bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240
Authors: Gohain Neelakshi , Tolbert William D. , Orlandi Chiara , Richard Jonathan , Ding Shilei , Chen Xishan , Bonsor Daniel A. , Sundberg Eric J. , Lu Wuyuan , Ray Krishanu , Finzi Andrés , Lewis George K. , Pazgier Marzena 
Published: November 2016

AbstractAntibody-dependent cell-mediated cytotoxicity (ADCC) by non-neutralizing antibodies (nnAbs) specific to the HIV envelope (Env) glycoproteins present at the surface of virus sensitized or infected cells plays a role in the effective adaptive immune response to HIV. Here, we explore the molecular basis for the epitope at the disulfide loop region (DLR) of the principal immunodominant domain of gp41, recognized by the well-known nnAb F240. Our structural studies reveal details of the F240-gp41 interface and describe a structure of DLR that is distinct from known conformations of this region studied in the context of either CD4-unliganded Env trimer or the gp41 peptide in the unbound state. These data coupled with binding and functional analyses indicate that F240 recognizes non-trimeric Env forms which are significantly overexpressed on intact virions but poorly represented at surfaces of cells infected with infectious molecular clones and endogenously-infected CD4 T cells from HIV-1-infected individuals. Furthermore, although we detect ADCC activities of F240 against cells spinoculated with intact virions, our data suggest that these activities result from F240 recognition of gp41 stumps or misfolded Env variants present on virions rather than its ability to recognize functional gp41 transition structures emerging on trimeric Env post CD4 receptor engagement.
Novel Culturing Techniques Select for Heterotrophs and Hydrocarbon Degraders in a Subantarctic Soil
Authors: van Dorst J. M. , Hince G. , Snape I. , Ferrari B. C. 
Published: November 2016

AbstractThe soil substrate membrane system (SSMS) is a novel micro-culturing technique targeted at terrestrial soil systems. We applied the SSMS to pristine and diesel fuel spiked polar soils, along with traditional solid media culturing and culture independent 454 tag pyrosequencing to elucidate the effects of diesel fuel on the soil community. The SSMS enriched for up to 76% of the total soil diversity within high diesel fuel concentration soils, in contrast to only 26% of the total diversity for the control soils. The majority of organisms originally recovered with the SSMS were lost in the transfer to solid media, with all 300 isolates belonging to Proteobacteria, Firmicutes, Actinobacteria or Bacteroidetes, the four phyla most frequently associated with soil culturing efforts. The soils spiked with high diesel fuel concentrations exhibited reduced species richness, diversity and a selection towards heterotrophs and hydrocarbon degraders in comparison to the control soils. Based on these observations and the unusually high level of overlap in microbial taxa observed between methods, we suggest the SSMS holds potential to exploit hydrocarbon degraders and other targets within simplified bacterial systems, yet is inadequate for soil ecology and ecotoxicology studies where identifying rare oligotrophic species is paramount.
Evidence for a dynamic role for mononuclear phagocytes during endometrial repair and remodelling
Authors: Cousins Fiona L. , Kirkwood Phoebe M. , Saunders Philippa T. K. , Gibson Douglas A. 
Published: November 2016

AbstractIn women, endometrial breakdown, which is experienced as menstruation, is characterised by high concentrations of inflammatory mediators and immune cells which account for ~40% of the stromal compartment during tissue shedding. These inflammatory cells are known to play a pivotal role in tissue breakdown but their contribution to the rapid scarless repair of endometrium remains poorly understood. In the current study we used a mouse model of menstruation to investigate dynamic changes in mononuclear phagocytes during endometrial repair and remodelling. Menstruation was simulated in MacGreen mice to allow visualisation of CSF1R+ mononuclear phagocytes. Immunohistochemistry revealed dynamic spatio-temporal changes in numbers and location of CSF1R-EGFP+ cells and Ly6G+ neutrophils. Flow cytometry confirmed a striking increase in numbers of GFP+ cells during repair (24 h): influxed cells were 66% F4/80+Gr-1+ and 30% F4/80−Gr-1+. Immunostaining identified distinct populations of putative ‘classical’ monocytes (GFP+F4/80−), monocyte-derived macrophages (GFP+F4/80+) and a stable population of putative tissue-resident macrophages (GFP-F4/80+) localised to areas of breakdown, repair and remodelling respectively. Collectively, these data provide the first compelling evidence to support a role for different populations of monocytes/macrophages in endometrial repair and provide the platform for future studies on the role of these cells in scarless healing.
PGE2 is a direct and robust mediator of anion/fluid secretion by human intestinal epithelial cells
Authors: Fujii Satoru , Suzuki Kohei , Kawamoto Ami , Ishibashi Fumiaki , Nakata Toru , Murano Tatsuro , Ito Go , Shimizu Hiromichi , Mizutani Tomohiro , Oshima Shigeru , Tsuchiya Kiichiro , Nakamura Tetsuya , Araki Akihiro , Ohtsuka Kazuo , Okamoto Ryuichi , Watanabe Mamoru 
Published: November 2016

AbstractIntestinal epithelial cells (IECs) play an indispensable role in maintaining body fluid balance partly through their ability to regulate anion/fluid secretion. Yet in various inflammatory gastrointestinal diseases, over-secretion of anions results in symptoms such as severe diarrhoea. Endogenous mediators, such as vasoactive intestinal peptide or prostaglandin E2 (PGE2), regulate intestinal anion/fluid secretion, but their direct effect on purified human IECs has never been described in detail. Based on a previously described intestinal organoid swelling model, we established a 3D-scanner-assisted quantification method to evaluate the anion/fluid secretory response of cultured human IECs. Among various endogenous secretagogues, we found that PGE2 had the lowest EC50 value with regard to the induction of swelling of the jejunal and colonic organoids. This PGE2-mediated swelling response was dependent on environmental Cl− concentrations as well as on several channels and transporters as shown by a series of chemical inhibitor studies. The concomitant presence of various inflammatory cytokines with PGE2 failed to modulate the PGE2-mediated organoid swelling response. Therefore, the present study features PGE2 as a direct and robust mediator of anion/fluid secretion by IECs in the human intestine.
Streptococcus pneumoniae resists intracellular killing by olfactory ensheathing cells but not by microglia
Authors: Macedo-Ramos Hugo , Ruiz-Mendoza Susana , Mariante Rafael M. , Guimarães Erick V. , Quadros-de-Souza Lucas C. , Paiva Mauricio M. , Ferreira Eliane de O. , Pinto Tatiana C. A. , Teixeira Lucia M. , Allodi Silvana , Baetas-da-Cruz Wagner 
Published: November 2016

AbstractOlfactory ensheathing cells (OECs) are a type of specialized glial cell currently considered as having a double function in the nervous system: one regenerative, and another immune. Streptococcus pneumoniae is a major agent of severe infections in humans, including meningitis. It is commonly found in the nasopharynx of asymptomatic carriers, and, under certain still unknown conditions, can invade the brain. We evaluated whether pneumococcal cells recovered from lysed OECs and microglia are able to survive by manipulating the host cell activation. An intracellular-survival assay of S. pneumoniae in OECs showed a significant number of bacterial CFU recovered after 3 h of infection. In contrast, microglia assays resulted in a reduced number of CFU. Electron-microscopy analysis revealed a large number of pneumococci with apparently intact morphology. However, microglia cells showed endocytic vesicles containing only bacterial cell debris. Infection of OEC cultures resulted in continuous NF-κB activation. The IFN-γ-induced increase of iNOS expression was reversed in infected OECs. OECs are susceptible to S. pneumoniae infection, which can suppress their cytotoxic mechanisms in order to survive. We suggest that, in contrast to microglia, OECs might serve as safe targets for pneumococci, providing a more stable environment for evasion of the immune system.
The Evolution of Material Signification: Tracing the Origins of Symbolic Body Ornamentation through a Pragmatic and Enactive Theory of Cognitive Semiotics
Authors: Iliopoulos Antonis 
Published: November 2016

AbstractPrehistoric archaeologists generally treat early body ornaments, such as the Blombos shell beads, as inherently symbolic artefacts that were created by symbolically capable brains. Essentially, they treat material signs in strictly linguistic terms and view them as the epiphenomenal products of internal representations that were used as templates. Yet material signification is neither inherently symbolic, nor the a priori product of innate neural structures. We must thus opt for a pragmatic semiotic theory that can describe the physical qualities and relations of material signs, and an enactive theory of cognition that can explain the anchoring of novel concepts to the material world. In synergistically fusing these strands, this article puts forth a pragmatic and enactive theory of cognitive semiotics. By applying this evolutionary epistemology to the case of early body ornamentation, this study traces the prehistoric process of semiotic scaffolding that eventually led to development of symbolic artefacts and practices.
Energetic particle driven geodesic acoustic mode in a toroidally rotating tokamak plasma
Authors: Ren Haijun 
Published: November 2016

Abstract
Energetic particle (EP) driven geodesic acoustic modes (EGAMs) in toroidally rotating tokamak plasmas are analytically investigated using the hybrid kinetic-fluid model and gyrokinetic equations. By ignoring high-order terms and ion Landau damping, the kinetic dispersion relation is reduced to the hybrid one in the large safety factor limit. There is one high-frequency branch with a frequency larger than

ω

t
0

, the transit frequency of EPs with initial energy, which is always stable. Two low-frequency solutions with a frequency smaller than

ω

t
0

are complex conjugates in the hybrid limit. In the presence of ion Landau damping, the growth rate of the unstable branch is decreased and the damping rate of the damped branch is increased. The toroidal Mach number is shown to increase

Ω

r

, the normalized real frequency of both branches. Although not affecting the instability critical condition, the Mach number decreases the growth rate when

Ω

r

is larger than a critical value

Ω

r

c
r
i

and enlarges the growth rate when

Ω

r

<

Ω

r

c
r
i

. The ion Landau damping effect is negligible for large M. But the discrepancy between the kinetic dispersion relation and the hybrid one becomes ignorable only for

q
≳
7

.
Determining the prediction limits of models and classifiers with applications for disruption prediction in JET
Authors: Murari A. , Peluso E. , Vega J. , Gelfusa M. , Lungaroni M. , Gaudio P. , Martínez F. J. 
Published: November 2016

Abstract
Understanding the many aspects of tokamak physics requires the development of quite sophisticated models. Moreover, in the operation of the devices, prediction of the future evolution of discharges can be of crucial importance, particularly in the case of the prediction of disruptions, which can cause serious damage to various parts of the machine. The determination of the limits of predictability is therefore an important issue for modelling, classifying and forecasting. In all these cases, once a certain level of performance has been reached, the question typically arises as to whether all the information available in the data has been exploited, or whether there are still margins for improvement of the tools being developed. In this paper, a theoretical information approach is proposed to address this issue. The excellent properties of the developed indicator, called the prediction factor (PF), have been proved with the help of a series of numerical tests. Its application to some typical behaviour relating to macroscopic instabilities in tokamaks has shown very positive results. The prediction factor has also been used to assess the performance of disruption predictors running in real time in the JET system, including the one systematically deployed in the feedback loop for mitigation purposes. The main conclusion is that the most advanced predictors basically exploit all the information contained in the locked mode signal on which they are based. Therefore, qualitative improvements in disruption prediction performance in JET would need the processing of additional signals, probably profiles.
The effects of a high-intensity functional exercise group on clinical outcomes in hospitalised older adults: an assessor-blinded, randomised-controlled trial
Authors: Raymond Melissa J. M. , Jeffs Kimberley J. , Winter Adele , Soh Sze-Ee , Hunter Peter , Holland Anne E. 
Published: November 2016

AbstractObjectiveto investigate a high-intensity functional exercise (HIFE) group in hospitalised older adults.Designassessor-blinded, randomised-controlled trial.Settingsub-acute wards at a metropolitan rehabilitation hospital.Participantsolder adults ≥65 years (n = 468) able to stand with minimum assistance or less from a chair and follow instructions.Intervention‘group’ participants were offered a standing HIFE group three times a week and individual physiotherapy sessions twice a week. Control participants were offered daily individual physiotherapy sessions.Main outcome measuresthe primary outcome measure was the Elderly Mobility Scale (EMS). Secondary measures included the Berg Balance Scale, gait speed, Timed Up and Go Test, falls, length of stay and discharge destination.Resultsparticipants’ mean age was 84.3 (7.1) years and 61% were female. There was no difference between groups for the improvement in EMS from admission to discharge (effect size −0.07, 95% confidence interval: −0.26 to 0.11, P = 0.446) and no difference in discharge destination, P = 0.904. Therapists saved 31–205 min/week treating group participants compared with control participants.Conclusionthe results suggest that a HIFE group programme combined with individual physiotherapy may improve mobility to a similar extent to individual physiotherapy alone in hospitalised older adults. Providing physiotherapy in a group setting resulted in increased therapist efficiency. A high-intensity exercise group with individual physiotherapy may be an effective and efficient method to provide care to older inpatients.
Immunoreceptor CD300a on mast cells and dendritic cells regulates neutrophil recruitment in a murine model of sepsis
Authors: Udayanga Kankanam Gamage Sanath , Nakamura Yoshiyuki , Nakahashi-Oda Chigusa , Shibuya Akira 
Published: November 2016

Abstract
Sepsis is a life-threatening syndrome caused by abnormal host immune responses against bacterial infection. Although innate immune cells are known to be important in the pathogenesis of sepsis, how their activation is regulated during sepsis remains incompletely understood. Here, we examined the role of the inhibitory immunoreceptor CD300a, which is expressed on various types of myeloid cells, in the pathogenesis of sepsis induced by cecal ligation and puncture (CLP). To this end, we used mice in which CD300a was specifically deleted on mast cells (MCs; Cd300afl/flMcpt5-Cre), dendritic cells (DCs; Cd300afl/flItgax-Cre), or macrophages and neutrophils (Cd300afl/flLyz2-Cre). We show that mice with CD300a-deleted MCs or DCs but not macrophages survived significantly longer than did control Cd300afl/fl mice. In addition, whereas neutrophil recruitment into the peritoneal cavity was increased within 1 h after CLP in mice with CD300a-deleted MCs, peritoneal neutrophils did not increase in number until the 12 h time point in mice with CD300a-deficient DCs. These results indicate that CD300a on MCs and DCs regulates neutrophil recruitment into the peritoneal cavity after CLP.
Genomic and Transcriptomic Resources for Marker Development inSynchytrium endobioticum, an Elusive but Severe Potato Pathogen
Authors: Busse Friederike , Bartkiewicz Annette , Terefe-Ayana Diro , Niepold Frank , Schleusner Yvonne , Flath Kerstin , Sommerfeldt-Impe Nicole , Lübeck Jens , Strahwald Josef , Tacke Eckhard , Hofferbert Hans-Reinhard , Linde Marcus , Przetakiewicz Jarosław , Debener Thomas 
Published: November 2016

Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host–pathogen interactions in this difficult pathosystem.[Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Epidemiology of Isolated Versus Nonisolated Mild Traumatic Brain Injury Treated in Emergency Departments in the United States, 2006-2012: Sociodemographic Characteristics
Authors: Cancelliere Carol , Coronado Victor G. , Taylor Christopher A. , Xu Likang 
Published: November 2016

Objectives:
To describe the frequencies and rates of mild traumatic brain injury (mTBI) emergency department (ED) visits, analyze the trend across the years, and compare sociodemographic characteristics of visits by mTBI type (ie, mTBI as the only injury, or present along with other injuries).

Design:
Population-based descriptive study using data from the Nationwide Emergency Department Sample (2006-2012).

Methods:
Joinpoint regression was used to calculate the average annual percent changes of mTBI incidence rates. Characteristics between isolated and nonisolated visits were compared, and the odds ratios were reported.

Results:
The rate per 100 000 population of mTBI ED visits in the United States increased significantly from 569.4 (in 2006) to 807.9 (in 2012). The highest rates were observed in 0- to 4-year-olds, followed by male 15- to 24-year-olds and females 65 years and older; the lowest rates were among 45- to 64-year-olds. The majority (70%) of all visits were nonisolated and occurred more frequently in residents of metropolitan areas. Falls were the leading external cause. Most visits were privately insured or covered by Medicare/Medicaid, and the injury occurred on weekdays in predominantly metropolitan hospitals in the South region.

Conclusions:
The burden of mTBI in US EDs is high. Most mTBI ED visits present with other injuries. Awareness of sociodemographic factors associated with nonisolated mTBI may help improve diagnosis in US EDs. This information has implications for resource planning and mTBI screening in EDs.
P300 Event-Related Potentials Differentiate Better Performing Individuals With Traumatic Brain Injury: A Preliminary Study of Semantic Processing
Authors: Davis Tara M. , Hill Benjamin D. , Evans Kelli J. , Tiffin Shelby , Stanley Nicholas , Fields Kelly , Russ Katherine , Bindele Huybrechts Frazier , Gordon-Hickey Susan 
Published: November 2016

Objective:
To measure the effect of traumatic brain injury on the cognitive processing of words, as measured by the P300, in a semantic categorization task.

Participants:
Eight adults with a history of moderate to severe traumatic brain injury and 8 age- and gender-matched controls.

Design:
A pilot study measuring cognitive event-related potentials in response to word pairs that were either in same or different semantic categories.

Main Measures:
The P300 (P3b) component of the auditory event-related potential and neuropsychological assessment.

Results:
Two patterns of P300 amplitude related to brain injury were observed. Participants with poorer performance on neuropsychological tests exhibited reduced P300 amplitude as compared to controls but showed the typical P300 parietal scalp distribution. In contrast, better performing participants demonstrated robust P300 amplitude but a substantially altered scalp distribution, characterized by the recruitment of anterior brain regions in addition to parietal activation.

Conclusions:
The recruitment of frontal areas after traumatic brain injury may represent compensatory neural mechanisms utilized to successfully maximize task performance. The P300 in a semantic processing paradigm may be a sensitive marker of neural plasticity that could be used to improve functional outcomes in cognitive remediation paradigms.
Anxiety and Posttraumatic Stress Disorder Among Medicare Beneficiaries After Traumatic Brain Injury
Authors: Albrecht Jennifer S. , Peters Matthew E. , Smith Gordon S. , Rao Vani 
Published: November 2016

Objective:
To estimate rates of anxiety and posttraumatic stress disorder (PTSD) diagnoses after traumatic brain injury (TBI) among Medicare beneficiaries, quantify the increase in rates relative to the pre-TBI period, and identify risk factors for diagnosis of anxiety and PTSD.

Participants:
A total of 96 881 Medicare beneficiaries hospitalized with TBI between June 1, 2006 and May 31, 2010.

Design:
Retrospective cohort study.

Measures:
Diagnosis of anxiety (International Classification of Diseases, Ninth Revision, Clinical Modification [ICD-9-CM] codes 300.0x) and/or PTSD (ICD-9-CM code 309.81).

Results:
After TBI, 16 519 (17%) beneficiaries were diagnosed with anxiety and 269 (0.3%) were diagnosed with PTSD. Rates of anxiety and PTSD diagnoses were highest in the first 5 months post-TBI and decreased over time. Pre-TBI diagnosis of anxiety disorder was significantly associated with post-TBI anxiety (risk ratio, 3.55; 95% confidence interval, 3.42–3.68) and pre-TBI diagnosis of PTSD was significantly associated with post-TBI PTSD (risk ratio 70.09; 95% confidence interval 56.29–111.12).

Conclusion:
This study highlights the increased risk of anxiety and PTSD after TBI. Routine screening for anxiety and PTSD, especially during the first 5 months after TBI, may help clinicians identify these important and treatable conditions, especially among patients with a history of psychiatric illness.