bluuebunny/crossref_metadata_2025 huggingface dataset:
Analyses of regulatory CD4+CD25+FOXP3+ T cells and observations from peripheral T cell subpopulation markers during the development of type 1 diabetes in children
Authors: Hamari S. , Kirveskoski T. , Glumoff V. , Kulmala P. , Simell O. , Knip M. , Veijola R.
Published: February 2016

Our aim was to study whether the aberrant amount or function of regulatory T cells is related to the development of type 1 diabetes (T1D) in children. We also set out to investigate the balance of different T cell subtype markers during the T1D autoimmune process. Treg cells were quantified with flow cytometric assay, and the suppression capacity was analysed with a carboxyfluorescein succinimidyl ester (CFSE)‐based T cell suppression assay in children in various phases of T1D disease process and in healthy autoantibody‐negative control children. The mRNA expression of different T cell subpopulation markers was analysed with real‐time qPCR method. The proportion and suppression capacity of regulatory T cells were similar in seroconverted children at an early stage of beta cell autoimmunity and also in children with T1D when compared to healthy and autoantibody‐negative children. Significant differences were observed in the mRNA expression of different T cell subpopulation markers in prediabetic children with multiple (≥2) autoantibodies and in children with newly diagnosed T1D when compared to the control children. In conclusion, there were no quantitative or functional differences in regulatory T cells between the case and control groups in any phase of the autoimmune process. Decreased mRNA expression levels of T cell subtype markers were observed in children with multiple islet autoantibodies and in those with newly diagnosed T1D, probably reflecting an exhaustion of the immune system after the strong immune activation during the autoimmune process or a generally aberrant immune response related to the progression of the disease.
Effects of submaximal and supramaximal interval training on determinants of endurance performance in endurance athletes
Authors: Paquette M. , Le Blanc O. , Lucas S. J. E. , Thibault G. , Bailey D. M. , Brassard P.
Published: February 2016

We compared the effects of submaximal and supramaximal cycling interval training on determinants of exercise performance in moderately endurance‐trained men. Maximal oxygen consumption (VO2max), peak power output (Ppeak), and peak and mean anaerobic power were measured before and after 6 weeks (3 sessions/week) of submaximal (85% maximal aerobic power [MP], HIIT85, n = 8) or supramaximal (115% MP, HIIT115, n = 9) interval training to exhaustion in moderately endurance‐trained men. High‐intensity training volume was 47% lower in HIIT115 vs HIIT85 (304 ± 77 vs 571 ± 200 min; P < 0.01). Exercise training was generally associated with increased VO2max (HIIT85: +3.3 ± 3.1 mL/kg/min; HIIT115: +3.3 ± 3.6 ml/kg/min; Time effect P = 0.002; Group effect: P = 0.95), Ppeak (HIIT85: +18 ± 9 W; HIIT115: +16 ± 27 W; Time effect P = 0.045; Group effect: P = 0.49), and mean anaerobic power (HIIT85: +0.42 ± 0.69 W/kg; HIIT115: +0.55 ± 0.65 W/kg; Time effect P = 0.01; Group effect: P = 0.18). Six weeks of submaximal and supramaximal interval training performed to exhaustion seems to equally improve VO2max and anaerobic power in endurance‐trained men, despite half the accumulated time spent at the target intensity.
Spatial analysis of long‐term effects of different tillage practices based on penetration resistance
Authors: Kuhwald M. , Blaschek M. , Minkler R. , Nazemtseva Y. , Schwanebeck M. , Winter J. , Duttmann R.
Published: February 2016

Measuring penetration resistance (PR) is a common technique for evaluating the effects of field management on soils. This study focuses on the effects of long‐term tillage on the spatial distribution of PR, comparing reduced and conventional tillage (CT) practices. The study site, located in Lower Saxony (Germany), has been subdivided into three plots, with one plot having been managed conventionally, whereas reduced tillage (RT) practices have been applied to the other two. In total, PR was measured at 63 randomly selected points. The PR data were stepwise interpolated using kriging with external drift. Core samples have been taken at 20 additional sites. The results show significant differences in PR between the different tillage practices. Within the conventionally managed plot, PR ranges to 2.3 MPa less in the topsoil than under RT. However, measured saturated hydraulic conductivity and amount of biopores at the depth of 30–35 cm are significantly greater under RT, indicating improved soil properties under RT. Comparisons between the headlands (HL) and the inner field point out the effects of intense field traffic in the HL, where maximum PR values of about 6 MPa have been measured. The spatial prediction of PR values show that long‐term effects of different tillage practices result in clearly structured patterns between CT and RT and the HL. Combining extensive PR measurements and point measurements of additional soil properties supports an adequate interpretation of PR data and can lead to fieldwide derivation of soil functions influenced by field management.
EXTENDING THE GLOBAL ACADEMIC TABLE: AN INTRODUCTION
Authors: Hastings Thomas John
Published: February 2016

Before commenting on the papers from a recent interdisciplinary gathering of scholars from China, Japan, Korea, and Taiwan, a case is made for regional academia conversations today, because international conferences, especially in the humanities and social sciences, are still dominated by “Western” traditions, discourse, and protocols. After touching on the relative stability or variability of phenomena and procedures in the natural sciences, humanities, and social sciences, political and cultural questions are considered along with some of the ongoing consequences of the East Asian adoption of the European model of the modern research university.
JUMPING TOGETHER: A WAY FROM SOCIOBIOLOGY TO BIO‐SOCIO‐HUMANITIES
Authors: Shin Ik Kang
Published: February 2016

Sociobiology is a grand narrative of evolutionary biology on which to build unified knowledge. Consilience is a metaphorical representation of that narrative. I take up the same metaphor but apply it differently. I evoke the image of jumping together, not on solid ground but on the strong, flexible canvas sheet of a trampoline, on which natural sciences, social sciences, and the humanities jump together. This image overlaps with the traditional East Asian way of understanding—that is, the “Heaven‐Earth‐Person Triad.” Using recent insights from cognitive science—metaphor, embodiment, and conceptual blending—I propose the alternative way of “bio‐socio‐humanities” to understand and experience the world.
Mechanisms of microglial activation in models of inflammation and hypoxia: Implications for chronic intermittent hypoxia
Authors: Kiernan Elizabeth A. , Smith Stephanie M. C. , Mitchell Gordon S. , Watters Jyoti J.
Published: February 2016

Chronic intermittent hypoxia (CIH) is a hallmark of sleep apnoea, a condition associated with diverse clinical disorders. CIH and sleep apnoea are characterized by increased reactive oxygen species formation, peripheral and CNS inflammation, neuronal death and neurocognitive deficits. Few studies have examined the role of microglia, the resident CNS immune cells, in models of CIH. Thus, little is known concerning their direct contributions to neuropathology or the cellular mechanisms regulating their activities during or following pathological CIH. In this review, we identify gaps in knowledge regarding CIH‐induced microglial activation, and propose mechanisms based on data from related models of hypoxia and/or hypoxia–reoxygenation. CIH may directly affect microglia, or may have indirect effects via the periphery or other CNS cells. Peripheral inflammation may indirectly activate microglia via entry of pro‐inflammatory molecules into the CNS, and/or activation of vagal afferents that trigger CNS inflammation. CIH‐induced release of damage‐associated molecular patterns from injured CNS cells may also activate microglia via interactions with pattern recognition receptors expressed on microglia. For example, Toll‐like receptors activate mitogen‐activated protein kinase/transcription factor pathways required for microglial inflammatory gene expression. Although epigenetic effects from CIH have not yet been studied in microglia, potential epigenetic mechanisms in microglial regulation are discussed, including microRNAs, histone modifications and DNA methylation. Epigenetic effects can occur during CIH, or long after it has ended. A better understanding of CIH effects on microglial activities may be important to reverse CIH‐induced neuropathology in patients with sleep disordered breathing.

image
Oscillations of a Meterstick on Two Rotating Shafts
Authors: Balta Nuri
Published: February 2016

Most students find real-world examples of harmonic oscillations interesting. Besides, normal and friction forces are the types of concepts in physics that are readily applicable to their everyday life. For instance, we depend on these forces to write, to drive cars, to pick up objects, and even to walk! And yet introductory physics students have too many misconceptions about them. Therefore, clarifying both forces with demonstrations is essential. In this paper, I will introduce an experiment that incorporates normal force, friction force, and oscillations. The demonstration will also confirm that sliding friction is proportional to the magnitude of the normal force.
Alfred P. Gage and the Introductory Physics Laboratory
Authors: Greenslade Thomas B.
Published: February 2016

This article is about a late 19th-century teacher of secondary school physics. I was originally interested in the apparatus that he sold. This led me to the physics books that he wrote, and these took me to his unusual ideas about ways to use laboratory time to introduce students to the phenomena of physics. More than 100 years later educational ideas have now come full circle, and it is time to bring Gage and his texts and ideas to 21st-century physics teachers.
The Qubit as Key to Quantum Physics Part II: Physical Realizations and Applications
Authors: Dür Wolfgang , Heusler Stefan
Published: February 2016

Using the simplest possible quantum system—the qubit—the fundamental concepts of quantum physics can be introduced. This highlights the common features of many different physical systems, and provides a unifying framework when teaching quantum physics at the high school or introductory level. In a previous TPT article and in a separate paper posted online, we introduced catchy visualizations of the qubit based on the Bloch sphere or just the unit circle (see also Refs. 3–8 for other approaches highlighting the importance of the qubit). These visualizations open the way to understand basic ideas of quantum physics even without knowledge of the underlying mathematical formalism. In addition, simple mathematics can be introduced to describe the qubit as an abstract object and basic unit of quantum information. This generalizes the digital bit as a basic unit of classical information. The proposed visualizations can be used even at the high school level, while the mathematical explanations are of importance when teaching quantum physics at the undergraduate university level. This approach provides a unified framework to introduce common features of all quantum systems, such as the stochastic behavior and state change of a superposition state under measurement.
Sharp Truncation of an Electric Field: An Idealized Model that Warrants Caution
Authors: Tu Hong , Zhu Jiongming
Published: February 2016

In physics, idealized models are often used to simplify complex situations. The motivation of the idealization is to make the real complex system tractable by adopting certain simplifications. In this treatment some unnecessary, negligible aspects are stripped away (so-called Aristotelian idealization), or some deliberate distortions are involved (so-called Galilean idealization). The most important principle in using an idealized model is to make sure that all the neglected aspects do not affect our analysis or result. Point charges, rigid bodies, simple pendulums, frictionless planes, and isolated systems are all frequently used idealized models. However, when they are applied to certain uncommon models, extra precautions should be taken. The possibilities and necessities of adopting the idealizations have to be considered carefully. Sometimes some factors neglected or ignored in the idealization could completely change the result, even make the treatment unphysical and conclusions unscientific.
Establishing a Student Research and Publishing Program in High School Physics
Authors: Eales Jonathan , Laksana Sangob
Published: February 2016

Student learning in science is improved by authentic personal experience of research projects and the publication of findings. Graduate students do this, but it is uncommon to find student research and publishing in high school science programs. We describe here the Student Research and Publishing Program (SRPP) established at International School Bangkok (ISB). We then discuss the effects of the SRPP on student attitudes and skills. Finally, we present a model detailing the criteria and processes recommended for the implementation of an SRPP in other high schools.
The role of various structures in the head on the formation of the biosonar beam of the baiji (Lipotes vexillifer)
Authors: Wei Chong , Au Whitlow W. L. , Song Zhongchang , Zhang Yu
Published: February 2016

The relative role of the various structures in the head of the baiji (Lipotes vexillifer) is examined. A finite element approach was applied to numerically simulate the acoustic propagation through a dolphin's head to examine the relative role of the skull, air sacs, and melon in the formation of the biosonar beam in the vertical plane. The beam pattern obtained with the whole head in place is compared with the beam pattern when the air sac is removed and the other structures (skull and melon) are in place, with only the skull removed, and finally with only the melon removed. The beam pattern with the air sacs and skull intact and the melon removed closely resembled the beam pattern for the complete head, suggesting that the melon has a minor role in the formation of the beam. The beam pattern for the other two cases had very little resemblance to the beam pattern for the whole head. The air sacs seem to have a role of directing propagation of the signal toward the front and the skull prevents the sound propagating below the rostrum. The beam patterns along with a correlation analysis showed that the melon had only a slight influence on the shape and direction of the beam. The resultant beam exiting the head of the dolphin is the result of complex reflection processes within the head of the animal.
Aerobic Fitness and Training in Children and Adolescents
Authors: Armstrong Neil
Published: February 2016

For ‘The Year that Was—2015’, I have selected 2 papers which review aspects of aerobic training. Studies of pediatric aerobic training generally focus on the effects of constant intensity exercise training (CIET) programs on peak oxygen uptake (VO2). The first paper has been chosen because it provides, for the first time, both a systematic review and a meta-analysis of the efficacy of high-intensity interval training (HIIT) in improving health-related fitness in adolescents. The second paper has been selected because it not only reviews both generic and sport-specific aerobic training studies of young team sport athletes, but also applies the analysis to the design of an evidence-based model of young athlete development. However, the primary reasons for highlighting these reviews is that they expose gaps in our knowledge of youth aerobic trainability, particularly between ‘pure’ and ‘applied’ pediatric sport science. They also identify areas where further research and appropriate data interpretation in relation to chronological age and biological maturation are required.
Chronic Diseases, Exercise, and Physical Activity in Childhood: 2015 in Review
Authors: Takken Tim
Published: February 2016

The year of 2015 was a fruitful year in the field of chronic diseases, exercise, and physical activity in childhood. Many interesting papers came out on this topic. Exercise testing and prescription in children with chronic disease and disability is an increasingly studied area in which many disciplines are involved including pediatric physical therapy, medicine, nursing, physical education, and exercise physiology. This multidisciplinary aspect is reflected in the journals in which my highlighted publications (below) were published. Because no single discipline has the ownership of exercise testing and prescription and because different disciplines use different jargon, it is difficult to have the scientific knowledge translated to the clinic. A few years ago we initiated the Pediatric Exercise Medicine Network (PEMNet) to close this knowledge translation gap.
Kinetics of Epstein-Barr Virus (EBV) Neutralizing and Virus-Specific Antibodies after Primary Infection with EBV
Authors: Bu Wei , Hayes Gregory M. , Liu Hui , Gemmell Lorraine , Schmeling David O. , Radecki Pierce , Aguilar Fiona , Burbelo Peter D. , Woo Jennifer , Balfour Henry H. , Cohen Jeffrey I.
Published: February 2016

Prospective studies of antibodies to multiple Epstein-Barr virus (EBV) proteins and EBV neutralizing antibodies in the same individuals before, during, and after primary EBV infection have not been reported. We studied antibody responses to EBV in college students who acquired primary EBV infection during prospective surveillance and correlated the kinetics of antibody response with the severity of disease. Neutralizing antibodies and enzyme-linked immunosorbent assay (ELISA) antibodies to gp350, the major target of neutralizing antibody, reached peak levels at medians of 179 and 333 days after the onset of symptoms of infectious mononucleosis, respectively. No clear correlation was found between the severity of the symptoms of infectious mononucleosis and the peak levels of antibody to individual viral proteins or to neutralizing antibody. In summary, we found that titers of neutralizing antibody and antibodies to multiple EBV proteins increase over many months after primary infection with EBV.
Comparison of the Copan eSwab System with an Agar Swab Transport System for Maintenance of Fastidious Anaerobic Bacterium Viability
Authors: Tyrrell Kerin L. , Citron Diane M. , Leoncio Eliza S. , Goldstein Ellie J. C.
Published: February 2016

We compared the eSwab system to a swab with an anaerobic transport semisolid agar system for their capacities to maintain the viability of 20 species of fastidious anaerobes inoculated on the bench and held at ambient or refrigerator temperature for 24 or 48 h. On average, both systems maintained similar viabilities among analogous groups of organisms at both temperatures, although there were quantitative differences among some species.
Evaluation of the Check-Points Check MDR CT103 and CT103 XL Microarray Kits by Use of Preparatory Rapid Cell Lysis
Authors: Cunningham Scott A. , Vasoo Shawn , Patel Robin
Published: February 2016

Using a rapid bacterial lysis method, the Check MDR CT103 and CT103 XL microarrays demonstrated accuracies of 98.1% and 94.2%, respectively, for detection of known resistance genes in 108 multidrug-resistant Gram-negative bacilli. In 45 isolates, 49 previously unrecognized extended-spectrum β-lactamase or plasmid AmpC targets were detected and confirmed by conventional PCR.
VP8, the Major Tegument Protein of Bovine Herpesvirus 1, Interacts with Cellular STAT1 and Inhibits Interferon Beta Signaling
Authors: Afroz Sharmin , Brownlie Robert , Fodje Michel , van Drunen Littel-van den Hurk Sylvia
Published: February 2016

The

U
L
47

gene product, VP8, is the most abundant tegument protein of bovine herpesvirus 1 (BoHV-1). Previously, we demonstrated that a

U
L
47

-deleted BoHV-1 mutant (BoHV1-ΔU
L
47) exhibits 100-fold-reduced virulence
in vitro
and is avirulent
in vivo
. In this study, we demonstrated that VP8 expression or BoHV-1 infection inhibits interferon beta (IFN-β) signaling by using an IFN-α/β-responsive plasmid in a luciferase assay. As transducer and activator of transcription (STAT) is an essential component in the IFN-signaling pathways, the effect of VP8 on STAT was investigated. An interaction between VP8 and STAT1 was established by coimmunoprecipitation assays in both VP8-transfected and BoHV-1-infected cells. Two domains of VP8, amino acids 259 to 482 and 632 to 686, were found to be responsible for its interaction with STAT1. The expression of VP8 did not induce STAT1 ubiquitination or degradation. Moreover, VP8 did not reduce STAT1 tyrosine phosphorylation to downregulate IFN-β signaling. However, the expression of VP8 or a version of VP8 (amino acids 219 to 741) that contains the STAT1-interacting domains but not the nuclear localization signal prevented nuclear accumulation of STAT1. Inhibition of nuclear accumulation of STAT1 also occurred during BoHV-1 infection, while nuclear translocation of STAT1 was observed in BoHV1-ΔU
L
47-infected cells. During BoHV-1 infection, VP8 was detected in the cytoplasm at 2 h postinfection without any
de novo
protein synthesis, at which time STAT1 was already retained in the cytoplasm. These results suggest that viral VP8 downregulates IFN-β signaling early during infection, thus playing a role in overcoming the antiviral response of BoHV-1-infected cells.

IMPORTANCE
Since VP8 is the most abundant protein in BoHV-1 virions and thus may be released in large amounts into the host cell immediately upon infection, we proposed that it might have a function in the establishment of conditions suitable for viral replication. Indeed, while nonessential
in vitro
, it is critical for BoHV-1 replication
in vivo
. In this study, we determined that VP8 plays a role in downregulation of the antiviral host response by inhibiting IFN-β signaling. VP8 interacted with and prevented nuclear accumulation of STAT1 at 2 h postinfection in the absence of
de novo
viral protein synthesis. Two domains of VP8, amino acids 259 to 482 and 632 to 686, were found to be responsible for this interaction. These results provide a new functional role for VP8 in BoHV-1 infection and a potential explanation for the lack of viral replication of the

U
L
47

deletion mutant in cattle.
The Proteolytic Activation of (H3N2) Influenza A Virus Hemagglutinin Is Facilitated by Different Type II Transmembrane Serine Proteases
Authors: Kühn Nora , Bergmann Silke , Kösterke Nadine , Lambertz Ruth L. O. , Keppner Anna , van den Brand Judith M. A. , Pöhlmann Stefan , Weiß Siegfried , Hummler Edith , Hatesuer Bastian , Schughart Klaus
Published: February 2016

Cleavage of influenza virus hemagglutinin (HA) by host cell proteases is necessary for viral activation and infectivity. In humans and mice, members of the type II transmembrane protease family (TTSP), e.g., TMPRSS2, TMPRSS4, and TMPRSS11d (HAT), have been shown to cleave influenza virus HA for viral activation and infectivity
in vitro
. Recently, we reported that inactivation of a single HA-activating protease gene,
Tmprss2
, in knockout mice inhibits the spread of H1N1 influenza viruses. However, after infection of
Tmprss2
knockout mice with an H3N2 influenza virus, only a slight increase in survival was observed, and mice still lost body weight. In this study, we investigated an additional trypsin-like protease, TMPRSS4. Both TMPRSS2 and TMPRSS4 are expressed in the same cell types of the mouse lung. Deletion of
Tmprss4
alone in knockout mice does not protect them from body weight loss and death upon infection with H3N2 influenza virus. In contrast,
Tmprss2
−/−
Tmprss4
−/−
double-knockout mice showed a remarkably reduced virus spread and lung pathology, in addition to reduced body weight loss and mortality. Thus, our results identified TMPRSS4 as a second host cell protease that, in addition to TMPRSS2, is able to activate the HA of H3N2 influenza virus
in vivo
.

IMPORTANCE
Influenza epidemics and recurring pandemics are responsible for significant global morbidity and mortality. Due to high variability of the virus genome, resistance to available antiviral drugs is frequently observed, and new targets for treatment of influenza are needed. Host cell factors essential for processing of the virus hemagglutinin represent very suitable drug targets because the virus is dependent on these host factors for replication. We reported previously that
Tmprss2
-deficient mice are protected against H1N1 virus infections, but only marginal protection against H3N2 virus infections was observed. Here we show that deletion of two host protease genes,
Tmprss2
and
Tmprss4
, strongly reduced viral spread as well as lung pathology and resulted in increased survival after H3N2 virus infection. Thus, TMPRSS4 represents another host cell factor that is involved in cleavage activation of H3N2 influenza viruses
in vivo
.
Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox
Authors: Kaever Thomas , Matho Michael H. , Meng Xiangzhi , Crickard Lindsay , Schlossman Andrew , Xiang Yan , Crotty Shane , Peters Bjoern , Zajonc Dirk M.
Published: February 2016

Vaccinia virus (VACV) A27 is a target for viral neutralization and part of the Dryvax smallpox vaccine. A27 is one of the three glycosaminoglycan (GAG) adhesion molecules and binds to heparan sulfate. To understand the function of anti-A27 antibodies, especially their protective capacity and their interaction with A27, we generated and subsequently characterized 7 murine monoclonal antibodies (MAbs), which fell into 4 distinct epitope groups (groups I to IV). The MAbs in three groups (groups I, III, and IV) bound to linear peptides, while the MAbs in group II bound only to VACV lysate and recombinant A27, suggesting that they recognized a conformational and discontinuous epitope. Only group I antibodies neutralized the mature virion in a complement-dependent manner and protected against VACV challenge, while a group II MAb partially protected against VACV challenge but did not neutralize the mature virion. The epitope for group I MAbs was mapped to a region adjacent to the GAG binding site, a finding which suggests that group I MAbs could potentially interfere with the cellular adhesion of A27. We further determined the crystal structure of the neutralizing group I MAb 1G6, as well as the nonneutralizing group IV MAb 8E3, bound to the corresponding linear epitope-containing peptides. Both the light and the heavy chains of the antibodies are important in binding to their antigens. For both antibodies, the L1 loop seems to dominate the overall polar interactions with the antigen, while for MAb 8E3, the light chain generally appears to make more contacts with the antigen.

IMPORTANCE
Vaccinia virus is a powerful model to study antibody responses upon vaccination, since its use as the smallpox vaccine led to the eradication of one of the world's greatest killers. The immunodominant antigens that elicit the protective antibodies are known, yet for many of these antigens, little information about their precise interaction with antibodies is available. In an attempt to better understand the interplay between the antibodies and their antigens, we generated and functionally characterized a panel of anti-A27 antibodies and studied their interaction with the epitope using X-ray crystallography. We identified one protective antibody that binds adjacent to the heparan sulfate binding site of A27, likely affecting ligand binding. Analysis of the antibody-antigen interaction supports a model in which antibodies that can interfere with the functional activity of the antigen are more likely to confer protection than those that bind at the extremities of the antigen.
Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies
Authors: Kaplan Gilad , Roitburd-Berman Anna , Lewis George K. , Gershoni Jonathan M.
Published: February 2016

The HIV envelope binds cellular CD4 and undergoes a range of conformational changes that lead to membrane fusion and delivery of the viral nucleocapsid into the cellular cytoplasm. This binding to CD4 reveals cryptic and highly conserved epitopes, the molecular nature of which is still not fully understood. The atomic structures of CD4 complexed with gp120 core molecules (a form of gp120 in which the V1, V2, and V3 loops and N and C termini have been truncated) have indicated that a hallmark feature of the CD4-bound conformation is the bridging sheet minidomain. Variations in the orientation of the bridging sheet hairpins have been revealed when CD4-liganded gp120 was compared to CD4-unliganded trimeric envelope structures. Hence, there appears to be a number of conformational transitions possible in HIV-1 monomeric gp120 that are affected by CD4 binding. The spectrum of CD4-bound conformations has been interrogated in this study by using a well-characterized panel of conditional, CD4-induced (CD4i) monoclonal antibodies (MAbs) that bind HIV-1 gp120 and its mutations under various conditions. Two distinct CD4i epitopes of the outer domain were studied: the first comprises the bridging sheet, while the second contains elements of the V2 loop. Furthermore, we show that the unliganded extended monomeric core of gp120 (core
e
) assumes an intermediate CD4i conformation in solution that further undergoes detectable rearrangements upon association with CD4. These discoveries impact both accepted paradigms concerning gp120 structure and the field of HIV immunogen design.

IMPORTANCE
Elucidation of the conformational transitions that the HIV-1 envelope protein undergoes during the course of entry into CD4
+
cells is fundamental to our understanding of HIV biology. The binding of CD4 triggers a range of gp120 structural rearrangements that could present targets for future drug design and development of preventive vaccines. Here we have systematically interrogated and scrutinized these conformational transitions using a panel of antibody probes that share a specific preference for the CD4i conformations. These have been employed to study a collection of gp120 mutations and truncations. Through these analyses, we propose 4 distinct sequential steps in CD4i transitions of gp120 conformations, each defined by antibody specificities and structural requirements of the HIV envelope monomer. As a result, we not only provide new insights into this dynamic process but also define probes to further investigate HIV infection.
New Monoclonal Antibodies against a Novel Subtype of Shiga Toxin 1 Produced by Enterobacter cloacae and Their Use in Analysis of Human Serum
Authors: Skinner Craig , Patfield Stephanie , Khalil Rowaida , Kong Qiulian , He Xiaohua
Published: February 2016

Stxs are among the most clinically important virulence factors of
Shigella
and enterohemorrhagic
Escherichia coli
. There are many varieties of Stx, and although Stx1a and Stx2a are the most common and widely distributed types of Stx, new variants of Stx are continually emerging. These new variants of Stx can be challenging to detect, since most Stx detection kits are optimized for the detection of Stx1a and Stx2a. Stx1e, recently discovered in an atypical host (
Enterobacter cloacae
), is undetectable by many Stx assays. To formulate new assays for the detection of Stx1e, we generated four new MAbs that recognize this Stx subtype. Using these antibodies, we generated an assay capable of detecting Stx1e at low picogram-per-milliliter concentrations. This assay is also compatible with a human serum matrix, suggesting that it may have utility for the clinical detection and diagnosis of Stx1e-associated infections.
Retained needle after cement injection during vertebral augmentation and its management strategy
Authors: Kosse Angelika , Nakhla Jonathan Pishoi , Yassari Reza , Abramowicz Apolonia Elisabeth , Brook Allan
Published: February 2016

A middle aged patient with multiple myeloma resulting in numerous pathological fractures underwent an L2, L3, and L5 vertebral cement augmentation for pain relief. After injection, the trocar at L2, the final level, could not be withdrawn despite several attempts of needle rotation, a second needle inserted to distract on, and rocking the needle on the pedicle. After a neurosurgical consultation, the patient was transferred to the operating room for open removal. As the needle protruded approximately 3 inches from the patient's back, the patient could not be positioned supine, and was anesthetized and intubated in the right semi-prone position prior to being placed prone on the operating room table. The needle was surgically exposed, cut off at the pedicular bone edge, and its free component was removed.
How do scientists perceive the current publication culture? A qualitative focus group interview study among Dutch biomedical researchers
Authors: Tijdink J K , Schipper K , Bouter L M , Maclaine Pont P , de Jonge J , Smulders Y M
Published: February 2016

Objective

To investigate the biomedical scientist's perception of the prevailing publication culture.

Design

Qualitative focus group interview study.

Setting

Four university medical centres in the Netherlands.

Participants

Three randomly selected groups of biomedical scientists (PhD, postdoctoral staff members and full professors).

Main outcome measures

Main themes for discussion were selected by participants.

Results

Frequently perceived detrimental effects of contemporary publication culture were the strong focus on citation measures (like the Journal Impact Factor and the H-index), gift and ghost authorships and the order of authors, the peer review process, competition, the funding system and publication bias. These themes were generally associated with detrimental and undesirable effects on publication practices and on the validity of reported results. Furthermore, senior scientists tended to display a more cynical perception of the publication culture than their junior colleagues. However, even among the PhD students and the postdoctoral fellows, the sentiment was quite negative. Positive perceptions of specific features of contemporary scientific and publication culture were rare.

Conclusions

Our findings suggest that the current publication culture leads to negative sentiments, counterproductive stress levels and, most importantly, to questionable research practices among junior and senior biomedical scientists.
Treatment of faecal incontinence using allogeneic-adipose-derived mesenchymal stem cells: a study protocol for a pilot randomised controlled trial
Authors: Park Eun Jung , Kang Jeonghyun , Baik Seung Hyuk
Published: February 2016

Introduction

Faecal incontinence is a distressing condition with recurrent uncontrolled passage of faecal material. Although faecal incontinence may cause psychological depression and social isolation, previous treatments have been limited. Recently, regenerative treatment has been developed using mesenchymal stem cells. Especially, there are possibilities that adipose-tissue-derived stem cells can be effective to treat a degenerated anal sphincter that is causing faecal incontinence. Therefore, this study aimed to investigate the safety and efficacy of using allogeneic-adipose-derived mesenchymal stem cells in the treatment of the anal sphincter of patients with faecal incontinence.

Methods and analysis

This study is a randomised, prospective, dose escalation, placebo-controlled, single-blinded, single-centre trial with two parallel groups. The safety test is performed by an injection of allogeneic-adipose-derived mesenchymal stem cells (ALLO-ASCs) into the anal sphincter with dose escalation (3×107, 6×107and 9×107cells, sequentially). After confirming the safety of the stem cells, an efficacy test is performed by this dose in the experimental group. The experimental group will receive ALLO-ASCs mixed with fibrin glue into the anal sphincter, and the placebo group will receive 0.9% normal saline injection mixed with fibrin glue. The primary end point is to assess the safety of ALLO-ASCs after the injection into the anal sphincter, and the secondary end point is to compare the efficacy of ALLO-ASC injection with fibrin glue in patients with faecal incontinence.

Ethics and dissemination

The study protocol was approved by the Ministry of Food and Drug Safety and the Ministry of Health & Welfare, in the Republic of Korea. The informed consent form was approved by the institutional review board of Gangnam Severance Hospital (IRB approval number 3-2014-0271). Dissemination of the results will be presented at a conference and in peer-reviewed publications.

Trial registration number

NCT02384499; Pre-results.
Using Monte Carlo simulation to assess variability and uncertainty of tobacco consumption in a city by sewage epidemiology
Authors: Wang De-Gao , Dong Qian-Qian , Du Juan , Yang Shuo , Zhang Yun-Jie , Na Guang-Shui , Ferguson Stuart G , Wang Zhuang , Zheng Tong
Published: February 2016

Objective

To use Monte Carlo simulation to assess the uncertainty and variability of tobacco consumption through wastewater analysis in a city.

Methods

A total of 11 wastewater treatment plants (WWTPs) (serving 2.2 million people; approximately 83% of urban population in Dalian) were selected and sampled. By detection and quantification of principal metabolites of nicotine, cotinine (COT) and trans-3′-hydroxycotinine (OH-COT), in raw wastewater, back calculation of tobacco use in the population of WWTPs can be realised.

Results

COT and OH-COT were detected in the entire set of samples with an average concentration of 2.33±0.30 and 2.76±0.91 µg/L, respectively. The mass load of absorbed NIC during the sampling period ranged from 0.25 to 4.22 mg/day/capita with an average of 1.92 mg/day/capita. Using these data, we estimated that smokers in the sampling area consumed an average of 14.6 cigarettes per day for active smoker. Uncertainty and variability analysis by Monte Carlo simulation were used to refine this estimate: the procedure concluded that smokers in Dalian smoked between 10 and 27 cigarettes per day. This estimate showed good agreement with estimates from epidemiological research.

Conclusions

Sewage-based epidemiology may be a useful additional tool for the large-scale monitoring of patterns of tobacco use. Probabilistic methods can be used to strengthen the reliability of estimated use generated from wastewater analysis.
ERK and AKT phosphorylation status in lung cancer and emphysema using nanocapillary isoelectric focusing
Authors: Crosbie Philip A J , Crosbie Emma J , Aspinall-O'Dea Mark , Walker Michael , Harrison Rebecca , Pernemalm Maria , Shah Rajesh , Joseph Leena , Booton Richard , Pierce Andrew , Whetton Anthony D
Published: February 2016

Background

Emphysema is an independent risk factor for the development of lung cancer in smokers. Activation of oncogenic signalling proteins AKT and ERK by phosphorylation has an established role in the development of lung cancer and has also been implicated in the pathogenesis of emphysema. The aim of this study was to compare the protein level and phosphorylation status of AKT and ERK in paired lung cancer and emphysema tissue using a highly sensitive phosphoprotein analysis approach.

Methods

An antibody-based, nanocapillary isoelectric focusing (cIEF) assay was used to determine the relative quantities and phosphorylation status of AKT and ERK in tumour and matched lung tissue from patients, with or without evidence of emphysema, undergoing curative resection for non-small cell lung cancer.

Results

20 patients with adenocarcinoma (n=9) or squamous cell carcinoma (n=11) of the lung were included (mean age 67.3 years (SD 7.5, range 47–80 years)), 12 were men and all were current (n=10) or former smokers (n=10). Paired macroscopically normal lung tissue was either histologically normal (n=7) or showed emphysema (n=13). Total and phosphorylated AKT levels were fourfold (p=0.0001) and fivefold (p=0.001) higher in tumour compared with matched lung, respectively. There was no correlation with tumour histology, stage or differentiation; however, total AKT signal in tumour was significantly correlated with fluorodeoxyglucose avidity on positron emission tomography-CT scan (r=0.53, p=0.035). Total ERK was not differentially expressed, but doubly phosphorylated (activated) ERK was threefold higher in emphysema (23.5%, SD 9.2) than either matched tumour (8.8%, SD 8.6) or normal lung tissue (8.3%, SD 9.0) and correlated with the histological severity of emphysema (p=0.005).

Conclusions

cIEF offers opportunities for quantifying subtle shifts in the phosphorylation status of oncoproteins in nanogram amounts of lung tissue. ERK activation is a feature of emphysema.
Building a taxonomy of integrated palliative care initiatives: results from a focus group
Authors: Ewert Benjamin , Hodiamont Farina , van Wijngaarden Jeroen , Payne Sheila , Groot Marieke , Hasselaar Jeroen , Menten Johann , Radbruch Lukas
Published: February 2016

Background

Empirical evidence suggests that integrated palliative care (IPC) increases the quality of care for palliative patients and supports professional caregivers. Existing IPC initiatives in Europe vary in their design and are hardly comparable. InSuP-C, a European Union research project, aimed to build a taxonomy of IPC initiatives applicable across diseases, healthcare sectors and systems.

Methods

The taxonomy of IPC initiatives was developed in cooperation with an international and multidisciplinary focus group of 18 experts. Subsequently, a consensus meeting of 10 experts revised a preliminary taxonomy and adopted the final classification system.

Results

Consisting of eight categories, with two to four items each, the taxonomy covers the process and structure of IPC initiatives. If two items in at least one category apply to an initiative, a minimum level of integration is assumed to have been reached. Categories range from thetype of initiative(items:pathway, modelorguideline) to patients’key contact(items:non-pc specialist, pc specialist,general practitioner). Experts recommended the inclusion of two new categories:level of care(items:primary, secondaryortertiary) indicating at which stage palliative care is integrated andprimary focus of interventiondescribing IPC givers’ different roles (items:treating function, advising/consulting or training) in the care process.

Conclusions

Empirical studies are required to investigate how the taxonomy is used in practice and whether it covers the reality of patients in need of palliative care. The InSuP-C project will test this taxonomy empirically in selected initiatives using IPC.
MARRIED-cocaine score: validating a tool for detecting the risk of ED revisit in cocaine users
Authors: Galicia Miguel , Nogué Santiago , Miró Òscar
Published: February 2016

Objective

According to a previous study, 17% of patients who attended an emergency department (ED) following cocaine use returned to the same ED over the next year for a problem related to drug use. This previous study proposed a scale (Multicenter Assessment of the Revisit Risk In the Emergency Department (MARRIED)-cocaine score) to quantify the risk of ED revisit. The aim of the present study was to validate this scale by analysing a new set of patients attending for cocaine use in nine Spanish EDs.

Methods

We performed a retrospective, multicentre, cohort study with consecutive patient inclusion, and without an intervention or control group. During 12 months (January–December 2010) we collected data from patients attending the ED after cocaine use. The MARRIED-cocaine score, ranging from 0 to 400 points, was calculated for each patient. The dependent variable was the identification of further visits associated with drug consumption to the same ED. Further analysis was performed to define risk categories.

Results

The study included 933 patients, with a mean follow-up of 466 (SD 189) days, and 185 patients returned to the same ED for problems related to drug consumption. The cumulative probability of ED revisit was 4.2%, 8.3%, 16.8% and 21.2% at 1 month, 3 months, 12 months and 24 months, respectively. The area under the curve receiver operating characteristic for the MARRIED-cocaine scale was 0.69 (p<0.001). Four categories for ED revisit risk were defined: low risk (0–40 points, n=416), moderate risk (41–100 points, n=235), high risk (101–210 points, n=71) and very high risk (210–400 points, n=211), with HRs for ED revisit (with respect to the low-risk group) of 1.82 (95% CI 1.18 to 2.80, p=0.007), 2.65 (95% CI 1.50 to 4.66, p=0.001) and 5.06 (95% CI 3.49 to 7.35, p<0.001), respectively.

Conclusions

The MARRIED-cocaine score has a moderate discriminative capacity to predict revisit among patients who attend the ED for cocaine drug-related emergencies, and allows classification of patients according to the risk of ED revisit.
Prospective comparison of ultrasound and CXR for confirmation of central vascular catheter placement
Authors: Weekes Anthony J , Keller Stephen M , Efune Bradley , Ghali Sama , Runyon Michael
Published: February 2016

Objective

To prospectively compare ultrasound (US) versus CXR for confirmation of central vascular catheter (CVC) placement. Secondary objective was to determine the incidence of pneumothorax (PTX) and compare US with CXR completion times.

Methods

Investigators performed the US saline flush echo test, and evaluated each anterior hemithorax for pleural sliding with US after subclavian or internal jugular CVC placement.

Measurements and main results

151 total (135 in the emergency department, 16 in the intensive care unit) patients after CVC placement, mean age 62.1±15.6 years and 83 (55%) female patients. The rapid atrial swirl sign ( RASS) was ultrasound finding of an immediate appearance of turbulence entering the right atrium via superior vena cava after a rapid saline flush of the distal CVC port. RASS was considered ‘negative’ for CVC malposition. US identified all correct CVC placements. Four suboptimal CVC tip placements were detected by CXR. US identified three of these misplacements (McNemar exact p value >0.99). There were no cases of PTX or abnormal pleural sliding by either CXR or US. Median times for US and CXR completion were 1.1 (IQR 0.7) minutes and 20 (IQR: 30) minutes, respectively, median difference 23.8 (95% CI 19.6 to 29.3) minutes, p<0.0001.

Conclusions

PTX and CVC tip malposition were rare after US-guided CVC placement. There was no significant difference between saline flush echo and CXR for the identification of catheter tip malposition. Benefits of US assessment for complications include reduced radiation exposure and time delays associated with CXR.