolyn G. 
Published: July 2019

AbstractThe microtubule cytoskeleton serves as a dynamic structural framework for mitosis in eukaryotic cells. TANGLED1 (TAN1) is a microtubule-binding protein that localizes to the division site and mitotic microtubules and plays a critical role in division plane orientation in plants. Here, in vitro experiments demonstrate that TAN1 directly binds microtubules, mediating microtubule zippering or end-on microtubule interactions, depending on their contact angle. Maizetan1mutant cells improperly position the preprophase band (PPB), which predicts the future division site. However, cell-shape-based modeling indicates that PPB positioning defects are likely a consequence of abnormal cell shapes and not due to TAN1 absence. Spindle defects in thetan1mutant suggest that TAN1-mediated microtubule zippering may contribute to metaphase spindle organization. In telophase, co-localization of growing microtubules ends from the phragmoplast with TAN1 at the division site suggests that TAN1 interacts with microtubule tips end-on. Together, our results suggest that TAN1 contributes to spindle and phragmoplast microtubule organization to ensure proper division plane orientation.
Collagen Production and Niche Engineering: A Novel Strategy for Cancer Cells to Survive Acidosis and Evolve
Authors: Damaghi Mehdi , Byrne Samantha , Xu Liping , Tafreshi Narges , Fang Bin , Koomen John M. , Karolak Aleksandra , Chen Tingan , Johnson Joseph , Gallant Nathan D. , Marusyk Andriy , Gillies Robert J. 
Published: July 2019

SummaryDuctal Carcinoma in situ (DCIS) is an avascular disease characterized by profound acidosis. Pre-malignant cells within this niche must adapt to acidosis to survive and thrive. A component of this acid-adaptation involves extracellular matrix remodeling leading to niche construction and remodeling. Using discovery proteomics, we identified that collagen producing enzyme PLODs are upregulated in acid-adapted breast cancer cells. Second harmonic generation microscopy showed significant collagen deposition within DCIS lesions of patients. In vitro analyses identified that acid-adaptation involves production of rare collagens that can be regulated by Ras and SMAD pathway. Secretome analysis showed upregulation ECM remodeling enzymes such as TGM2 and LOXL2. Comparison of acid induced collagens in vitro and in patient data showed correlation between rare collagens production and survival of patients. We conclude acidosis induces collagen production by cancer cells and promote growth independent of basal membrane attachment. The independently produced collagen can be used for niche construction and engineering as an adaptation strategy of cancer cells to survive and evolve.
Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles
Authors: Ramsbottom Kerry A , Carr Daniel F , Rigden Daniel J , Jones Andrew R 
Published: July 2019

AbstractAdverse drug reactions have been linked with HLA alleles in different studies. These HLA proteins play an essential role in the adaptive immune response for the presentation of self and non-self peptides. Anti-thyroid drugs methimazole and propylthiouracil have been associated with drug induced agranulocytosis (severe lower white blood cell count) in patients with B*27:05, B*38:02 and DRB1*08:03 alleles in different populations: Taiwanese, Vietnamese, Han Chinese and Caucasian.In this study, informatics methods were used to investigate if any sequence or structural similarities exist between the two associated HLA-B alleles, compared with a set of “control” alleles assumed not be associated, which could help explain the molecular basis of the adverse drug reaction. We demonstrated using MHC Motif Viewer and MHCcluster that the two alleles do not have a propensity to bind similar peptides, and thus at a gross level the structure of the antigen presentation region of the two alleles are not similar. We also performed multiple sequence alignment to identify polymorphisms shared by the risk but not by the control alleles and molecular docking to compare the predicted binding positions of the drug-allele combinations.Two residues, Cys67 and Thr80, were identified from the multiple sequence alignments to be unique to these risk alleles alone. The molecular docking showed the poses of the risk alleles to favour the F-pocket of the peptide binding groove, close to the Thr80 residue, with the control alleles generally favouring a different pocket. The data are thus suggestive that Thr80 may be a critical residue in HLA-mediated anti-thyroid drug induced agranulocytosis, and thus can guide future research and risk assessment.
Social networks with strong spatial embedding generate non-standard epidemic dynamics driven by higher-order clustering
Authors: Haw David J. , Pung Rachael , Read Jonathan M. , Riley Steven 
Published: July 2019

AbstractSome directly transmitted human pathogens such as influenza and measles generate sustained exponential growth in incidence, and have a high peak incidence consistent with the rapid depletion of susceptible individuals. Many do not. While a prolonged exponential phase typically arises in traditional disease-dynamic models, current quantitative descriptions of non-standard epidemic profiles are either abstract, phenomenological or rely on highly skewed offspring distributions in network models. Here, we create large socio-spatial networks to represent contact behaviour using human population density data, a previously developed fitting algorithm, and gravity-like mobility kernels. We define a basic reproductive numberR0for this system analogous to that used for compartmental models. Controlling forR0, we then explore networks with a household-workplace structure in which between-household contacts can be formed with varying degrees of spatial correlation, determined by a single parameter from the gravity-like kernel. By varying this single parameter and simulating epidemic spread, we are able to identify how more frequent local movement can lead to strong spatial correlation and thus induce sub-exponential outbreak dynamics with lower, later epidemic peaks. Also, the ratio of peak height to final size was much smaller when movement was highly spatially correlated. We investigate the topological properties of our networks via a generalized clustering coefficient that extends beyond immediate neighbourhoods, identifying very strong correlations between 4th order clustering and non-standard epidemic dynamics. Our results motivate the joint observation of incidence and socio-spatial human behaviour during epidemics that exhibit non-standard incidence patterns.Author SummaryEpidemics are typically described using a standard set of mathematical models that do not capture social interactions or the way those interactions are determined by geography. Here we propose a model that can reflect social networks influenced strongly by the way people travel and we show that they lead to very different epidemic profiles. This type of model will likely be useful for forecasting.
L1EM: A tool for accurate locus specific LINE-1 RNA quantification
Authors: McKerrow Wilson , Fenyö David 
Published: July 2019

AbstractMotivationLINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify RNA at specific LINE-1 loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA.ResultsWe provide a tool, L1-EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1-EM on simulated data and against long read sequencing from HEK cells.AvailabilityL1-EM is written in python. The source code along with the necessary annotations are available athttps://github.com/FenyoLab/L1EMand distributed under GPLv3.Contactwilson.mckerrow@nyulangone.org,david@fenyolab.org
Changes in gene expression during female reproductive development in a colour polymorphic insect
Authors: Willink B. , Duryea M. C. , Wheat C. , Svensson E. I. 
Published: July 2019

AbstractPleiotropy (multiple phenotypic effects of single genes) and epistasis (gene interaction) have key roles in the development of complex phenotypes, especially in polymorphic taxa. The development of discrete and heritable phenotypic polymorphisms often emerges from major-effect genes that interact with other loci and have pleiotropic effects on multiple traits. We quantified gene expression changes during ontogenetic colour development in a polymorphic insect (damselfly:Ischnura elegans), with three heritable female morphs, one being a male mimic. This female colour polymorphism is maintained by male mating harassment and sexual conflict. Using transcriptome sequencing andde novoassembly, we demonstrate that all three morphs downregulate gene expression during early colour development. The morphs become increasingly differentiated during sexual maturation and when developing adult colouration. These different ontogenetic trajectories arise because the male-mimic shows accelerated (heterochronic) development, compared to the other female morphs. Many loci with regulatory functions in reproductive development are differentially regulated in the male-mimic, including upstream and downstream regulators of ecdysone signalling and transcription factors potentially influencing sexual differentiation. Our results suggest that long-term sexual conflict does not only maintain this polymorphism, but has also modulated the evolution of gene expression profiles during colour development of these sympatric female morphs.
Lipid Droplets Mediate Salt Stress Tolerance in Parachlorella kessleri
1
Authors: You Zaizhi , Zhang Qi , Peng Zhou , Miao Xiaoling 
Published: July 2019

Abstract
Microalgae are known to respond to salinity stress via mechanisms that include accumulation of compatible solutes and synthesis of antioxidants. Here, we describe a salinity-tolerance mechanism mediated by lipid droplets (LDs). In the alga Parachlorella kessleri grown under salt-stress conditions, we observed significant increases in cell size and LD content. LDs that were closely grouped along the plasma membrane shrank as the plasma membrane expanded, and some LDs were engulfed by vacuoles. Transcriptome analysis showed that genes encoding lysophospholipid acyltransferases (LPLATs) and phospholipase A2 were significantly up-regulated following salt stress. Diacylglycerol kinase and LPLAT were identified in the proteome of salt-induced LDs, alongside vesicle trafficking and plastidial proteins and histone H2B. Analysis of fatty acid composition revealed an enrichment of C18:1 and C18:2 at the expense of C18:3 in response to salt stress. Pulse-chase experiments further suggested that variations of fatty acid composition were associated with LDs. Acetate stimulation research further confirmed a positive role of LDs in cell growth under salt stress. These results suggest that LDs play important roles in salt-stress tolerance, through harboring proteins, participating in cytoplasmic component recycling, and providing materials and enzymes for membrane modification and expansion.
Design and analysis of output feedback constraint control for antilock braking system based on Burckhardt’s model
Authors: He Youguo , Lu Chuandao , Shen Jie , Yuan Chaochun 
Published: July 2019

Purpose
The purpose of this study is to improve vehicles’ brake stability, the problem of constraint control for an antilock braking system (ABS) with asymmetric slip ratio constraints is concerned. A nonlinear control method based on barrier Lyapunov function (BLF) is proposed not only to track the optimal slip ratio but also to guarantee no violation on slip ratio constraints.

Design/methodology/approach
A quarter vehicle braking model and Burckhardt’s tire model are considered. The asymmetric BLF is introduced into the controller for solving asymmetric slip ratio constraint problems.

Findings
The proposed controller can implement ABS zero steady-state error tracking of the optimal wheel slip ratio and make slip ratio constraints flexible for various runway surfaces and runway transitions. Simulation and experimental results show that the control scheme can guarantee no violation on slip ratio constraints and avoid self-locking.

Originality/value
The slip rate equation with uncertainties is established, and BLF is introduced into the design process of the constrained controller to realize the slip rate constrained control.
Legitimacy theory
Authors: Deegan Craig Michael 
Published: July 2019

Purpose
The purpose of this paper is to reflect upon the contributions made to the social and environmental accounting literature by papers that comprised a 2002 Special Issue of Accounting, Auditing and Accountability Journal (AAAJ) entitled social and environmental reporting and its role in maintaining or creating organisational legitimacy. This paper will also provide insights into the origins of legitimacy theory as used in the social and environmental accounting literature as well as providing reflections about the strengths, and shortcomings, of the theory. Suggestions are made with respect to the ongoing application, and development, of legitimacy theory.

Design/methodology/approach
As a commentary, this paper utilises a review of the social and environmental accounting and institutional literature across a number of decades to reveal insights about the development and use of legitimacy theory as a basis to explain social and environmental reporting practices. Citation data are also used to indicate the potential impact that the papers in the 2002 Special Issue had upon subsequent research.

Findings
This commentary shows that the 2002 Special Issue is the most highly cited issue in the history of AAAJ. It also shows that individually, some of the papers in the Special Issue represent some of the most highly cited papers in the social and environmental accounting literature. The commentary provides arguments to suggest that the development of legitimacy theory is in need of further refinement, and suggests a way in which this refinement might take place.

Research limitations/implications
This paper is largely based on the opinions of one researcher, and the evidence presented in the paper is selected on the basis that it is deemed sufficient to support the opinions being projected. The paper also relies on citation data as an indicator of “impact”. The implication of the research is that it identifies a “way forward” for the development of theory applicable to the understanding of organisational social and environmental reporting practices.

Originality/value
The study provides evidence to show that the 2002 Special Issue was significant within the context of AAAJ, and also within the context of the evolution of the social and environmental accounting literature. The description of the history of the development of legitimacy theory, and of the theory’s subsequent application, provides a solid impetus for future refinements to the theory.
Corrosion behavior of N80 steel in CO2-saturated formation water
Authors: Qiu Zhichao , Xiong Chunming , Ye Zhengrong , Zhou Xiang , Wang Rui , Lin Xueqiang , Sui Pengfei 
Published: July 2019

Purpose
This paper aims to explore the influence of CO2 partial pressure, flow rate and water cut on N80 steel corrosion behaviors in the displacement process of oil in glutenite reservoir by CO2 injection.

Design/methodology/approach
A self-made 3 L high-temperature and high-pressure autoclave was used to conduct corrosion simulation experiments of N80 steel in different CO2 partial pressures, flow rates and water cut (the independently developed oil and water mixing approach can ensure the uniform mixing of oil and water in experiments). Techniques like weight loss and surface analysis were used to analyze the corrosion behaviors of N80 steel under different conditions.

Findings
Results showed that the average corrosion rate of N80 steel accelerated at varying degrees with the increase of CO2 partial pressure, flow rate and water cut. Excluding that the samples showed uniform corrosion under the two conditions of 0.5MPa CO2 partial pressure and static corrosion, they displayed mesa attack corrosion under other conditions. Besides, with the increase of CO2 partial pressure, the pH value of solution dropped and the matrix corrosion speed rose, hence leading to the increased Fe2+ and CO32− concentration. Meanwhile, a lowered pH value improved the FeCO3 critical supersaturation, thereby leading to an increased nucleation rate/growth rate and ultimately causing the decrease of the dimension of FeCO3 crystallites formed on the surface of the samples.

Originality/value
The results can be helpful in targeted anti-corrosion measures for CO2/oil/water corrosive environment.