bluuebunny/crossref_metadata_2025_split huggingface dataset:
B cell Compartmentalization in Blood and Cerebrospinal Fluid of HIV-Infected Ugandans with Cryptococcal Meningitis
Authors: Okurut Samuel , Meya David B. , Bwanga Freddie , Olobo Joseph , Eller Michael A. , Cham-Jallow Fatim , Bohjanen Paul R. , Pratap Harsh , Palmer Brent E. , Hullsiek Katharine H. , Manabe Yukari C. , Boulware David R. , Janoff Edward N. 
Published: September 2019

AbstractBackgroundActivated B cells modulate infection by differentiating into pathogen-specific antibody-producing effector plasmablasts/plasma cells, memory cells and immune regulatory B cells. In this context, the B cell phenotypes that infiltrate the central nervous system during HIV and cryptococcal meningitis co-infection are ill defined.MethodsWe characterized clinical parameters, mortality and B cell phenotypes in blood and CSF by flow cytometry in HIV-infected adults with cryptococcal (n=31), and non-cryptococcal meningitis (n=12), and heathy control subjects with neither infection (n=10).ResultsActivation of circulating B cells (CD21low) was significantly higher in blood of subjects with HIV infection compared with healthy controls, and greater yet in matched CSF B cells (p<0.001). Among B cell subsets, elevated frequencies of memory and plasmablasts/plasma cells most clearly distinguished the CSF from blood compartments. With cryptococcal meningitis, lower frequencies of expression of the regulatory protein PD-1 on plasmablasts/plasma cells in blood (median 7%) at presentation was associated with significantly decreased 28-day survival (29% (4/14 subjects)), whereas higher PD-1 expression (median 46%) characterized subjects with higher survival (88% (14/16 subjects)).ConclusionWith HIV infection, B cell differentiation and regulatory markers are discrete elements of the circulating and CSF compartments with clinical implications for cryptococcal disease outcome, potentially due to their effects on the fungus and other local immune cells.
Parameter fitting using time-scale analysis for vector-borne diseases with spatial dynamics
Authors: Sartori Larissa M. , Pereira Marcone C. , Oliva Sergio M. 
Published: September 2019

AbstractVector-borne diseases are becoming increasingly widespread in a growing number of countries and it has the potential to invade new areas and habitats, either associated to changes in vectors habitats, human circulation or climate changes. From the dynamical point of view, the spatial-temporal interaction of models that try to adjust to such events are rich and challenging. The first challenges are to address the dynamics of the vectors (very fast and local) and the dynamics of humans (very heterogeneous and non-local). The objective of the present paper is to use the well-known Ross-Macdonald models, incorporating spatial movements, identifying different times scales and estimate in a suitable way the parameters. We will concentrate in a practical example, a simplified space model, and apply to Dengue’s spread in the state of Rio de Janeiro, Brazil.
Tuber yield and processing quality response of French fried potatoes to nitrogen fertilization
Authors: Jiang Lili , Wang Ziquan , Jin Guanghui , Zhang Guizhi , Zhang Chunyu 
Published: September 2019

AbstractNitrogen (N) is an important factor that influences potato production; appropriate N fertilizer management can optimize tuber yield and quality and thus reduce the risk of environmental N losses. The present study aimed to evaluate the effects of different nitrogen (N) application rates (0, 75, 150, 225, 300, and 375 kg ha−1) on the total tuber yield, marketable yield, dry matter content, reducing sugar content, sucrose content of tuber, and fry color index of two potato cultivars (Kennebec and Shepody) in 2016 and 2017. N supply significantly affected tuber yield and processing quality, but these effects depended on the year and/or cultivar. The results indicated that low (75 kg ha−1) and medium-N application rates (150 or 225 kg ha−1) had a positive effect on tuber yield and processing quality; however, high-N application rates (300 and 375 kg ha−1) resulted in lower yield and poor quality. Total and marketable yields responded quadratically to N, and they were optimized at 150 kg ha−1for Kennebec and 225 kg ha−1for Shepody in both the years. The processing quality of tubers also responded quadratically with increasing N application rates. The optimal range of N application was approximately 145–185.83 kg ha−1for Kennebec and approximately 93.44–288.67 kg ha−1for Shepody according to the processing quality standards of French fried potatoes in China. To achieve the goals of high yield and high quality, N application rates should be 150 kg ha−1for Kennebec and 225 kg ha−1for Shepody.
Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme
Authors: Alzamrooni Afnan , Vieira Petra Mendes , Murciano Nicoletta , Wolton Matthew , Schubert Frank R. , Robson Samuel C. , Dietrich Susanne 
Published: September 2019

AbstractThe vertebrate head mesoderm provides the heart, the great vessels, some smooth and most head skeletal muscle, in addition to parts of the skull. It has been speculated that the ability to generate cardiac and smooth muscle is the evolutionary ground-state of the tissue. However, whether indeed the entire head mesoderm has generic cardiac competence, how long this may last, and what happens as cardiac competence fades, is not clear.Bone morphogenetic proteins (Bmps) are known to promote cardiogenesis. Using 41 different marker genes in the chicken embryo, we show that the paraxial head mesoderm that normally does not engage in cardiogenesis has the ability to respond to Bmp for a long time. However, Bmp signals are interpreted differently at different time points. Up to early head fold stages, the paraxial head mesoderm is able to read Bmps as signal to engage in the cardiac programme; the ability to upregulate smooth muscle markers is retained slightly longer. Notably, as cardiac competence fades, Bmp promotes the head skeletal muscle programme instead. The switch from cardiac to skeletal muscle competence is Wnt-independent as Wnt caudalises the head mesoderm and also suppresses Msc-inducing Bmp provided by the prechordal plate, thus suppressing both the cardiac and the head skeletal muscle programmes.Our study for the first time suggests a specific transition state in the embryo when cardiac competence is replaced by skeletal muscle competence. It sets the stage to unravel the cardiac-skeletal muscle antagonism that is known to partially collapse in heart failure.Summary statementThe head mesoderm has generic cardiac competence until early head fold stages. Thereafter, cardiac competence fades in the paraxial region, and Bmp promotes head skeletal muscle programmes instead of cardiac programmes.
Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models
Authors: Scarborough Matthew J. , Hamilton Joshua J. , Erb Elizabeth A. , Donohue Timothy J. , Noguera Daniel R. 
Published: September 2019

ABSTRACTMulti-species microbial communities determine the fate of materials in the environment and can be harnessed to produce beneficial products from renewable resources. In a recent example, fermentations by microbial communities have produced medium-chain fatty acids (MCFAs). Tools to predict, assess, and improve the performance of these communities, however, are limited. To provide such tools, we constructed two metabolic models of MCFA-producing microbial communities based on available genomic, transcriptomic and metabolomic data. The first model is a unicellular model (iFermCell215), while the second model (iFermGuilds789) separates fermentation activities into functional guilds. Ethanol and lactate are fermentation products known to serve as substrates for MCFA production, while acetate is another common co-metabolite during MCFA production. Simulations with iFermCell215 predict that low molar ratios of acetate-to-ethanol favor MCFA production, whereas the products of lactate and acetate co-utilization are less dependent on the acetate-to-lactate ratio. In simulations of an MCFA-producing community fed a complex organic mixture derived from lignocellulose, iFermGuilds789 predicted that lactate was an extracellular co-metabolite that served as a substrate for butyrate (C4) production. Extracellular hexanoic (C6) and octanoic acids (C8) were predicted by iFermGuilds789 to be from community members that directly metabolize sugars. Modeling results provide several hypotheses that can improve our understanding of microbial roles in a MCFA-producing microbiome and inform strategies to increase MCFA production. Further, these models represent novel tools for exploring the role of mixed microbial communities in carbon recycling in the environment, as well as on beneficial reuse of organic residues.IMPORTANCEMicrobiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three medium-chain fatty acid-producing guilds and identified potential strategies to increase production of medium-chain fatty acids. This work demonstrates the role of metabolic models in augmenting multi-omic studies to gain greater insights into microbiome behavior.
Correlated evolution of large DNA fragments in the 3D genome of Arabidopsis thaliana
Authors: Yan Yubin , Li Zhaohong , Li Ye , Wu Zefeng , Yang Ruolin 
Published: September 2019

AbstractIn eukaryotes, the three-dimensional (3D) conformation of the genome is far from random, and this nonrandom chromatin organization is strongly correlated with gene expression and protein function, which are two critical determinants of the selective constraints and evolutionary rates of genes. However, whether genes and other elements that are located close to each other in the 3D genome evolve in a coordinated way has not been investigated in any organism. To address this question, we constructed chromatin interaction networks (CINs) in Arabidopsis thaliana based on high-throughput chromosome conformation capture (Hi-C) data and demonstrated that adjacent large DNA fragments in the CIN indeed exhibit more similar levels of polymorphism and evolutionary rates than random fragment pairs. Using simulations that account for the linear distance between fragments, we proved that the 3D chromosomal organization plays a role in the observed correlated evolution. Spatially interacting fragments also exhibit more similar mutation rates and functional constraints in both coding and noncoding regions than the random expectations, indicating that the correlated evolution between 3D neighbors is a result of combined evolutionary forces. A collection of 39 genomic and epigenomic features can explain much of the variance in genetic diversity and evolutionary rates across the genome. Moreover, features that have a greater effect on the evolution of regional sequences tend to show higher similarity between neighboring fragments in the CIN, suggesting a pivotal role of epigenetic modifications and chromatin organization in determining the correlated evolution of large DNA fragments in the 3D genome.
Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018-Impact and Lessons Learned
Authors: Zhu YanChun , O’Brien Brittany , Leach Lynn , Clark Alexandra , Bates Marian , Adams Eleanor , Ostrowsky Belinda , Quinn Monica , Dufort Elizabeth , Southwick Karen , Erazo Richard , Haley Valerie B. , Bucher Coralie , Chaturvedi Vishnu , Limberger Ronald J. , Blog Debra , Lutterloh Emily , Chaturvedi Sudha 
Published: September 2019

ABSTRACTCandida auris is a multidrug-resistant yeast which has emerged in healthcare facilities worldwide, however little is known about identification methods, patient colonization, spread, environmental survival, and drug resistance. Colonization on both biotic and abiotic surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in NY from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/non-selective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of ribosomal genes for C. auris genotyping. Results included: a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates, as well as identification of 277 clinical cases and 350 colonized cases from 151 healthcare facilities including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, c) demonstration of relatively heavier colonization of C. auris in nares compared to the axilla/groin, and d) predominance of the South Asia Clade I with intrinsic resistance to fluconazole and elevated minimum inhibitory concentration (MIC) to voriconazole (81%), amphotericin B (61%), 5-FC (3%) and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.
FRA1 modulates cortical microtubule localization of CMU proteins
Authors: Ganguly Anindya , Zhu Chuanmei , Chen Weizu , Dixit Ram 
Published: September 2019

ABSTRACTConstruction of the cell wall demands harmonized deposition of cellulose and matrix polysaccharides. Cortical microtubules orient the deposition of cellulose by guiding the trajectory of plasma membrane-embedded cellulose synthase complexes. Vesicles containing matrix polysaccharides are thought to be transported by the FRA1 kinesin to facilitate their secretion along cortical microtubules. The cortical microtubule cytoskeleton thus provides a platform to coordinate the delivery of cellulose and matrix polysaccharides, but the underlying molecular mechanisms remain unknown. Here, we show that the tail region of the FRA1 kinesin physically interacts with CMU proteins which are important for the microtubule-dependent guidance of cellulose synthase complexes. Interaction with CMUs did not affect microtubule binding or motility of the FRA1 kinesin but had an opposing effect on the cortical microtubule localization of CMU1 and CMU2 proteins, thus regulating the lateral stability of cortical microtubules. Phosphorylation of the FRA1 tail region by CKL6 inhibited binding to CMUs and consequently reversed the extent of cortical microtubule decoration by CMU1 and CMU2. Genetic experiments demonstrated the significance of this interaction to the growth and reproduction ofArabidopsis thalianaplants. We propose that modulation of CMU’s microtubule localization by FRA1 provides a mechanism to control the coordinated deposition of cellulose and matrix polysaccharides.
Does skin surface temperature variation account for Buruli ulcer lesion distribution?
Authors: Sexton-Oates Nicola K. , Stewardson Andrew J. , Yerramilli Arvind , Johnson Paul D.R. 
Published: September 2019

AbstractBackgroundBuruli ulcer is a necrotising infection of skin and soft tissue caused by Mycobacterium ulcerans (M. ulcerans). Buruli ulcer most often occurs on limbs, and it is hypothesized this is explained by direct exposure to the environment. However, even on exposed areas Buruli ulcer is not randomly distributed. M. ulcerans prefers an in vitro temperature of 30-33°C and growth is inhibited at higher temperatures. This study investigated whether variations in skin surface temperature distribution in healthy volunteers could partly account for Buruli ulcer lesion distribution.Methodology/Principal FindingsIn this observational study, a thermal camera (FLIR E8) was used to measure skin surface temperature at the sternal notch and at 44 predetermined locations on the limbs of 18 human participants. Body locations of high, middle and low Buruli ulcer incidence were identified from existing density maps of lesion distribution. Skin temperature of the three incidence location groups were compared, and differences in age and sex groups were also analysed.We found an inverse relationship between skin temperature and lesion distribution, where high incidence locations were significantly cooler and low incidence locations significantly warmer (Kruskal-Wallis test p<0.0001). Linear mixed effects regression analysis estimated that skin surface temperature accounts for 9.5% of the variance in Buruli ulcer lesion distribution (marginal R-squared = 0.095). Men had warmer upper and lower limbs than females (Mann-Whitney U test p=0.0003 and p<0.0001 respectively).Conclusions/SignificanceWe have found an inverse relationship between skin temperature and Buruli ulcer lesion distribution, however this association is weak. Additional unknown factors are likely to be involved that explain the majority of the variation in Buruli lesion distribution.Author SummaryBuruli ulcer is a destructive soft tissue infection caused by the bacterium Mycobacterium ulcerans. The precise mode of transmission remains unknown. One theory proposes that transmission occurs by direct contact with a contaminated environment. Lesions occur mostly on limbs, and it is hypothesized this is explained by direct exposure to the environment. However even on exposed areas, lesions are not randomly distributed. This study investigated whether skin surface temperature can partly explain Buruli ulcer lesion distribution. We measured the skin surface temperature of 18 healthy participants using a thermal camera and compared temperature distribution to the distribution of Buruli ulcer lesions investigated in a previously published study. We found that there is a negative correlation between skin temperature and Buruli ulcer lesion incidence. However, the association is weak and other factors e.g. clothing choice and insect biting patterns may explain the majority of Buruli ulcer lesion distribution.
An analysis of CEE equity market integration and their volatility spillover effects
Authors: Hung Ngo Thai 
Published: September 2019

PurposeThe purpose of this paper is to examine the conditional correlations and spillovers of volatilities across CEE markets, namely, Hungary, Poland, the Czech Republic, Romania and Croatia, in the post-2007 financial crisis period.Design/methodology/approachThe authors use five-dimensional GARCH-BEKK alongside with the CCC and DCC models.FindingsThe estimation results of the three models generally demonstrate that the correlations between these markets are particularly significant. Also, own-volatility spillovers are generally lower than cross-volatility spillovers for all markets.Practical implicationsThese results recommend that investors should take caution when investing in the CEE equity markets as well as diversifying their portfolios so as to minimize risk.Originality/valueUnlike the previous studies in this field, this paper is the first study using multivariate GARCH-BEKK alongside with CCC and DCC models. The study makes an outstanding contribution to the existing literature on spillover effects and conditional correlations in the CEE financial stock markets.
Human remains as documents: implications for repatriation
Authors: Berryman Jim 
Published: September 2019

Purpose
The purpose of this paper is twofold. First, to investigate the documentality of human remains in museum and research collections. Second, to provide a rationale for a processual model of documentation, which can account for their repatriation and eventual burial.

Design/methodology/approach
This paper uses a multidisciplinary approach to examine the repatriation issue. It considers an ethical argument developed to support claims for repatriation: the nominal identification of a body as a universal criterion for its burial. Based on Igor Kopytoff’s processual model of commoditisation, it looks to cultural anthropology to help explain how objects can move between a document and non-document state.

Findings
Human remains can be understood as examples of information-as-thing. However, while document theory can readily account for the expanding realm of documentation, it cannot adequately accommodate instances where documentality is revoked, and when something ceases to be a document. When a human biological specimen is returned, the process that made it serve as a document is effectively reversed. When remains are interred, they revert to their primary standing, as people. The process of becoming a document is therefore not unidirectional, and document status not permanent.

Research limitations/implications
The implications of a processual model of documentation are discussed. Such a model must be able to account for things as they move into and out of the document state, and where the characteristics of documentality change through time.

Originality/value
This paper explores problematic material not usually discussed in relation to document theory. The repatriation movement poses a challenge to a discourse predicated on documentation as a progressively expanding field.
Maturing research data services and the transformation of academic libraries
Authors: Cox Andrew M. , Kennan Mary Anne , Lyon Liz , Pinfield Stephen , Sbaffi Laura 
Published: September 2019

PurposeA major development in academic libraries in the last decade has been recognition of the need to support research data management (RDM). The purpose of this paper is to capture how library research data services (RDS) have developed and to assess the impact of this on the nature of academic libraries.Design/methodology/approachQuestionnaire responses from libraries in Australia, Canada, Germany, Ireland, the Netherlands, New Zealand, the UK and USA from 2018 are compared to a previous data set from 2014.FindingsThe evidence supports a picture of the spread of RDS, especially advisory ones. However, future ambitions do not seem to have seen much evolution. There is limited evidence of organisational change and skills shortages remain. Most service development can be explained as the extension of traditional library services to research data. Yet there remains the potential for transformational impacts, when combined with the demands implied by other new services such as around text and data mining, bibliometrics and artificial intelligence. A revised maturity model is presented that summarises typical stages of development of services, structures and skills.Research limitations/implicationsThe research models show how RDS are developing. It also reflects on the extent to which RDM represents a transformation of the role of academic libraries.Practical implicationsPractitioners working in the RDM arena can benchmark their current practices and future plans against wider patterns.Originality/valueThe study offers a clear picture of the evolution of research data services internationally and proposes a maturity model to capture typical stages of development. It contributes to the wider discussion of how the nature of academic libraries are changing.