bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germinal center responses to complex antigens
Authors: Finney Joel , Yeh Chen‐Hao , Kelsoe Garnett , Kuraoka Masayuki 
Published: June 2018

SummaryGerminal centers (GCs) are the primary sites of antibody affinity maturation, sites where B‐cell antigen‐receptor (BCR) genes rapidly acquire mutations and are selected for increasing affinity for antigen. This process of hypermutation and affinity‐driven selection results in the clonal expansion of B cells expressing mutated BCRs and acts to hone the antibody repertoire for greater avidity and specificity. Remarkably, whereas the process of affinity maturation has been confirmed in a number of laboratories, models for how affinity maturation in GCs operates are largely from studies of genetically restricted B‐cell populations competing for a single hapten epitope. Much less is known about GC responses to complex antigens, which involve both inter‐ and intraclonal competition for many epitopes. In this review, we (i) compare current methods for analysis of the GC B‐cell repertoire, (ii) describe recent studies of GC population dynamics in response to complex antigens, discussing how the observed repertoire changes support or depart from the standard model of clonal selection, and (iii) speculate on the nature and potential importance of the large fraction of GC B cells that do not appear to interact with native antigen.
iReceptor: A platform for querying and analyzing antibody/B‐cell and T‐cell receptor repertoire data across federated repositories
Authors: Corrie Brian D. , Marthandan Nishanth , Zimonja Bojan , Jaglale Jerome , Zhou Yang , Barr Emily , Knoetze Nicole , Breden Frances M. W. , Christley Scott , Scott Jamie K. , Cowell Lindsay G. , Breden Felix 
Published: June 2018

SummaryNext‐generation sequencing allows the characterization of the adaptive immune receptor repertoire (AIRR) in exquisite detail. These large‐scale AIRR‐seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune and infectious disease, and monitoring novel therapeutics against cancer. However, at present there is no easy way to compare these AIRR‐seq data sets across studies and institutions. The ability to combine and compare information for different disease conditions will greatly enhance the value of AIRR‐seq data for improving biomedical research and patient care. The iReceptor Data Integration Platform (gateway.ireceptor.org) provides one implementation of the AIRR Data Commons envisioned by the AIRR Community (airr‐community.org), an initiative that is developing protocols to facilitate sharing and comparing AIRR‐seq data. The iReceptor Scientific Gateway links distributed (federated) AIRR‐seq repositories, allowing sequence searches or metadata queries across multiple studies at multiple institutions, returning sets of sequences fulfilling specific criteria. We present a review of the development of iReceptor, and how it fits in with the general trend toward sharing genomic and health data, and the development of standards for describing and reporting AIRR‐seq data. Researchers interested in integrating their repositories of AIRR‐seq data into the iReceptor Platform are invited to contact support@ireceptor.org.
How infrastructures anchor open entrepreneurship: The case of Bitcoin and stigma
Authors: Ingram Bogusz Claire , Morisse Marcel 
Published: June 2018

AbstractThis paper delves into the question: How does an entrepreneur commercialising an open source technology (an “open entrepreneur”) respond when an underlying infrastructure that is maintained by a distributed and heterogeneous community become stigmatised, particularly when the source of the stigma is unclear? Research has found that, when faced with stigma, the most effective and robust strategy for established nondigital firms is to try to and create a distance from it. Open entrepreneurs with different ideologies would likely benefit from similar actions; however, the interdependencies created when they rely upon a digital infrastructure may make this strategy impossible. Given the tensions between ideological heterogeneity and a shared infrastructure, how—and why—do open entrepreneurs respond to stigma? This paper extends existing literature on stigma by developing a model of ideologically mediated responses to stigma by open entrepreneurs through an inductive study based upon interviews, archival, and forum data. We further contribute to extant literature on open entrepreneurship by proposing a model of ideologically mediated responses to stigma, which is grounded in group identity theory. We also build on digital infrastructure literature by proposing the concept of digital infrastructure anchoring. Lastly, we show how ideological heterogeneity leads to business model heterogeneity among open entrepreneurs and discuss the practical implications of this research.
OsPKpα1 encodes a plastidic pyruvate kinase that affects starch biosynthesis in the rice endosperm
Authors: Cai Yue , Zhang Wenwei , Jin Jie , Yang Xiaoming , You Xiaoman , Yan Haigang , Wang Liang , Chen Jie , Xu Jiahuan , Chen Weiwei , Chen Xingang , Ma Jing , Tang Xiaojie , Kong Fei , Zhu Xiaopin , Wang Guoxiang , Jiang Ling , Terzaghi William , Wang Chunming , Wan Jianmin 
Published: June 2018

AbstractPyruvate kinase (PK) is a key enzyme in glycolysis and carbon metabolism. Here, we isolated a rice (Oryza sativa) mutant, w59, with a white‐core floury endosperm. Map‐based cloning of w59 identified a mutation in OsPKpα1, which encodes a plastidic isoform of PK (PKp). OsPKpα1 localizes to the amyloplast stroma in the developing endosperm, and the mutation of OsPKpα1 in w59 decreases the plastidic PK activity, resulting in dramatic changes to the lipid biosynthesis in seeds. The w59 grains were also characterized by a marked decrease in starch content. Consistent with a decrease in number and size of the w59 amyloplasts, large empty spaces were observed in the central region of the w59 endosperm, at the early grain‐filling stage. Moreover, a phylogenetic analysis revealed four potential rice isoforms of OsPKp. We validated the in vitro PK activity of these OsPKps through reconstituting active PKp complexes derived from inactive individual OsPKps, revealing the heteromeric structure of rice PKps, which was further confirmed using a protein–protein interaction analysis. These findings suggest a functional connection between lipid and starch synthesis in rice endosperm amyloplasts.
Genome‐wide screening of long non‐coding RNAs involved in rubber biosynthesis in Eucommia ulmoides
Authors: Liu Huimin , Lu Yan , Wang Juan , Hu Jingjing , Wuyun Tana 
Published: June 2018

AbstractIncreasing evidence indicates that long non‐coding RNAs (lncRNAs) play pivotal roles in regulatory networks controlling plant and animal gene expression. However, lncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber (Eu‐rubber), are currently unknown. Here, we report on RNA deep‐sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,103 lncRNAs and 9,048 transcripts of uncertain coding potential (TUCPs) were identified. Two differentially expressed (DE) TUCPs appear to simultaneously regulate 12 protein‐coding genes involved in Eu‐rubber biosynthesis (GIEBs), as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu‐rubber is synthesized. A model is proposed in which “commanders” (DE TUCPs) direct the “builders” (DE genes) to construct a “storehouse” of materials needed for Eu‐rubber synthesis, and the “workers” (GIEBs) to synthesize Eu‐rubber. These findings provide insights into both cis‐ and trans‐polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.
Modulation of synaptic inputs in magnocellular neurones in a rat model of cancer cachexia
Authors: Yokoyama Toru , Terawaki Kiyoshi , Minami Kouichiro , Miyano Kanako , Nonaka Miki , Uzu Miaki , Kashiwase Yohei , Yanagihara Kazuyoshi , Ueta Yoichi , Uezono Yasuhito 
Published: June 2018

In cancer cachexia, abnormal metabolism and neuroendocrine dysfunction cause anorexia, tissue damage and atrophy, which can in turn alter body fluid balance. Arginine vasopressin, which regulates fluid homeostasis, is secreted by magnocellular neurosecretory cells (MNCs) of the hypothalamic supraoptic nucleus. Arginine vasopressin secretion by MNCs is regulated by both excitatory and inhibitory synaptic activity, alterations in plasma osmolarity and various peptides, including angiotensin II. In the present study, we used whole‐cell patch‐clamp recordings of brain slices to determine whether hyperosmotic stimulation and/or angiotensin II potentiate excitatory synaptic input in a rat model of cancer cachexia, similar to their effects in normal (control) rats. Hyperosmotic (15 and 60 mmol L‐1 mannitol) stimulation and angiotensin II (0.1 μmol L‐1) increased the frequency, but not the amplitude, of miniature excitatory postsynaptic currents in normal rats; in model rats, both effects were significantly attenuated. These results suggest that cancer cachexia alters supraoptic MNC sensitivity to osmotic and angiotensin II stimulation.
The price of journeying towards the prize—Commencing nursing students' experiences of working and studying: A qualitative study
Authors: Salamonson Yenna , Priddis Holly , Woodmass Joel M , Everett Bronwyn , Lynch Joan , Curtis Elizabeth , Ramjan Lucie M 
Published: June 2018

AbstractAims and objectivesTo explore the experiences of commencing first‐year undergraduate nursing students who were studying full time while engaging in 20 or more hours of paid work each week.MethodUsing a qualitative exploratory design, commencing full‐time nursing students who were employed in paid work for at least 20 hr per week were interviewed between May–June 2016. Data were thematically analysed using the following approach: data familiarisation, generating initial codes independently, searching and reviewing themes and subthemes, and defining and naming these themes and subthemes.ResultsFour main themes were identified which illustrated students' experiences of working and studying: (a) “Work is a necessity…not a choice” identified how students relied heavily on the financial income from paid work to support themselves and others during their studies, (b) “Something's got to give” highlighted the sacrifices that needed to be made to avoid negative effects on their studies, (c) “It's a balancing act!” demonstrated how students studied strategically and balanced their workload despite challenges, and lastly (d) “Being supported to work and study” described the overwhelming support from others for students to succeed academically.ConclusionsDespite support, working 20 hr or more per week while studying full time often overwhelmed students' personal resources and negatively impacted on course grades. Inflexible University timetables compounded the challenges experienced by students who struggled to balance work and study commitments.Relevance to clinical practiceNursing employers play a pivotal role in enabling students to juggle effectively their work‐study commitments, through providing work flexibility. Students may also benefit if the nursing workforce advocates that they be awarded exclusion from selected clinical placement requirements, particularly if the clinical placement focus is closely related to their current nursing employment.
Evaluation of three pain assessment scales used for ventilated neonates
Authors: Huang Xiao‐Zhi , Li Li , Zhou Jun , He Fang , Zhong Chun‐Xia , Wang Bin 
Published: June 2018

Aims and objectivesTo compare and evaluate the reliability, validity, feasibility, clinical utility, and nurses’ preference of the Premature Infant Pain Profile‐Revised, the Neonatal Pain, Agitation, and Sedation Scale, and the Neonatal Infant Acute Pain Assessment Scale used for procedural pain in ventilated neonates.BackgroundProcedural pain is a common phenomenon but is undermanaged and underassessed in hospitalised neonates. Information for clinician selecting pain measurements to improve neonatal care and outcomes is still limited.DesignA prospective observational study was used.MethodsA total of 1,080 pain assessments were made at 90 neonates by two nurses independently, using three scales viewing three phases of videotaped painful (arterial blood sampling) and nonpainful procedures (diaper change). Internal consistency, inter‐rater reliability, discriminant validity, concurrent validity and convergent validity of scales were analysed. Feasibility, clinical utility and nurses’ preference of scales were also investigated.ResultsAll three scales showed excellent inter‐rater coefficients (from 0.991–0.992) and good internal consistency (0.733 for the Premature Infant Pain Profile‐Revised, 0.837 for the Neonatal Pain, Agitation, and Sedation Scale and 0.836 for the Neonatal Infant Acute Pain Assessment Scale, respectively). Scores of painful and nonpainful procedures on the three scales changed significantly across the phases. There was a strong correlation between the three scales with adequate limits of agreement. The mean scores of the Neonatal Pain, Agitation, and Sedation Scale for feasibility and utility were significantly higher than those of the Neonatal Infant Acute Pain Assessment Scale, but not significantly higher than those of the Premature Infant Pain Profile‐Revised. The Neonatal Pain, Agitation, and Sedation Scale was mostly preferred by 55.9% of the nurses, followed by the Neonatal Infant Acute Pain Assessment Scale (23.5%) and the Premature Infant Pain Profile‐Revised (20.6%).ConclusionsThe three scales are all reliable and valid, but the Neonatal Pain, Agitation, and Sedation Scale and the Neonatal Infant Acute Pain Assessment Scale perform better in reliability. The Neonatal Pain, Agitation, and Sedation Scale appears to be a better choice for frontier nurses to assess procedural pain in ventilated neonates based on its good feasibility, utility and nurses’ preference.Relevance to clinical practiceChoosing a valid, reliable, feasible and practical measurement is the key step for better management of procedural pain for ventilated newborns. Using the right and suitable tool is helpful to accurately identify pain, ultimately improve the neonatal care and outcomes.
Characteristics of interruptions during medication administration: An integrative review of direct observational studies
Authors: Schroers Ginger 
Published: June 2018

Aims and objectivesTo synthesise and summarise data gathered by direct observation of the characteristics of interruptions in the context of nursing medication administration (MA) in hospital settings.BackgroundInterruptions are prevalent during the MA process performed by nurses in hospital settings and have been found to be associated with an increase in frequency and severity of nursing MA errors. In addition, interruptions decrease task efficiency, leading to longer MA completion times.DesignIntegrative review.MethodsThe electronic databases Cumulative Index to Nursing and Allied Health Literature (CINAHL), PubMed, PsycARTICLES and Google Scholar were searched using the terms “interruptions” AND “medication administration” AND “direct observation.” Nine articles met the inclusion criteria.ResultsInterruptions are likely to occur at least once during nursing MA processes in hospital settings. This finding applies to medication administered to one patient, termed a medication pass, and medication administered to multiple patients, termed a medication round. Interruptions are most commonly caused by another nurse or staff member or are self‐initiated, and last approximately 1 min in length.ConclusionsA raised awareness among staff of the most common sources of interruptions may encourage changes that lead to a decrease in the occurrence of interruptions. In addition, nurse leaders can apply an understanding of the common characteristics of interruptions to guide research, policies and educational methods aimed at interruption management strategies.Relevance to clinical practiceThe findings from this review can be used to guide the identification and development of targeted interventions and strategies that would have the most substantial impact to reduce and manage interruptions during MA. Interruption management strategies have the potential to lead to a decrease in medication errors and an increase in task efficiency.
Paediatric cardiopulmonary resuscitation: Knowledge and perceptions of surf lifeguards
Authors: Webber Jonathon , Moran Kevin , Cumin David 
Published: June 2018

AimTo conduct a comprehensive analysis of surf lifeguards' real and perceived ability in paediatric cardiopulmonary resuscitation (CPR), knowledge of child resuscitation protocols and technical competency during a simulated CPR scenario.MethodsSurf lifeguards aged 16 years and over were invited to complete a written survey and simulated test of five cycles of single‐rescuer CPR on a paediatric manikin. In accordance with the latest Australia and New Zealand Committee on Resuscitation (ANZCOR) guidelines, practical skills were assessed by trained observers. A manikin fitted with electronic data‐collection capability recorded technical compression and ventilation skills.ResultsA total of 244 participants were entered into the study. Most previous CPR training did not include a paediatric component (53%). Lifeguards rated their ability to perform CPR on an adult as ‘highly effective’ or ‘effective’ in 56% of responses. Less than a quarter (23%), however, gave this response when compared to a child. Observed CPR skills were mostly compliant with ANZCOR guidelines (80–99%). Manikin data provided a median compression rate of 115.6 min−1, compression depth of 3.7 cm and tidal volume of 220.0 mL. Almost half of ventilations were too little (45%), and around one fifth were too much (22%).ConclusionsSurf lifeguards are less confident in paediatric CPR. The overall performance of observed and technical CPR skills, which were mostly ANZCOR guideline compliant, suggests that performance could be improved if paediatric‐specific training is provided to supplement the adult‐focused methods currently in use. The use of electronic feedback manikins is recommended to address the technical compression and ventilation issues identified in this study.
Diversity of fungal latent pathogens and true endophytes associated with fruit trees in Uruguay
Authors: Sessa Lucía , Abreo Eduardo , Lupo Sandra 
Published: June 2018

AbstractWe have explored the fungal diversity in asymptomatic twigs of apple, peach, pear and blueberry trees, with the objective of discerning between true endophytes and latent pathogens. Several fungal genera containing known bark pathogens were found. Seven Diaporthe species—D. oxe, D. infecunda, D. serafiniae, D. phaseolorum, D. terebinthifolii, D. foeniculina and D. brasiliensis—were identified, along with Botryosphaeria dothidea, Neofusicoccum parvum, Neofusicoccum australe, Cytospora sp., Cytospora acaciae and Pestalotiopsis spp. A pathogenicity trial was undertaken to determine the role of these species on apple, pear, blueberry and peach shoots. Diaporthe brasiliensis, D. foeniculina, Diaporthe inconspicua, D. terebinthifolii, Diaporthe sp.1, Cytospora‐like isolates and Pestalotiopsis spp. isolates produced no lesions on inoculated shoots, suggesting that they could be considered true endophytes on their respective hosts. Meanwhile, some of the isolates of Diaporthe—D. oxe, Diaporthe sp.2, D. infecunda and D. serafiniae, B. dothidea, N. parvum and N. australe could be regarded as latent pathogens in their respective hosts as they produced sunken cankers and necrosis on inoculated shoots. These results demonstrate that apple, pear, blueberry and peach healthy shoots can host many known endophytic fungi along with potential wood disease‐causing fungi that should be regarded as latent pathogens.
Comparison of temperature effects on the in vitro growth and disease development in potato tubers inoculated with bacteria Pectobacterium atrosepticum, P carotovorum subsp. carotovorum and Dickeya solani
Authors: Lebecka Renata , Flis Bogdan , Murawska Zofia 
Published: June 2018

AbstractThe relationship between the rate of in vitro growth of bacterial isolates of Pectobacterium atrosepticum, P. carotovorum subsp. carotovorum and Dickeya solani and their pathogenicity was investigated in tubers of two potato cultivars at four temperatures ranging from 18°C to 30°C. The rate of in vitro growth was highly positively correlated with the number of rotted tubers (r ranged from 0.91 to 0.93) and with the weight of macerated potato tissue, which, however, was only found for P. carotovorum and D. solani (r = 0.76; r = 0.91, respectively) and not for P. atrosepticum. The weight of macerated tissue increased with the temperature, but significant differences between species of bacteria were observed only at 26°C and above, at which temperatures D. solani was the most aggressive, followed by P. carotovorum and P. atrosepticum. Almost all potato tubers inoculated with bacteria showed symptoms of soft rot at 26°C and 30°C, but the number of rotting tubers at lower temperatures (22°C and 18°C) decreased significantly. The lowest disease incidence, 11% of tubers with symptoms, was observed for the D. solani and cultivar Sonda at 18°C, what was also confirmed in a separate experiment with tubers from four potato cultivars inoculated with the highly aggressive isolate of D. solani. At temperatures from 18°C to 30°C, the differences in disease severity between potato cultivars with various resistance to bacteria increased in line with temperature, while the differences in disease incidence decreased.
Flavonoids of Artocarpus heterophyllus Lam. heartwood inhibit the innate immune responses of human phagocytes
Authors: Septama Abdi Wira , Jantan Ibrahim , Panichayupakaranant Pharkphoom 
Published: June 2018

Abstract

Objectives
To investigate the effects of flavonoids isolated from Artocarpus heterophyllus. heartwood on chemotaxis, phagocytosis, reactive oxygen species (ROS) production and myeloperoxidase (MPO) activity of human phagocytes.

Methods
Chemotaxis was evaluated using a modified Boyden chamber and phagocytosis was determined by flowcytometer. Respiratory burst was investigated by luminol-based chemiluminescence assay while MPO activity was determined by colorimetric assay.

Key findings
Artocarpanone and artocarpin strongly inhibited all steps of phagocytosis. Artocarpanone and artocarpin showed strong chemotactic activity with IC50 values of 6.96 and 6.10 μm, respectively, which were lower than that of ibuprofen (7.37 μm). Artocarpanone was the most potent compound in inhibiting ROS production of polymorphonuclear leucocytes and monocytes with IC50 values comparable to those of aspirin. Artocarpin at 100 μg/ml inhibited phagocytosis of opsonized bacteria (28.3%). It also strongly inhibited MPO release with an IC50 value (23.3 μm) lower than that of indomethacin (69 μm). Structure–activity analysis indicated that the number of hydroxyl group, the presence of prenyl group and variation of C-2 and C-3 bonds might contribute towards their phagocytosis.

Conclusions
Artocarpanone and artocarpin were able to suppress strongly the phagocytosis of human phagocytes at different steps and have potential to be developed into potent anti-inflammatory agents.