bluuebunny/crossref_metadata_2025 huggingface dataset:
Teaching Critical Thinking: Sense-Making, Explanations, Language, and Habits
Authors: Maloney David
Published: September 2015

The conjunction of three events has encouraged me to devote significant time to thinking about the pedagogical framework in my introductory courses. The three events were: doing a workshop addressing the Advanced Placement restructuring of the Physics B course with a stronger focus on critical thinking, finding out that TPT was planning an issue about the “science and art” of teaching, and dealing with a course that I haven't taught in about a decade, where the students behaved very differently from students in the same course in the past.
Respecting Our Students
Authors: Gavrin Andy
Published: September 2015

Giving our students the respect they deserve will improve their performance, our mutual interactions, and our satisfaction as teachers. This is obvious to many TPT readers, but there are times when we all, myself included, forget. There are times when our judgment is clouded by institutional culture, or our best intentions are subverted by the vexations of our roles as instructors. This essay is based on my own experience teaching physics (primarily at a public urban university, primarily at the introductory level), and on conversations with many colleagues here and elsewhere. I hope this essay will serve as a reminder to all of us that we must treat our students with respect, and that the rewards of doing so are worth the effort of rethinking some of our behaviors.
Bringing (Century-Old) Technology into the Classroom, Part I: Teaching Mechanics and Thermodynamics with Antiques
Authors: Jewett John W.
Published: September 2015

The notion of bringing technology into the classroom has been the subject of many recent presentations at conferences and papers in physics teaching journals. The use of devices such as laptops, smartphones, tablets, and clickers is rising in today's classrooms and laboratories. PhET simulations have been available online for over a decade. A column in The Physics Teacher, called “iPhysicsLabs,” was begun in February of 2012 and describes experiments to be carried out with smartphones and tablets. Students have become familiar with the operation and application of such technology. But are they aware of the underlying physics necessary to make the devices and the online simulations work? Much of the physics is hidden at the microscopic level in tiny circuit chips or in the workings of a distant server.
Defining and Developing “Critical Thinking” Through Devising and Testing Multiple Explanations of the Same Phenomenon
Authors: Etkina Eugenia , Planinšič Gorazd
Published: September 2015

Most physics teachers would agree that one of the main reasons for her/his students to take physics is to learn to think critically. However, for years we have been assessing our students mostly on the knowledge of physics content (conceptually and quantitatively). Only recently have science educators started moving systematically towards achieving and assessing this critical thinking goal. In this paper we seek to show how guiding students to devise and test multiple explanations of observed phenomena can be used to improve their critical thinking.
The sound of church bells: Tracking down the secret of a traditional arts and crafts trade
Authors: Vogt Patrik , Kasper Lutz , Burde Jan-Philipp
Published: September 2015

The sound of church bells is part of most people's everyday life and can easily be examined with smartphones. Similar to other experiments of this column, we use a suitable iOS app. The underlying physical theory of church bells proves to be difficult. A reliable prediction of their natural frequencies based on their exact dimensions is only possible using the finite element method. If you ask bell founders how they calculate the rib of a bell (half longitudinal section of a bell, which completely determines the acoustic properties, Fig. 1) in order to get a church bell with the desired frequency spectrum, you will certainly not get an answer: the art of bell casting is based on centuries of experience and knowledge of the rib structure is only shared with direct descendants. We want to have a closer look at these well-guarded secrets, knowing full well that we cannot fully unravel them. This article presents simple mathematical models and a comparison with a data set of almost 700 bells.
Long-Term Immunogenicity and Safety of a Conventional Influenza Vaccine in Patients with Type 2 Diabetes
Authors: Seo Yu Bin , Baek Ji Hyeon , Lee Jacob , Song Joon Young , Lee Jin Soo , Cheong Hee Jin , Kim Woo Joo
Published: September 2015

No previous studies have assessed the persistence of immune responses in individuals with diabetes. We conducted this study to evaluate the long-term immunogenicity and safety of an influenza vaccine in type 2 diabetic subjects compared with nondiabetic controls. A randomized and controlled study was conducted at two university hospitals during the 2012-2013 influenza season. The study vaccine was a standard-dose trivalent subunit inactivated intramuscular vaccine. Serum hemagglutination-inhibiting (HI) antibodies were measured at the time of vaccination and 1 month and 6 months after vaccination. Local and systemic reactions were recorded for 7 days. A total of 105 diabetic patients and 108 controls were included in the analysis. One month after vaccination, both the diabetic and nondiabetic groups satisfied all of the criteria of the Committee for Medical Products for Human Use (CHMP), and the immunogenicity profiles were statistically similar between the two groups. Although the vaccine was well tolerated, and all adverse reactions were mild to moderate, there was a tendency toward a reduced incidence of local reactions in the diabetic group. All values in the long-term immunogenicity profiles were statistically similar between the two groups, except for the seroprotection rate for the A/H1N1 influenza virus strain, which was significantly lower in the elderly diabetic group than that in the elderly nondiabetic group. However, in multivariate analysis, long-term immunogenicity was associated with age and prevaccination titer, regardless of diabetes status. (This study has been registered at CRIS [
https://cris.nih.go.kr/cris/en/
] under registration no. KCT0001423.)
Evaluation of Selected Borrelia burgdorferi lp54 Plasmid-Encoded Gene Products Expressed during Mammalian Infection as Antigens To Improve Serodiagnostic Testing for Early Lyme Disease
Authors: Weiner Zachary P. , Crew Rebecca M. , Brandt Kevin S. , Ullmann Amy J. , Schriefer Martin E. , Molins Claudia R. , Gilmore Robert D.
Published: September 2015

Laboratory testing for the diagnosis of Lyme disease is performed primarily by serologic assays and is accurate for detection beyond the acute stage of the infection. Serodiagnostic assays to detect the early stages of infection, however, are limited in their sensitivity, and improvement is warranted. We analyzed a series of
Borrelia burgdorferi
proteins known to be induced within feeding ticks and/or during mammalian infection for their utility as serodiagnostic markers against a comprehensive panel of Lyme disease patient serum samples. The antigens were assayed for IgM and IgG reactivity in line immunoblots and separately by enzyme-linked immunosorbent assay (ELISA), with a focus on reactivity against early Lyme disease with erythema migrans (EM), early disseminated Lyme neuroborreliosis, and early Lyme carditis patient serum samples. By IgM immunoblotting, we found that recombinant proteins BBA65, BBA70, and BBA73 reacted with early Lyme EM samples at levels comparable to those of the OspC antigen used in the current IgM blotting criteria. Additionally, these proteins reacted with serum samples from patients with early neuroborreliosis and early carditis, suggesting value in detecting early stages of this disease progression. We also found serological reactivity against recombinant proteins BBA69 and BBA73 with early-Lyme-disease samples using IgG immunoblotting and ELISA. Significantly, some samples that had been scored negative by the Centers for Disease Control and Prevention-recommended 2-tiered testing algorithm demonstrated positive reactivity to one or more of the antigens by IgM/IgG immunoblot and ELISA. These results suggest that incorporating additional
in vivo
-expressed antigens into the current IgM/IgG immunoblotting tier in a recombinant protein platform assay may improve the performance of early-Lyme-disease serologic testing.
Human Memory CD4
+
T Cell Immune Responses against Giardia lamblia
Authors: Saghaug Christina Skår , Sørnes Steinar , Peirasmaki Dimitra , Svärd Staffan , Langeland Nina , Hanevik Kurt
Published: September 2015

The intestinal protozoan parasite
Giardia lamblia
may cause severe prolonged diarrheal disease or pass unnoticed as an asymptomatic infection. T cells seem to play an important role in the immune response to
Giardia
infection, and memory responses may last years. Recently, T
H
17 responses have been found in three animal studies of
Giardia
infection. The aim of this study was to characterize the human CD4
+
T cell responses to
Giardia
. Peripheral blood mononuclear cells (PBMCs) were obtained from 21 returning travelers with recent or ongoing giardiasis and 12 low-risk healthy controls and stimulated
in vitro
with
Giardia lamblia
proteins. Production of tumor necrosis factor alpha (TNF-α), gamma interferon, interleukin-17A (IL-17A), IL-10, and IL-4 was measured in CD4
+
effector memory (EM) T cells after 24 h by flow cytometry. After 6 days of culture, activation and proliferation were measured by flow cytometry, while an array of inflammatory cytokine levels in supernatants were measured with multiplex assays. We found the number of IL-17A-producing CD4
+
EM T cells, as well as that of cells simultaneously producing both IL-17A and TNF-α, to be significantly elevated in the
Giardia
-exposed individuals after 24 h of antigen stimulation. In supernatants of PBMCs stimulated with
Giardia
antigens for 6 days, we found inflammation-associated cytokines, including 1L-17A, as well as CD4
+
T cell activation and proliferation, to be significantly elevated in the
Giardia
-exposed individuals. We conclude that symptomatic
Giardia
infection in humans induces a CD4
+
EM T cell response of which IL-17A production seems to be an important component.
Attenuation of Replication-Competent Adenovirus Serotype 26 Vaccines by Vectorization
Authors: Maxfield Lori F. , Abbink Peter , Stephenson Kathryn E. , Borducchi Erica N. , Ng'ang'a David , Kirilova Marinela M. , Paulino Noelix , Boyd Michael , Shabram Paul , Ruan Qian , Patel Mayank , Barouch Dan H.
Published: September 2015

Replication-competent adenovirus (rcAd)-based vaccine vectors may theoretically provide immunological advantages over replication-incompetent Ad vectors, but they also raise additional potential clinical and regulatory issues. We produced replication-competent Ad serotype 26 (rcAd26) vectors by adding the E1 region back into a replication-incompetent Ad26 vector backbone with the E3 or E3/E4 regions deleted. We assessed the effect of vectorization on the replicative capacity of the rcAd26 vaccines. Attenuation occurred in a stepwise fashion, with E3 deletion, E4 deletion, and human immunodeficiency virus type 1 (HIV-1) envelope (Env) gene insertion all contributing to reduced replicative capacity compared to that with the wild-type Ad26 vector. The rcAd26 vector with E3 and E4 deleted and containing the Env transgene exhibited 2.7- to 4.4-log-lower replicative capacity than that of the wild-type Ad26
in vitro
. This rcAd26 vector is currently being evaluated in a phase 1 clinical trial. Attenuation as a result of vectorization and transgene insertion has implications for the clinical development of replication-competent vaccine vectors.
Detection of Polyclonality among Clinical Isolates from Prosthetic Joint Infections
Authors: De-la-Fuente Marta , Martinez-Perez Marta , Gonzalez-Pallares Iris , Esteban Jaime
Published: September 2015

Prosthetic joint infection (PJI) is an increasingly important health concern in the Western world due to the rising number of joint arthroplasties. Although most infections are considered to be monomicrobial, the introduction of sonication procedures has led to an increase in the detection of polymicrobial infections. To date, no published studies have investigated the presence of different clones of the same species in the infected patient. The objective of this study was to analyze whether the phenomenon of polyclonality, or the appearance of different clones in the same sample, occurs in PJI. Bacteria isolated by sonication of the retrieved implant from patients with theoretically monomicrobial PJI were included in the study. Two techniques (random amplified polymorphic DNA [RAPD] and matrix-assisted laser desorption ionization–time of flight [MALDI-TOF] mass spectrometry) were used to determine the presence of several clones in the same sample. Results were analyzed to determine bacterial species and infection type (acute versus chronic). RAPD showed a predominance of polyclonal cases (16 of 19). However, when performing the analysis with MALDI-TOF, all cases were shown to be polyclonal. We were unable to establish any relationship between the two methodologies. Polyclonality is a common phenomenon in acute and chronic PJI. Further studies are needed to establish the potential implications of this phenomenon on patient outcomes.
Direct Repeat Unit (
dru
) Typing of Methicillin-Resistant Staphylococcus pseudintermedius from Dogs and Cats
Authors: Kadlec Kristina , Schwarz Stefan , Goering Richard V. , Weese J. Scott
Published: September 2015

Methicillin-resistant
Staphylococcus pseudintermedius
(MRSP) has emerged in a remarkable manner as an important problem in dogs and cats. However, limited molecular epidemiological information is available. The aims of this study were to apply direct repeat unit (
dru
) typing in a large collection of well-characterized MRSP isolates and to use
dru
typing to analyze a collection of previously uncharacterized MRSP isolates. Two collections of MRSP isolates from dogs and cats were included in this study. The first collection comprised 115 well-characterized MRSP isolates from North America and Europe. The data for these isolates included multilocus sequence typing (MLST) and staphylococcal protein A gene (
spa)
typing results as well as SmaI macrorestriction patterns after pulsed-field gel electrophoresis (PFGE). The second collection was a convenience sample of 360 isolates from North America. The
dru
region was amplified by PCR, sequenced, and analyzed. For the first collection, the discriminatory indices of the typing methods were calculated. All isolates were successfully
dru
typed. The discriminatory power for
dru
typing (
D
= 0.423) was comparable to that of
spa
typing (
D
= 0.445) and of MLST (
D
= 0.417) in the first collection. Occasionally,
dru
typing was able to further discriminate between isolates that shared the same
spa
type. Among all 475 isolates, 26 different
dru
types were identified, with 2 predominant types (dt9a and dt11a) among 349 (73.4%) isolates. The results of this study underline that
dru
typing is a useful tool for MRSP typing, being an objective, standardized, sequence-based method that is relatively cost-efficient and easy to perform.
Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing
Authors: de Gier Camilla , Kirkham Lea-Ann S. , Nørskov-Lauritsen Niels
Published: September 2015

Nonhemolytic variants ofHaemophilus haemolyticusare difficult to differentiate fromHaemophilus influenzaedespite a wide difference in pathogenic potential. A previous investigation characterized a challenging set of 60 clinical strains using multiple PCRs for marker genes and described strains that could not be unequivocally identified as either species. We have analyzed the same set of strains by multilocus sequence analysis (MLSA) and near-full-length 16S rRNA gene sequencing. MLSA unambiguously allocated all study strains to either of the two species, while identification by 16S rRNA sequence was inconclusive for three strains. Notably, the two methods yielded conflicting identifications for two strains. Most of the “fuzzy species” strains were identified asH. influenzaethat had undergone complete deletion of the fucose operon. Such strains, which are untypeable by theH. influenzaemultilocus sequence type (MLST) scheme, have sporadically been reported and predominantly belong to a single branch ofH. influenzaeMLSA phylogenetic group II. We also found evidence of interspecies recombination betweenH. influenzaeandH. haemolyticuswithin the 16S rRNA genes. Establishing an accurate method for rapid and inexpensive identification ofH. influenzaeis important for disease surveillance and treatment.
Diagnostic Accuracy of Seven Commercial Assays for Rapid Detection of Group A Rotavirus Antigens
Authors: Kaplon Jérôme , Fremy Céline , Pillet Sylvie , Mendes Martins Lucile , Ambert-Balay Katia , Aho Serge L. , Pothier Pierre
Published: September 2015

Seven commercial immunochromatographic assays intended for the detection of group A rotavirus antigens in human stool samples were evaluated. These assays showed similar levels of diagnostic accuracy and were suitable for the detection of rotavirus in patients with acute gastroenteritis but missed some asymptomatic rotavirus shedding identified by real-time reverse transcription-PCR.
Successful Treatment of Peritoneal Dialysis Catheter-Related Polymicrobial Peritonitis Involving Clostridium difficile
Authors: Bharti Sheena , Malhotra Prashant , Juretschko Stefan
Published: September 2015

Clostridium difficile
is one of the most common nosocomial pathogens and the cause of pseudomembranous colitis in cases of prior antimicrobial exposure. Extraintestinal manifestations of
C. difficile
are uncommon and rarely reported. We report the first successfully treated case of catheter-related
C. difficile
peritonitis in a patient undergoing peritoneal dialysis.
Rapid Detection of Subtype H10N8 Influenza Virus by One-Step Reverse Transcription–Loop-Mediated Isothermal Amplification Methods
Authors: Bao Hongmei , Feng Xiaoxiao , Ma Yong , Shi Jianzhong , Zhao Yuhui , Gu Linlin , Wang Xiurong , Chen Hualan
Published: September 2015

We developed hemagglutinin- and neuraminidase-specific one-step reverse transcription–loop-mediated isothermal amplification assays for detecting the H10N8 virus. The detection limit of the assays was 10 copies of H10N8 virus, and the assays did not amplify nonspecific RNA. The assays can detect H10N8 virus from chicken samples with high sensitivity and specificity, and they can serve as an effective tool for detecting and monitoring H10N8 virus in live poultry markets.
Commentary: The Race Is On To Shorten the Turnaround Time for Diagnosis of Multidrug-Resistant Tuberculosis
Authors: Somoskovi Akos , Salfinger Max
Published: September 2015

To realize the most benefit from multidrug-resistant tuberculosis (MDR-TB) screening, all nucleic acid amplification test (NAAT)-positive respiratory specimens should be universally tested. Once an MDR-TB diagnosis is established, additional testing is warranted to provide details about the detected mutations. The lab-on-chip technology described by A. M. Cabibbe et al. (J Clin Microbiol 53:3876–3880, 2015,
http://dx.doi.org/10.1128/JCM.01824-15
) potentially provides this much needed information.
Retargeting Oncolytic Vesicular Stomatitis Virus to Human T-Cell Lymphotropic Virus Type 1-Associated Adult T-Cell Leukemia
Authors: Betancourt Dillon , Ramos Juan Carlos , Barber Glen N.
Published: September 2015

Adult T cell leukemia/lymphoma (ATL) is an aggressive cancer of CD4/CD25
+
T lymphocytes, the etiological agent of which is human T-cell lymphotropic virus type 1 (HTLV-1). ATL is highly refractory to current therapies, making the development of new treatments a high priority. Oncolytic viruses such as vesicular stomatitis virus (VSV) are being considered as anticancer agents since they readily infect transformed cells compared to normal cells, the former appearing to exhibit defective innate immune responses. Here, we have evaluated the efficacy and safety of a recombinant VSV that has been retargeted to specifically infect and replicate in transformed CD4
+
cells. This was achieved by replacing the single VSV glycoprotein (G) with human immunodeficiency virus type 1 (HIV-1) gp160 to create a hybrid fusion protein, gp160G. The resultant virus, VSV-gp160G, was found to only target cells expressing CD4 and retained robust oncolytic activity against HTLV-1 actuated ATL cells. VSV-gp160G was further noted to be highly attenuated and did not replicate efficiently in or induce significant cell death of primary CD4
+
T cells. Accordingly, VSV-gp160G did not elicit any evidence of neurotoxicity even in severely immunocompromised animals such as NOD/Shi-scid, IL-2Rγ-c-null (NSG) mice. Importantly, VSV-gp160G effectively exerted potent oncolytic activity in patient-derived ATL transplanted into NSG mice and facilitated a significant survival benefit. Our data indicate that VSV-gp160G exerts potent oncolytic efficacy against CD4
+
malignant cells and either alone or in conjunction with established therapies may provide an effective treatment in patients displaying ATL.

IMPORTANCE
Adult T cell leukemia (ATL) is a serious form of cancer with a high mortality rate. HTLV-1 infection is the etiological agent of ATL and, unfortunately, most patients succumb to the disease within a few years. Current treatment options have failed to significantly improve survival rate. In this study, we developed a recombinant strain of vesicular stomatitis virus (VSV) that specifically targets transformed CD4
+
T cells through replacement of the G protein of VSV with a hybrid fusion protein, combining domains from gp160 of HIV-1 and VSV-G. This modification eliminated the normally broad tropism of VSV and restricted infection to primarily the transformed CD4
+
cell population. This effect greatly reduced neurotoxic risk associated with VSV infection while still allowing VSV to effectively target ATL cells.
RIG-I Signaling Is Essential for Influenza B Virus-Induced Rapid Interferon Gene Expression
Authors: Mäkelä Sanna M. , Österlund Pamela , Westenius Veera , Latvala Sinikka , Diamond Michael S. , Gale Michael , Julkunen Ilkka
Published: September 2015

Influenza B virus causes annual epidemics and, along with influenza A virus, accounts for substantial disease and economic burden throughout the world. Influenza B virus infects only humans and some marine mammals and is not responsible for pandemics, possibly due to a very low frequency of reassortment and a lower evolutionary rate than that of influenza A virus. Influenza B virus has been less studied than influenza A virus, and thus, a comparison of influenza A and B virus infection mechanisms may provide new insight into virus-host interactions. Here we analyzed the early events in influenza B virus infection and interferon (IFN) gene expression in human monocyte-derived macrophages and dendritic cells. We show that influenza B virus induces IFN regulatory factor 3 (IRF3) activation and IFN-λ1 gene expression with faster kinetics than does influenza A virus, without a requirement for viral protein synthesis or replication. Influenza B virus-induced activation of IRF3 required the fusion of viral and endosomal membranes, and nuclear accumulation of IRF3 and viral NP occurred concurrently. In comparison, immediate early IRF3 activation was not observed in influenza A virus-infected macrophages. Experiments with RIG-I-, MDA5-, and RIG-I/MDA5-deficient mouse fibroblasts showed that RIG-I is the critical pattern recognition receptor needed for the influenza B virus-induced activation of IRF3. Our results show that innate immune mechanisms are activated immediately after influenza B virus entry through the endocytic pathway, whereas influenza A virus avoids early IRF3 activation and IFN gene induction.

IMPORTANCE
Recently, a great deal of interest has been paid to identifying the ligands for RIG-I under conditions of natural infection, as many previous studies have been based on transfection of cells with different types of viral or synthetic RNA structures. We shed light on this question by analyzing the earliest step in innate immune recognition of influenza B virus by human macrophages. We show that influenza B virus induces IRF3 activation, leading to IFN gene expression after viral RNPs (vRNPs) are released into the cytosol and are recognized by RIG-I receptor, meaning that the incoming influenza B virus is already able to activate IFN gene expression. In contrast, influenza A (H3N2) virus failed to activate IRF3 at very early times of infection, suggesting that there are differences in innate immune recognition between influenza A and B viruses.
Replication and Transmission of the Novel Bovine Influenza D Virus in a Guinea Pig Model
Authors: Sreenivasan Chithra , Thomas Milton , Sheng Zizhang , Hause Ben M. , Collin Emily A. , Knudsen David E. B. , Pillatzki Angela , Nelson Eric , Wang Dan , Kaushik Radhey S. , Li Feng
Published: September 2015

Influenza D virus (FLUDV) is a novel influenza virus that infects cattle and swine. The goal of this study was to investigate the replication and transmission of bovine FLUDV in guinea pigs. Following direct intranasal inoculation of animals, the virus was detected in nasal washes of infected animals during the first 7 days postinfection. High viral titers were obtained from nasal turbinates and lung tissues of directly inoculated animals. Further, bovine FLUDV was able to transmit from the infected guinea pigs to sentinel animals by means of contact and not by aerosol dissemination under the experimental conditions tested in this study. Despite exhibiting no clinical signs, infected guinea pigs developed seroconversion and the viral antigen was detected in lungs of animals by immunohistochemistry. The observation that bovine FLUDV replicated in the respiratory tract of guinea pigs was similar to observations described previously in studies of gnotobiotic calves and pigs experimentally infected with bovine FLUDV but different from those described previously in experimental infections in ferrets and swine with a swine FLUDV, which supported virus replication only in the upper respiratory tract and not in the lower respiratory tract, including lung. Our study established that guinea pigs could be used as an animal model for studying this newly emerging influenza virus.

IMPORTANCE
Influenza D virus (FLUDV) is a novel emerging pathogen with bovine as its primary host. The epidemiology and pathogenicity of the virus are not yet known. FLUDV also spreads to swine, and the presence of FLUDV-specific antibodies in humans could indicate that there is a potential for zoonosis. Our results showed that bovine FLUDV replicated in the nasal turbinate and lungs of guinea pigs at high titers and was also able to transmit from an infected animal to sentinel animals by contact. The fact that bovine FLUDV replicated productively in both the upper and lower respiratory tracts of guinea pigs, similarly to virus infection in its native host, demonstrates that guinea pigs would be a suitable model host to study the replication and transmission potential of bovine FLUDV.
Deficiencies in Cellular Processes Modulated by the Retinoblastoma Protein Do Not Account for Reduced Human Cytomegalovirus Replication in Its Absence
Authors: VanDeusen Halena R. , Kalejta Robert F.
Published: September 2015

Despite encoding multiple viral proteins that modulate the retinoblastoma (Rb) protein in a manner classically defined as inactivation, human cytomegalovirus (HCMV) requires the presence of the Rb protein to replicate efficiently. In uninfected cells, Rb controls numerous pathways that the virus also commandeers during infection. These include cell cycle progression, senescence, mitochondrial biogenesis, apoptosis, and glutaminolysis. We investigated whether a potential inability of HCMV to regulate these Rb-controlled pathways in the absence of the Rb protein was the reason for reduced viral productive replication in Rb knockdown cells. We found that HCMV was equally able to modulate these pathways in the parental Rb-expressing and Rb-depleted cells. Our results suggest that Rb may be required to enhance a specific viral process during HCMV productive replication.

IMPORTANCE
The retinoblastoma (Rb) tumor suppressor is well established as a repressor of E2F-dependent transcription. Rb hyperphosphorylation, degradation, and binding by viral oncoproteins are also codified. Recent reports indicate Rb can be monophosphorylated, repress the transcription of antiviral genes in association with adenovirus E1A, modulate cellular responses to polycomb-mediated epigenetic methylations in human papillomavirus type 16 E7 expressing cells, and increase the efficiency of human cytomegalovirus (HCMV) productive replication. Since Rb function also now extends to regulation of mitochondrial function (apoptosis, metabolism), it is clear that our current understanding of this protein is insufficient to explain its roles in virus-infected cells and tumors. Work here reinforces this concept, showing the known roles of Rb are insufficient to explain its positive impact on HCMV replication. Therefore, HCMV, along with other viral systems, provide valuable tools to probe functions of Rb that might be modulated with therapeutics for cancers with viral or nonviral etiologies.
Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
Authors: Rujas Edurne , Gulzar Naveed , Morante Koldo , Tsumoto Kouhei , Scott Jamie K. , Nieva José L. , Caaveiro Jose M. M.
Published: September 2015

The 4E10 antibody recognizes the membrane-proximal external region (MPER) of the HIV-1 Env glycoprotein gp41 transmembrane subunit, exhibiting one of the broadest neutralizing activities known to date. The neutralizing activity of 4E10 requires solvent-exposed hydrophobic residues at the apex of the complementarity-determining region (CDR) H3 loop, but the molecular basis for this requirement has not been clarified. Here, we report the cocrystal structures and the energetic parameters of binding of a peptide bearing the 4E10-epitope sequence (4E10ep) to nonneutralizing versions of the 4E10 Fab. Nonneutralizing Fabs were obtained by shortening and decreasing the hydrophobicity of the CDR-H3 loop (termed ΔLoop) or by substituting the two tryptophan residues of the CDR-H3 apex with Asp residues (termed WDWD), which also decreases hydrophobicity but preserves the length of the loop. The analysis was complemented by the first crystal structure of the 4E10 Fab in its ligand-free state. Collectively, the data ruled out major conformational changes of CDR-H3 at any stage during the binding process (equilibrium or transition state). Although these mutations did not impact the affinity of wild-type Fab for the 4E10ep in solution, the two nonneutralizing versions of 4E10 were deficient in binding to MPER inserted in the plasma membrane (mimicking the environment faced by the antibody
in vivo
). The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear α-helical epitope and likely constrained by the viral membrane lipids.

IMPORTANCE
The broadly neutralizing anti-HIV-1 4E10 antibody blocks infection caused by nearly all viral strains and isolates examined thus far. However, 4E10 (or 4E10-like) antibodies are rarely found in HIV-1-infected individuals or elicited through vaccination. Impediments to the design of successful 4E10 immunogens are partly attributed to an incomplete understanding of the structural and binding characteristics of this class of antibodies. Since the broadly neutralizing activity of 4E10 is abrogated by mutations of the tip of the CDR-H3, we investigated their impact on binding of the MPER-epitope at the atomic and energetic levels. We conclude that the difference between neutralizing and nonneutralizing antibodies of 4E10 is neither structural nor energetic but is related to the capacity to recognize the HIV-1 gp41 epitope inserted in biological membranes. Our findings strengthen the idea that to elicit similar neutralizing antibodies, the suitable MPER vaccine must be “delivered” in a membrane environment.
A Novel Tricyclic Polyketide, Vanitaracin A, Specifically Inhibits the Entry of Hepatitis B and D Viruses by Targeting Sodium Taurocholate Cotransporting Polypeptide
Authors: Kaneko Manabu , Watashi Koichi , Kamisuki Shinji , Matsunaga Hiroki , Iwamoto Masashi , Kawai Fumihiro , Ohashi Hirofumi , Tsukuda Senko , Shimura Satomi , Suzuki Ryosuke , Aizaki Hideki , Sugiyama Masaya , Park Sam-Yong , Ito Takayoshi , Ohtani Naoko , Sugawara Fumio , Tanaka Yasuhito , Mizokami Masashi , Sureau Camille , Wakita Takaji
Published: September 2015

Anti-hepatitis B virus (HBV) drugs are currently limited to nucleos(t)ide analogs (NAs) and interferons. A challenge of drug development is the identification of small molecules that suppress HBV infection from new chemical sources. Here, from a fungus-derived secondary metabolite library, we identify a structurally novel tricyclic polyketide, named vanitaracin A, which specifically inhibits HBV infection. Vanitaracin A inhibited the viral entry process with a submicromolar 50% inhibitory concentration (IC
50
) (IC
50
= 0.61 ± 0.23 μM), without evident cytotoxicity (50% cytotoxic concentration of >256 μM; selectivity index value of >419) in primary human hepatocytes. Vanitaracin A did not affect the HBV replication process. This compound was found to directly interact with the HBV entry receptor sodium taurocholate cotransporting polypeptide (NTCP) and impaired its bile acid transport activity. Consistent with this NTCP targeting, antiviral activity of vanitaracin A was observed with hepatitis D virus (HDV) but not hepatitis C virus. Importantly, vanitaracin A inhibited infection by all HBV genotypes tested (genotypes A to D) and clinically relevant NA-resistant HBV isolate. Thus, we identified a fungal metabolite, vanitaracin A, which was a potent, well-tolerated, and broadly active inhibitor of HBV and HDV entry. This compound, or its related analogs, could be part of an antiviral strategy for preventing reinfection with HBV, including clinically relevant nucleos(t)ide analog-resistant virus.

IMPORTANCE
For achieving better treatment and prevention of hepatitis B virus (HBV) infection, anti-HBV agents targeting a new molecule are in great demand. Although sodium taurocholate cotransporting polypeptide (NTCP) has recently been reported to be an essential host factor for HBV entry, there is a limited number of reports that identify new compounds targeting NTCP and inhibiting HBV entry. Here, from an uncharacterized chemical library, we isolated a structurally new compound, named vanitaracin A, which inhibited the process of entry of HBV and hepatitis D virus (HDV). This compound was suggested to directly interact with NTCP and inhibit its transporter activity. Importantly, vanitaracin A inhibited the entry of all HBV genotypes examined and of a clinically relevant nucleos(t)ide analog-resistant HBV isolate.
Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia
Authors: Eden John-Sebastian , Read Andrew J. , Duckworth Janine A. , Strive Tanja , Holmes Edward C.
Published: September 2015

To resolve the evolutionary history of rabbit hemorrhagic disease virus (RHDV), we performed a genomic analysis of the viral stocks imported and released as a biocontrol measure in Australia, as well as a global phylogenetic analysis. Importantly, conflicts were identified between the sequences determined here and those previously published that may have affected evolutionary rate estimates. By removing likely erroneous sequences, we show that RHDV emerged only shortly before its initial description in China.
Mimivirus Fibrils Are Important for Viral Attachment to the Microbial World by a Diverse Glycoside Interaction Repertoire
Authors: Rodrigues Rodrigo Araújo Lima , dos Santos Silva Ludmila Karen , Dornas Fábio Pio , de Oliveira Danilo Bretas , Magalhães Thais Furtado Ferreira , Santos Daniel Assis , Costa Adriana Oliveira , de Macêdo Farias Luiz , Magalhães Paula Prazeres , Bonjardim Cláudio Antônio , Kroon Erna Geessien , La Scola Bernard , Cortines Juliana Reis , Abrahão Jônatas Santos
Published: September 2015

Acanthamoeba polyphaga mimivirus
(APMV) is a giant virus from the
Mimiviridae
family. It has many unusual features, such as a pseudoicosahedral capsid that presents a starfish shape in one of its vertices, through which the ∼1.2-Mb double-stranded DNA is released. It also has a dense glycoprotein fibril layer covering the capsid that has not yet been functionally characterized. Here, we verified that although these structures are not essential for viral replication, they are truly necessary for viral adhesion to amoebae, its natural host. In the absence of fibrils, APMV had a significantly lower level of attachment to the
Acanthamoeba castellanii
surface. This adhesion is mediated by glycans, specifically, mannose and
N
-acetylglucosamine (a monomer of chitin and peptidoglycan), both of which are largely distributed in nature as structural components of several organisms. Indeed, APMV was able to attach to different organisms, such as Gram-positive bacteria, fungi, and arthropods, but not to Gram-negative bacteria. This prompted us to predict that (i) arthropods, mainly insects, might act as mimivirus dispersers and (ii) by attaching to other microorganisms, APMV could be ingested by amoebae, leading to the successful production of viral progeny. To date, this mechanism has never been described in the virosphere.

IMPORTANCE
APMV is a giant virus that is both genetically and structurally complex. Its size is similar to that of small bacteria, and it replicates inside amoebae. The viral capsid is covered by a dense glycoprotein fibril layer, but its function has remained unknown, until now. We found that the fibrils are not essential for mimivirus replication but that they are truly necessary for viral adhesion to the cell surface. This interaction is mediated by glycans, mainly
N
-acetylglucosamine. We also verified that APMV is able to attach to bacteria, fungi, and arthropods. This indicates that insects might act as mimivirus dispersers and that adhesion to other microorganisms could facilitate viral ingestion by amoebae, a mechanism never before described in the virosphere.
Monoclonal Antibodies Directed toward the Hepatitis C Virus Glycoprotein E2 Detect Antigenic Differences Modulated by the N-Terminal Hypervariable Region 1 (HVR1), HVR2, and Intergenotypic Variable Region
Authors: Alhammad Yousef , Gu Jun , Boo Irene , Harrison David , McCaffrey Kathleen , Vietheer Patricia T. , Edwards Stirling , Quinn Charles , Coulibaly Fásseli , Poumbourios Pantelis , Drummer Heidi E.
Published: September 2015

Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 form a heterodimer and mediate receptor interactions and viral fusion. Both E1 and E2 are targets of the neutralizing antibody (NAb) response and are candidates for the production of vaccines that generate humoral immunity. Previous studies demonstrated that N-terminal hypervariable region 1 (HVR1) can modulate the neutralization potential of monoclonal antibodies (MAbs), but no information is available on the influence of HVR2 or the intergenotypic variable region (igVR) on antigenicity. In this study, we examined how the variable regions influence the antigenicity of the receptor binding domain of E2 spanning HCV polyprotein residues 384 to 661 (E2
661
) using a panel of MAbs raised against E2
661
and E2
661
lacking HVR1, HVR2, and the igVR (Δ123) and well-characterized MAbs isolated from infected humans. We show for a subset of both neutralizing and nonneutralizing MAbs that all three variable regions decrease the ability of MAbs to bind E2
661
and reduce the ability of MAbs to inhibit E2-CD81 interactions. In addition, we describe a new MAb directed toward the region spanning residues 411 to 428 of E2 (MAb24) that demonstrates broad neutralization against all 7 genotypes of HCV. The ability of MAb24 to inhibit E2-CD81 interactions is strongly influenced by the three variable regions. Our data suggest that HVR1, HVR2, and the igVR modulate exposure of epitopes on the core domain of E2 and their ability to prevent E2-CD81 interactions. These studies suggest that the function of HVR2 and the igVR is to modulate antibody recognition of glycoprotein E2 and may contribute to immune evasion.

IMPORTANCE
This study reveals conformational and antigenic differences between the Δ123 and intact E2
661
glycoproteins and provides new structural and functional data about the three variable regions and their role in occluding neutralizing and nonneutralizing epitopes on the E2 core domain. The variable regions may therefore function to reduce the ability of HCV to elicit NAbs directed toward the conserved core domain. Future studies aimed at generating a three-dimensional structure for intact E2 containing HVR1, and the adjoining NAb epitope at residues 412 to 428, together with HVR2, will reveal how the variable regions modulate antigenic structure.
Corresponding waist circumference and body mass index values based on 10-year absolute type 2 diabetes risk in an Australian Aboriginal community
Authors: Adegbija Odewumi , Hoy Wendy E , Wang Zhiqiang
Published: September 2015

Objective

There is a lack of waist circumference (WC) thresholds to identify Aboriginal individuals at high risk of type 2 diabetes. We generated gender-specific WC values with equivalent 10-year absolute risk of type 2 diabetes as body mass index (BMI) points in an Australian Aboriginal community to contribute to guidelines needed for establishing WC cut-off points for Aboriginals.

Research design and methods

A cohort of 803 adult participants free from type 2 diabetes in an Aboriginal community was followed up for up to 20 years. We derived WC values with absolute risks equivalent for the development of type 2 diabetes as BMI values (20–35 kg/m2) using the Weibull accelerated failure-time model.

Results

After a mean follow-up of 15.7 years, 110 participants developed type 2 diabetes. Absolute risk of type 2 diabetes increased as WC increased, ranging from 3.52% (WC=77.5 cm) to 14.14% (WC=119.9 cm) in males, and 5.04% (WC=79.5 cm) to 24.25% (WC=113.7 cm) in females. In males, WC values with same absolute risks of type 2 diabetes as BMI values were 77.5 cm for BMI=20 kg/m2, 91.5 cm for BMI=25 kg/m2(overweight threshold), 105.7 cm for BMI=30 kg/m2(obesity threshold) and 119.9 cm for BMI=35 kg/m2. In females, WC values were 79.5 cm for BMI=20 kg/m2, 90.9 cm for BMI=25 kg/m2, 102.3 cm for BMI=30 kg/m2and 113.7 cm for BMI=35 kg/m2. Interaction between WC and gender was not statistically significant (p=0.53).

Conclusions

The absolute risk of type 2 diabetes increased with higher WC measured at baseline screening. Males were not significantly different from females in the association between WC and type 2 diabetes. Our findings are useful contributions for future establishment of WC cut-off points for identifying high-risk individuals in Aboriginal people.
Factors influencing obesogenic dietary intake in young children (0–6 years): systematic review of qualitative evidence
Authors: Mazarello Paes Veena , Ong Ken K , Lakshman Rajalakshmi
Published: September 2015

Background

Obesogenic dietary intake is prevalent in young children and is associated with obesity and other adverse health outcomes in childhood and later in life.

Objective

To describe the barriers to and facilitators of obesogenic dietary intake in early childhood, in order to inform interventions and public health policies to prevent obesity.

Design

Systematic review of qualitative literature on factors influencing obesogenic diets in children aged 0–6 years.

Data sources

MEDLINE, EMBASE, CINAHL, PsycINFO, Web of Knowledge, British Nursing Index, ASSIA and Sociological Abstracts.

Review methods

Qualitative studies meeting the inclusion criteria were synthesised. Data were analysed by creating a thematic framework, underpinned by the socioecological model, which included familiarisation of data across the studies, indexing, charting, mapping and interpretation.

Results

20 studies from the USA (10), Europe (6) and Australia (4) included the views of 1067 participants (901 parents/caregivers, 37 children, 87 teachers, 15 dieticians and 27 nursery staff). Study designs included focus groups (n=16), individual interviews (n=6) and ethnography (n=1) with some studies using more than one design. Despite wide differences in the study context and focus, several consistent themes emerged. Parental factors increasing young children's obesogenic diets were: negative parent/family/peer modelling, lack of knowledge, time constraints, using food as reward, affordability and concerns about child's health. Child preferences also increased intake. Environmental factors increasing intake include: availability, advertising, societal, cultural and preschool/childcare influences.

Conclusions

Future intervention strategies should aim to promote modelling of positive behaviours, create home and preschool environments that promote healthy diets, and simultaneously target factors at the family and preschool/childcare levels.

Trial registration number

This review is one of a series of systematic reviews on the determinants of obesogenic behaviours in young children, registered with the International Prospective Register for Systematic Reviews (PROSPERO), CRD42012002881.
Older people, the natural environment and common mental disorders: cross-sectional results from the Cognitive Function and Ageing Study
Authors: Wu Yu-Tzu , Prina A Matthew , Jones Andy , Matthews Fiona E , Brayne Carol ,   MRC CFAS
Published: September 2015

Objectives

To explore the hypothesis that higher exposure to natural environments in local areas is associated with a lower odds of depression and anxiety in later life.

Design

A cross-sectional study based on the year-10 interview of the Medical Research Council Cognitive Function and Ageing Study (CFAS), a population-based study of ageing in the UK. Postcodes of the CFAS participants were mapped onto small geographic units, lower-layer super output areas (LSOAs) and linked to environmental data from government databases. The natural environment was characterised as the percentage of green space and private gardens in each LSOA based on the UK Generalised Land Use 2001 Dataset.

Participants

2424 people aged 74 and over in the CFAS year-10 follow-up interview (2001) from 4 English centres (Cambridgeshire, Nottingham, Newcastle and Oxford).

Main outcome measures

Depression and anxiety; clinical and subthreshold cases were identified using the Geriatric Mental State Examination (GMS) package and its associated diagnostic algorithm: the Automated Geriatric Examination for Computer Assisted Taxonomy.

Results

Compared with the lowest quartile, living in the highest quartile of neighbourhood natural environment provision was associated with a reduced odds of subthreshold depression (OR 0.66, 95% CI 0.46 to 0.95), anxiety symptoms (OR 0.62, 95% CI 0.46 to 0.83) and their co-occurrence (OR 0.55, 95% CI 0.35 to 0.84) after adjusting for individual-level factors. Controlling for area deprivation attenuated the strength of associations for subthreshold depression by 20% but not for anxiety symptoms or for co-occurrence of the conditions.

Conclusions

A high exposure to natural environments (green space and gardens) in communities was associated with fewer mental disorders among older people. Increasing provision of green environments in local areas could be a potential population-level intervention to improve mental health among older people.