bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in teacher–student relationships
Authors: Gehlbach Hunter , Brinkworth Maureen E. , Harris Anna D.
Published: December 2011

Background.Although teacher–student relationships lie at the heart of students’ schooling experience, fundamental questions regarding these relationships remain unanswered.

Aims.This study investigates three related questions about these relationships: To what extent do they change from the beginning to the end of a school year? Are any emergent changes associated with shifts in students’ academic or motivational outcomes? Are certain ‘upstream’ factors associated with improvements or declines in teacher–student relationships?

Sample.We investigate these questions with a sample of middle school students (N =119) and their teachers (N =30).

Methods.Through a novel approach which accounts for both perspectives within teacher–student relationships, we assess these relationships at the beginning and end of the school year. Using multi‐level models, we examine how changes in these relationships are associated with changes in students’ grades, homework completion rates, self‐efficacy, and effort. In addition, we examine associations with two potential precursors to teacher–student relationships: students’ accuracy in taking their teachers’ perspective and their perceptions of similarity to their teachers.

Results.We find that substantial changes occur in these relationships from the beginning to the end of the year; these changes are associated with shifts in important student outcomes; and changes in students’ social perspective taking accuracy and perceived similarity to their teachers correspond with changes in teacher–student relationships.

Conclusions.Given the malleability of teacher–student relationships and their importance for key achievement and motivational outcomes, we advocate for researchers to conduct field experiments to inform how to improve these critical relationships.
Perceptual equivalence of psychological climates within groups: When agreement indices do not agree
Authors: Beus Jeremy M. , Jarrett Steven M. , Bergman Mindy E. , Payne Stephanie C.
Published: December 2011

Individual climate perceptions (i.e., psychological climates) are often aggregated to form group‐level climates without considering the equivalence of the meaning of climate within groups. Confirming perceptual equivalence across faultlines – within‐group dividing lines that can create subgroups based on the alignment of group member attributes (Lau & Murnighan, 1998) – is a particularly important concern given that sense‐making processes and subsequent psychological climates are likely to differ across faultlines. Using safety climate as an exemplar, we demonstrate the importance of assessing qualitative perceptual equivalence (i.e., perceptions of what a climate is) within groups instead of solely relying on traditional agreement indices (e.g., rwg, intraclass correlation [ICC]) to make aggregation decisions. Specifically, we tested for perceptual equivalence across context‐specific faultlines (hierarchical level and organizational heritage) in a large, multinational organization using multi‐group hierarchical confirmatory factor analyses and found that although traditional agreement indices universally supported aggregation decisions, tests of perceptual equivalence in 8 of 12 separate subgroup analyses failed to support aggregation. These findings confirm the importance of testing for perceptual equivalence within groups before aggregating psychological climates to the group level.

Practitioner points

• Our findings underscore the value for organizations to consider the potential existence of faultlines and to examine their possible influence on employee climate perceptions.

• These findings also point to the need for organizations to promote qualitative equivalence of climate perceptions among employees independent of the potential existence of faultlines.
Inhibition of voltage‐gated proton channels by local anaesthetics in GMI‐R1 rat microglia
Authors: Matsuura Tadashi , Mori Takashi , Hasaka Megumi , Kuno Miyuki , Kawawaki Junko , Nishikawa Kiyonobu , Narahashi Toshio , Sawada Makoto , Asada Akira
Published: December 2011

Non‐technical summary  Lidocaine and bupivacaine are the most commonly used local anaesthetics in clinical practices such as neuraxial anaesthesia and local infiltration. They are known to suppress phagocytosis and the production of reactive oxygen species in immune cells. Voltage‐gated proton channels are abundantly expressed in immune cells, including microglia, and play crucial roles in sustaining phagocytosis. We show that both lidocaine and bupivacaine increase the intracellular pH of microglia by their weak base properties and, consequently, inhibit proton channels. This is a novel mechanism underlying actions of local anaesthetics. Our results also indicate that the proton channel is a useful tool for monitoring the behaviours of lidocaine and bupivacaine across the cellular membrane.
Quantifying Individual Losses in a Direct Methanol Fuel Cell
Authors: García-Díaz Brenda L. , Patterson Jennifer R. , Weidner John W.
Published: December 2011

Studying the performance of a direct methanol fuel cell (DMFC) is complicated by the complex interactions of kinetic and transport processes. As a result, changes in one aspect of the cell have consequences in other aspects, which are difficult to elucidate from full-cell polarization (i.e., voltage versus current) behavior. This study outlines a strategy to use current and voltage relationships from anode half-cells, cathode half-cells, and hydrogen pump coupled with methanol crossover data and a mathematical model. In this way, all the kinetic and transport processes have been quantified, and the cell voltage was deconstructed (i.e., individual voltage losses were quantified). This data analysis accounts for all of the voltage losses observed during the operation of the full cell. As expected, the anode and cathode overpotentials accounted for most of the losses (i.e., 92% on average). Also, the cathode flow rate has been shown to affect the methanol crossover by diffusion. Cells operated at constant stoichiometry or where the cathode flow rate is small can show a parabolic shape in the methanol crossover because the electroosmotic drag dominates over diffusion as the primary transport mechanism for methanol through the membrane. Decrease in the methanol crossover was observed for cells with high compression and thicker cathode electrodes. The one-dimensional model, developed previously (García et al., 2004, “Mathematical Model of a Direct Methanol Fuel Cell,” J. Fuel Cell Sci. Technol., 1(1), pp. 43–48), was improved by: (1) including methanol transport from the anode flow channel to the backing layer using a mass transfer resistance and (2) accounting for the unreacted methanol transport through the cathode. The model was able to reasonably predict the anode, cathode, full-cell polarization, and methanol crossover data for methanol concentrations between 0.05 M and 2 M at all operating currents.
Role of ions, photons, and radicals in inducing plasma damage to ultra low-k dielectrics
Authors: Shi Hualiang , Huang Huai , Bao Junjing , Liu Junjun , Ho Paul S. , Zhou Yifeng , Pender Jeremy T. , Armacost Michael D. , Kyser David
Published: December 2011

The damage induced by CO2 and O2 plasmas to an ultra low-k (ULK) dielectric film with a dielectric constant (κ) of 2.2 was investigated. The dielectric constant was observed to increase due to methyl depletion, moisture uptake, and surface densification. A gap structure was used to delineate the role of ions, photons and radicals in inducing the damage, where the experimental variables included an optical mask (MgF2, fused silica, and Si), a gap height, an inductively coupled plasma power source, a bias power on the bottom electrode, variable chamber pressure, and variable substrate temperature. The plasma radical density distribution inside the gap between the optical mask and the ULK film was simulated. The simulation was based on radical diffusion, reaction, and recombination inside the gap. The experimental results and the numerical simulation showed that the oxygen radicals played an important role in plasma induced damage which was found to be proportional to the oxygen radical density and enhanced byvacuum ultraviolet (VUV) photon radiation. Under certain experimental conditions, ion bombardment can induce surface densification and suppress radical diffusion. The role of UV and VUV photons in induced damage was investigated with Ar plasma using the gap structure and it was found that the photons can induce surface damage directly.
Resource Letter EM-1: Electromagnetic Momentum
Authors: Griffiths David J.
Published: December 2011

This Resource Letter surveys the literature on momentum in electromagnetic fields, including the general theory, the relation between electromagnetic momentum and vector potential, “hidden” momentum, the 4/3 problem for electromagnetic mass, and the Abraham–Minkowski controversy regarding the field momentum in polarizable and magnetizable media.
Electrostatic clocks
Authors: Zypman Fredy R.
Published: December 2011

We consider the motion of a charged ring in the presence of the electric field produced by an infinite line of charge. We first introduce a clock based on small oscillations of the ring which oscillates with a period in the range of seconds. The same system is next considered beyond the small angle approximation, an integrable problem in classical mechanics. The partition function for an ensemble of these oscillators is also obtained, making the system a fruitful playground for courses in thermodynamics and statistical mechanics. Finally, we consider purely spinning motion of the ring to gain insight into the effective mass, a concept useful in condensed matter physics.
Introductory physics going soft
Authors: Langbeheim Elon , Livne Shelly , Safran Samuel A. , Yerushalmi Edit
Published: December 2011

We describe an elective course on soft matter at the level of introductory physics. Soft matter physics serves as a context that motivates the presentation of basic ideas in statistical thermodynamics and their applications. It also is an example of a contemporary field that is interdisciplinary and touches on chemistry, biology, and physics. We outline a curriculum that uses the lattice gas model as a quantitative and visual tool, initially to introduce entropy, and later to facilitate the calculation of interactions. We demonstrate how free energy minimization can be used to teach students to understand the properties of soft matter systems such as the phases of fluid mixtures, wetting of interfaces, self-assembly of surfactants, and polymers. We discuss several suggested activities in the form of inquiry projects which allow students to apply the concepts they have learned to experimental systems.
From Flat Foot to Fat Foot: Structure, Ontogeny, Function, and Evolution of Elephant “Sixth Toes”
Authors: Hutchinson John R. , Delmer Cyrille , Miller Charlotte E. , Hildebrandt Thomas , Pitsillides Andrew A. , Boyde Alan
Published: December 2011

Elephants have an extra bone in their feet that can be traced through their fossil record to reveal a transition from flat to raised feet.
Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
Authors: Carothers James M. , Goler Jonathan A. , Juminaga Darmawi , Keasling Jay D.
Published: December 2011

Evidence is presented for the feasibility of computer-aided design of biological circuits for regulation of gene expression.
The Art and Craft of Portraying Data
Visualize This
The FlowingData Guide to Design, Visualization, and Statistics

by Nathan Yau

Wiley, Indianapolis, 2011. 384 pp. Paper, $39.99, C$47.99. ISBN 9780470944882.
Visual Complexity
Mapping Patterns of Information

by Manuel Lima

Princeton Architectural Press, New York, 2011. 272 pp., $50, £35. ISBN 9781568989365.
Authors: Kosara Robert
Published: December 2011

Lima presents a collection of exemplary visualizations of data, and Yau offers hands-on guidance for effectively displaying information.
An Exit Strategy for Measles Virus
Authors: Racaniello Vincent
Published: December 2011

A receptor for measles virus on epithelial cells reveals how the virus accesses the respiratory tract.
Seroprevalence of Serum Bactericidal Antibodies against Group W135 and Y Meningococci in England in 2009
Authors: Trotter Caroline L. , Findlow Helen , Borrow Ray
Published: December 2011

Serological surveillance has been used in the United Kingdom to inform vaccine policy for several infections, including those with group C meningococci. Meningococcal conjugate vaccines, containing capsular groups A, W135, and Y in addition to C, are now available, but their use in the United Kingdom is restricted to at-risk groups and travelers to areas of endemicity. The aim of this study was to establish a baseline for natural immunity for groups W135 and Y. Serum samples collected in 2009 from individuals of all ages were obtained from the Health Protection Agency Seroepidemiology Unit, which collects residual sera from participating laboratories across the country. Serum bactericidal antibody (SBA) activity against two reference strains, representing groups Y (strain M03 241125) and W135 (strain M01 240070), was determined with 1,191 sera using a standardized complement-mediated SBA assay, with complement derived from baby rabbits (rSBA). The age-specific geometric mean titers (GMTs) and percentages of individuals with rSBA titers of ≥8 were calculated, together with 95% confidence intervals (CI). Overall, 18.4% and 19.6% had rSBA titers of ≥8 for groups W135 and Y, respectively. Antibody prevalence varied by age. In general, rSBA titers were low for younger children, with serum samples from 7% and 13% of children under 5 years achieving titers of ≥8 against groups W135 and Y, respectively. GMTs peaked for 20- to 24-year-olds for group W135 (GMT, 7.1; 95% CI, 4.7, 10.9) and for 30- to 44-year-olds for group Y (GMT, 8.6; 95% CI, 5.9, 12.7). Unlike seroprevalence against group B meningococci, there was not an obvious peak in SBA titers in samples from teenagers. Natural immunity against group W135 and Y meningococci in England appears to be low.
Phase 1 Study of a Recombinant Mutant Protective Antigen of Bacillus anthracis
Authors: Bellanti Joseph A. , Lin Feng-Ying C. , Chu Chiayung , Shiloach Joseph , Leppla Stephen H. , Benavides German A. , Karpas Arthur , Moayeri Mahtab , Guo Chunyan , Robbins John B. , Schneerson Rachel
Published: December 2011

A phase 1 study of a recombinant mutant protective antigen (rPA) vaccine was conducted in 186 healthy adults aged 18 to 45 years. Volunteers were randomized to receive one of three formulations of rPA (formalin treated, alum adsorbed, or both), in 10- or 20-μg dosages each, or the licensed vaccine, AVA. Three injections were given at 2-month intervals and a 4th 1 year after the 3rd. Vaccinees were examined at the clinic once following each injection, at 48 to 72 h postinjection. Adverse reactions were recorded in diaries for 7 days. Sera were collected before each injection and 1 week after the 1st, 2 weeks after the 3rd and 4th, and 1 year after the 4th. Serum anti-PA IgG was assayed by enzyme-linked immunosorbent assay (ELISA) and toxin neutralization assay (TNA). All formulations at both dosages were safe and immunogenic, inducing booster responses, with the highest antibody levels following the 4th injection (354 to 732 μg/ml). The lowest levels were induced by the formalin-only-treated rPA; there was no statistical difference between levels induced by alum-adsorbed and formalin-treated/alum-adsorbed rPA or by the two dosages. The antibody levels declined in all groups during the 1-year intervals after the 3rd and 4th injections but less so during the 2nd year, after the 4th injection (fold decreases were 10 to 25 versus 3.4 to 7.0,
P
< 0.001). There were too few AVA recipients for statistical comparisons, but their antibody levels followed those of rPA. Anti-rPA measured by ELISA correlated with TNA titers (
r
= 0.97). These data support studying alum-adsorbed rPA in children.
Humoral and Cellular Immune Responses to Yersinia pestis Infection in Long-Term Recovered Plague Patients
Authors: Li Bei , Du Chunhong , Zhou Lei , Bi Yujing , Wang Xiaoyi , Wen Li , Guo Zhaobiao , Song Zhizhong , Yang Ruifu
Published: December 2011

Plague is one of the most dangerous diseases and is caused by
Yersinia pestis
. Effective vaccine development requires understanding of immune protective mechanisms against the bacterium in humans. In this study, the humoral and memory cellular immune responses in plague patients (
n
= 65) recovered from
Y. pestis
infection during the past 16 years were investigated using a protein microarray and an enzyme-linked immunosorbent spot assay (ELISpot). The seroprevalence to the F1 antigen in all recovered patients is 78.5%. In patients infected more than a decade ago, the antibody-positive rate still remains 69.5%. There is no difference in the antibody presence between gender, age, and infected years, but it seems to be associated with the F1 antibody titers during infection (
r
= 0.821;
P
< 0.05). Except F1 antibody, the antibodies against LcrV and YopD were detected in most of the patients, suggesting they could be the potential diagnostic markers for detecting the infection of F1-negative strains. Regarding cellular immunity, the cell number producing gamma interferon (IFN-γ), stimulated by F1 and LcrV, respectively,
in vitro
to the peripheral blood mononuclear cells of 7 plague patients and 4 negative controls, showed no significant difference, indicating F1 and LcrV are not dominant T cell antigens against plague for a longer time in humans. Our findings have direct implications for the future design and development of effective vaccines against
Y. pestis
infection and the development of new target-based diagnostics.
Genotypic Diversity of Coxiella burnetii in the 2007-2010 Q Fever Outbreak Episodes in The Netherlands
Authors: Tilburg Jeroen J. H. C. , Rossen John W. A. , van Hannen Erik J. , Melchers Willem J. G. , Hermans Mirjam H. A. , van de Bovenkamp Jeroen , Roest Hendrik Jan I. J. , de Bruin Arnout , Nabuurs-Franssen Marrigje H. , Horrevorts Alphons M. , Klaassen Corné H. W.
Published: December 2011

The genotypic diversity of
Coxiella burnetii
in clinical samples obtained from the Dutch Q fever outbreak episodes of 2007-2010 was determined by using a 6-locus variable-number tandem repeat analysis panel. The results are consistent with the introduction of one founder genotype that is gradually diversifying over time while spreading throughout The Netherlands.
Association between Helicobacter pylori Virulence Factors and Gastroduodenal Diseases in Okinawa, Japan
Authors: Matsunari Osamu , Shiota Seiji , Suzuki Rumiko , Watada Masahide , Kinjo Nagisa , Murakami Kazunari , Fujioka Toshio , Kinjo Fukunori , Yamaoka Yoshio
Published: December 2011

The incidence of gastric cancer in Okinawa is lowest in Japan. Some previous reports using small number of strains suggested that the high prevalence of
Helicobacter pylori
with Western-type
cagA
in Okinawa compared to other areas in Japan might contribute to the low incidence of gastric cancer. It has still not been confirmed why the prevalence of Western-type
cagA
strains is high in Okinawa. We examined the association between the virulence factors of
H. pylori
and gastroduodenal diseases in Okinawa. The genotypes of
cagA
and
vacA
of 337
H. pylori
strains were determined by PCR and gene sequencing. The genealogy of these Western-type
cagA
strains in Okinawa was analyzed by multilocus sequence typing (MLST). Overall, 86.4% of the strains possessed
cagA
: 70.3% were East-Asian type and 16.0% were Western type. After adjustment by age and sex, the presence of East-Asian-type
cagA
/
vacA
s1m1 genotypes was significantly associated with gastric cancer compared to gastritis (odds ratio = 6.68, 95% confidence interval = 1.73 to 25.8). The structure of Western-type CagA in Okinawa was different from that of typical Western-type CagA found in Western countries. Intriguingly, MLST analysis revealed that the majority of Western-type
cagA
strains formed individual clusters but not hpEurope. Overall, low prevalence of gastric cancer in Okinawa may result from the high prevalence of non-East-Asian-type
cagA
strains. The origin of Western-type
cagA
strains in Okinawa may be different from those of Western countries.
Emergence of Hospital- and Community-Associated Panton-Valentine Leukocidin-Positive Methicillin-Resistant Staphylococcus aureus Genotype ST772-MRSA-V in Ireland and Detailed Investigation of an ST772-MRSA-V Cluster in a Neonatal Intensive Care Unit
Authors: Brennan Gráinne I. , Shore Anna C. , Corcoran Suzanne , Tecklenborg Sarah , Coleman David C. , O'Connell Brian
Published: December 2011

Sequence type 22 (ST22) methicillin-resistantStaphylococcus aureus(MRSA) harboring staphylococcal cassette chromosomemec(SCCmec) IV (ST22-MRSA-IV) has predominated in Irish hospitals since the late 1990s. Six distinct clones of community-associated MRSA (CA-MRSA) have also been identified in Ireland. A new strain of CA-MRSA, ST772-MRSA-V, has recently emerged and become widespread in India and has spread into hospitals. In the present study, highly similar MRSA isolates were recovered from seven colonized neonates in a neonatal intensive care unit (NICU) in a maternity hospital in Ireland during 2010 and 2011, two colonized NICU staff, one of their colonized children, and a NICU environmental site. The isolates exhibited multiantibiotic resistance,spatype t657, and were assigned to ST772-MRSA-V by DNA microarray profiling. All isolates encoded resistance to macrolides [msr(A) andmpb(BM)] and aminoglycosides (aacA-aphDandaphA3) and harbored the Panton-Valentine leukocidin toxin genes (lukF-PVandlukS-PV), enterotoxin genes (sea,sec,sel, andegc), and one of the immune evasion complex genes (scn). One of the NICU staff colonized by ST772-MRSA-V was identified as the probable index case, based on recent travel to India. Seven additional hospital and CA-ST772-MRSA-V isolates recovered from skin and soft tissue infections in Ireland between 2009 and 2011 exhibiting highly similar phenotypic and genotypic characteristics to the NICU isolates were also identified. The clinical details of four of these patients revealed connections with India through ethnic background or travel. Our study indicates that hospital-acquired and CA-ST772-MRSA-V is currently emerging in Ireland and may have been imported from India on several occasions.
Molecular Characterization of Escherichia coli Strains That Cause Symptomatic and Asymptomatic Urinary Tract Infections
Authors: Abraham Sam , Chapman Toni A. , Zhang Ren , Chin James , Mabbett Amanda N. , Totsika Makrina , Schembri Mark A.
Published: December 2011

The differences between
Escherichia coli
strains associated with symptomatic and asymptomatic urinary tract infections (UTIs) remain to be properly determined. Here we examined the prevalence of plasmid types and bacteriocins, as well as genetic relatedness, in a defined collection of
E. coli
strains that cause UTIs. Comparative analysis identified a subgroup of strains with a high number of virulence genes (VGs) and microcins M/H47. We also identified associations between microcin genes, VGs, and specific plasmid types.
The Human Adenovirus Type 5 E1B 55-Kilodalton Protein Is Phosphorylated by Protein Kinase CK2
Authors: Ching Wilhelm , Dobner Thomas , Koyuncu Emre
Published: December 2011

The human adenovirus type 5 (HAdV5) early region 1B 55-kDa protein (E1B-55K) is a multifunctional phosphoprotein playing several critical roles during adenoviral productive infection, e.g., degradation of host cell proteins, viral late mRNA export, and inhibition of p53-mediated transcription. Many of these functions are apparently regulated at least in part by the phosphorylation of E1B-55K occurring at a stretch of amino acids resembling a potential CK2 consensus phosphorylation motif. We therefore investigated the potential role of CK2 phosphorylation upon E1B-55K during adenoviral infection. A phosphonegative E1B-55K mutant showed severely reduced virus progeny production, although viral early, late, and structural protein levels and viral DNA replication were not obviously affected. Binding studies revealed an interaction between the CK2α catalytic subunit and wild-type E1B-55K, which is severely impaired in the phosphonegative E1B mutant. In addition,in situthe α-catalytic subunit is redistributed into ring-like structures surrounding E1B-55K nuclear areas and distinct cytoplasmic accumulations, where a significant amount of CK2α colocalizes with E1B-55K. Furthermore, inin vitrophosphorylation assays, wild-type E1B-55K glutathioneS-transferase fusion proteins were readily phosphorylated by the CK2α subunit but inefficiently phosphorylated by the CK2 holoenzyme. Addition of the CK2-specific inhibitors TBB (4,5,6,7-tetrabromobenzotriazole) and DMAT (2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole) to infected cells confirmed that CK2α binding to E1B-55K is necessary for efficient phosphorylation of E1B-55K. In summary, our data show that CK2α interacts with and phosphorylates HAdV5 E1B-55K at residues S490/491 and T495 and that these posttranslational modifications are essential for E1B-55K lytic functions.
Molecular Signatures Associated with Mx1-Mediated Resistance to Highly Pathogenic Influenza Virus Infection: Mechanisms of Survival
Authors: Cilloniz Cristian , Pantin-Jackwood Mary J. , Ni Chester , Carter Victoria S. , Korth Marcus J. , Swayne David E. , Tumpey Terrence M. , Katze Michael G.
Published: December 2011

Understanding the role of host factors during lethal influenza virus infection is critical to deciphering the events that determine the fate of the host. One such factor is encoded by the Mx1 gene, which confers resistance to influenza virus infection. Here, we compared pathology and global gene expression profiles in lung tissue from BALB/c (Mx1
−
) and BALB · A2G-Mx1 mice (Mx1
+/+
) infected with the fully reconstructed 1918 pandemic influenza virus. Mx1
+/+
mice showed less tissue damage than Mx
−
animals, and pathology and mortality were further reduced by treating the mice with interferon prior to infection. Using global transcriptional profiling, we identified distinct molecular signatures associated with partial protection, complete protection, and the contribution of interferon to the host response. In the absence of interferon treatment, partial protection was characterized by the generation of an acute response with the upregulation of genes associated with apoptosis, reactive oxygen species, and cell migration. Complete protection was characterized by the downregulation of cytokine and chemokine genes previously associated with influenza virus pathogenesis. The contribution of interferon treatment to total protection in virus-infected Mx1
+/+
mice was characterized by the altered regulation of cell cycle genes. These genes were upregulated in Mx1
+/+
mice treated with interferon but downregulated in the absence of interferon treatment. Our results suggest that Mx1
+/+
mice generate a protective antiviral response by controlling the expression of key modulator molecules associated with influenza virus lethality.
Baculovirus-Encoded Protein BV/ODV-E26 Determines Tissue Tropism and Virulence in Lepidopteran Insects
Authors: Katsuma Susumu , Kobayashi Jun , Koyano Yasue , Matsuda-Imai Noriko , Kang WonKyung , Shimada Toru
Published: December 2011

Lepidopteran nucleopolyhedroviruses (NPVs) show distinct tissue tropism in host insect larvae. However, the molecular mechanism of this tropism is largely unknown. We quantitatively investigated NPV tissue tropism by measuring mRNA levels of viral genes in 16 tissues from
Bombyx mori
NPV (BmNPV)-infected
B. mori
larvae and found clear tissue tropism, i.e., BmNPV replicates poorly in the silk glands, midgut, and Malpighian tubule compared with other larval tissues. We next identified the viral genes determining tissue tropism in NPV infection by investigating the phenotypes of larvae infected with 44 BmNPV mutants in which one gene was functionally disrupted by a
LacZ
cassette insertion. We found that occlusion body (OB) production was markedly enhanced compared with that of the wild type in the middle silk glands (MSGs) of larvae infected with three mutants in which one of three tandemly arrayed genes (
Bm7
,
Bm8
, and
Bm9
) was disrupted. We generated additional mutants in which one or two genes of this gene cluster were partially deleted and showed that Bm8, also known as BV/ODV-E26, was solely required for the suppression of OB production in the MSGs of BmNPV-infected
B. mori
larvae. Western blotting showed that a
LacZ
cassette insertion in
Bm7
or
Bm9
resulted in aberrant expression of Bm8, presumably leading to abnormal OB production in the MSGs. Larval bioassays also revealed that disruption of
Bm8
accelerated the death of
B. mori
larvae. These results suggest that the group I NPV-specific protein BV/ODV-E26 determines tissue tropism and virulence in host lepidopteran insects.
In Vitro
-Selected Drug-Resistant Varicella-Zoster Virus Mutants in the Thymidine Kinase and DNA Polymerase Genes Yield Novel Phenotype-Genotype Associations and Highlight Differences between Antiherpesvirus Drugs
Authors: Andrei G. , Topalis D. , Fiten P. , McGuigan C. , Balzarini J. , Opdenakker G. , Snoeck R.
Published: December 2011

Varicella zoster virus (VZV) is usually associated with mild to moderate illness in immunocompetent patients. However, older age and immune deficiency are the most important risk factors linked with virus reactivation and severe complications. Treatment of VZV infections is based on nucleoside analogues, such as acyclovir (ACV) and its valyl prodrug valacyclovir, penciclovir (PCV) as its prodrug famciclovir, and bromovinyldeoxyuridine (BVDU; brivudin) in some areas. The use of the pyrophosphate analogue foscarnet (PFA) is restricted to ACV-resistant (ACV
r
) VZV infections. Since antiviral drug resistance is an emerging problem, we attempt to describe the contributions of specific mutations in the viral thymidine kinase (TK) gene identified following selection with ACV, BVDU and its derivative BVaraU (sorivudine), and the bicyclic pyrimidine nucleoside analogues (BCNAs), a new class of potent and specific anti-VZV agents. The string of 6 Cs at nucleotides 493 to 498 of the VZV TK gene appeared to function as a hot spot for nucleotide insertions or deletions. Novel amino acid substitutions (G24R and T86A) in VZV TK were also linked to drug resistance. Six mutations were identified in the “palm domain” of VZV DNA polymerase in viruses selected for resistance to PFA, PCV, and the 2-phophonylmethoxyethyl (PME) purine derivatives. The investigation of the contributions of specific mutations in VZV TK or DNA polymerase to antiviral drug resistance and their impacts on the structures of the viral proteins indicated specific patterns of cross-resistance and highlighted important differences, not only between distinct classes of antivirals, but also between ACV and PCV.
Ultrastructural Characterization of Arterivirus Replication Structures: Reshaping the Endoplasmic Reticulum To Accommodate Viral RNA Synthesis
Authors: Knoops Kèvin , Bárcena Montserrat , Limpens Ronald W. A. L. , Koster Abraham J. , Mommaas A. Mieke , Snijder Eric J.
Published: December 2011

Virus-induced membrane structures support the assembly and function of positive-strand RNA virus replication complexes. The replicase proteins of arteriviruses are associated with double-membrane vesicles (DMVs), which were previously proposed to derive from the endoplasmic reticulum (ER). Using electron tomography, we performed an in-depth ultrastructural analysis of cells infected with the prototypic arterivirus equine arteritis virus (EAV). We established that the outer membranes of EAV-induced DMVs are interconnected with each other and with the ER, thus forming a reticulovesicular network (RVN) resembling that previously described for the distantly related severe acute respiratory syndrome (SARS) coronavirus. Despite significant morphological differences, a striking parallel between the two virus groups, and possibly all members of the order
Nidovirales
, is the accumulation in the DMV interior of double-stranded RNA, the presumed intermediate of viral RNA synthesis. In our electron tomograms, connections between the DMV interior and cytosol could not be unambiguously identified, suggesting that the double-stranded RNA is compartmentalized by the DMV membranes. As a novel approach to visualize and quantify the RNA content of viral replication structures, we explored electron spectroscopic imaging of DMVs, which revealed the presence of phosphorus in amounts equaling on average a few dozen copies of the EAV RNA genome. Finally, our electron tomograms revealed a network of nucleocapsid protein-containing protein tubules that appears to be intertwined with the RVN. This potential intermediate in nucleocapsid formation, which was not observed in coronavirus-infected cells, suggests that arterivirus RNA synthesis and assembly are coordinated in intracellular space.
Baculovirus GP64-Mediated Entry into Mammalian Cells
Authors: Kataoka Chikako , Kaname Yuuki , Taguwa Shuhei , Abe Takayuki , Fukuhara Takasuke , Tani Hideki , Moriishi Kohji , Matsuura Yoshiharu
Published: December 2011

The baculovirus
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) serves as an efficient viral vector, not only for abundant gene expression in insect cells, but also for gene delivery into mammalian cells. Lentivirus vectors pseudotyped with the baculovirus envelope glycoprotein GP64 have been shown to acquire more potent gene transduction than those with vesicular stomatitis virus (VSV) envelope glycoprotein G. However, there are conflicting hypotheses about the molecular mechanisms of the entry of AcMNPV. Moreover, the mechanisms of the entry of pseudotyped viruses bearing GP64 into mammalian cells are not well characterized. Determination of the entry mechanisms of AcMNPV and the pseudotyped viruses bearing GP64 is important for future development of viral vectors that can deliver genes into mammalian cells with greater efficiency and specificity. In this study, we generated three pseudotyped VSVs, NPVpv, VSVpv, and MLVpv, bearing envelope proteins of AcMNPV, VSV, and murine leukemia virus, respectively. Depletion of membrane cholesterol by treatment with methyl-β-cyclodextrin, which removes cholesterol from cellular membranes, inhibited GP64-mediated internalization in a dose-dependent manner but did not inhibit attachment to the cell surface. Treatment of cells with inhibitors or the expression of dominant-negative mutants for dynamin- and clathrin-mediated endocytosis abrogated the internalization of AcMNPV and NPVpv into mammalian cells, whereas inhibition of caveolin-mediated endocytosis did not. Furthermore, inhibition of macropinocytosis reduced GP64-mediated internalization. These results suggest that cholesterol in the plasma membrane, dynamin- and clathrin-dependent endocytosis, and macropinocytosis play crucial roles in the entry of viruses bearing baculovirus GP64 into mammalian cells.
Risk factors for injury in rugby union football in New Zealand: a cohort study
Authors: Chalmers David J , Samaranayaka Ari , Gulliver Pauline , McNoe Bronwen
Published: December 2011

Objective

To identify risk factors for injury in amateur club rugby.

Design

Prospective cohort design; with follow-up over the 2004 season.

Setting

Amateur club rugby in New Zealand.

Participants

Seven hundred and four male rugby players, aged 13 years and over.

Assessment of risk factors

The study investigated the independent effect on injury incidence of age, ethnicity, rugby experience, height, weight, body mass index, physical activity, cigarette smoking, previous injury, playing while injured, grade, position, training, time of season, warm-up, foul play, weather conditions, ground conditions and protective equipment. Generalised Poisson regression was used to estimate the effect of each factor after adjusting for all other factors.

Main outcome measures

Game injury, defined as ‘any event that resulted in an injury requiring medical attention or causing a player to miss at least one scheduled game or team practice’.

Results

A total of 704 players, representing 6263 player-games, contributed information on injury and exposure. Evidence was obtained of the effect on injury incidence of increasing age, Pacific Island versus Maori ethnicity (injury rate ratio (IRR)=1.48, 1.03–2.13), ≥40 h strenuous physical activity per week (IRR=1.54, 1.11–2.15), playing while injured (IRR=1.46, 1.20–1.79), very hard ground condition (IRR=1.50, 1.13–2.00), foul-play (IRR=1.87, 1.54–2.27) and use of headgear (IRR=1.23, 1.00–1.50).

Conclusions

Opportunities for injury prevention might include promoting injury-prevention measures more vigorously among players of Pacific Island ethnicity, ensuring injured players are fully rehabilitated before returning to play, reducing the effects of ground hardness through ground preparation and stricter enforcement of the laws relating to foul play.
Modified state-surface approach to the study of unsaturated soil behavior. Part III: Modeling of coupled hydromechanical effect
Authors: Zhang Xiong , Lytton Robert L.
Published: December 2011

A modified state-surface approach (MSSA) was proposed in the authors’ previous study to investigate volume change of the soil skeleton for unsaturated soils. This paper discussed the coupling effect between volume changes of soil skeleton, water phase, and air phase for unsaturated soils based on the proposed MSSA and experimental results presented by other researchers. The MSSA was further extended to study the coupled hydromechanical behavior for unsaturated soils. Besides void ratio constitutive surface, conventional unique water content and degree of saturation constitutive surfaces were also divided into elastic and plastic regions by loading–collapse (LC) yield curves and simultaneously used to describe the coupled hydromechanical behavior for unsaturated soils. A general theoretic formulation was derived for the simultaneous use of the MSSA under isotropic conditions. Based on the derived formulation, existing elastoplastic models were reviewed, and compatibility and consistency in modeling the mechanical and hydraulic behavior of unsaturated soils were discussed. Afterwards, the results of a number of suction-controlled laboratory isotropic compression tests at different suctions were used to demonstrate the ability of the proposed approach to reproduce the observed soil behavior quantitatively and soil behavior under undrained conditions qualitatively.
A PHYSICS-BASED TUNNELING MODEL FOR SB-HETEROSTRUCTURE BACKWARD TUNNEL DIODE MILLIMETER-WAVE DETECTORS
Authors: ZHANG ZE , CAO YU , KELLY MICHELLE , JENA DEBDEEP , FAY PATRICK , RAJAVEL RAJESH , DEELMAN PETER
Published: December 2011

InAs / AlSb / GaSb heterostructure backward tunnel diodes are sensitive millimeter-wave detectors that achieve their high sensitivity by leveraging interband tunneling current in a broken-gap heterostructure. A new physics-based tunneling model that accurately reproduces experimental results is proposed in this work. This model, which uses Kane's eight-band k · p band structures and tunneling coefficients calculated using the transfer matrix method, predicts IV curves that closely match measured data. It also predicts critical device parameters for detector performance (including curvature coefficient and junction resistance) as a function of device structure, and good agreement with experiment results has been obtained. It accurately predicts the junction resistance's exponential dependence on tunnel barrier thickness, as well as more subtle effects such as the impact of cathode doping profile adjustment and anode ternary composition. The predictive capabilities of this model are promising to provide guidance for future detector heterostructure optimization and may be useful in modeling the characteristics of other heterostructure designs and devices using 6.1 Å lattice constant materials.
A NOVEL SUBWAVELENGTH MICROBOLOMETER FOR TERAHERTZ SENSING
Authors: MEIERBACHTOL COLLIN S. , CHAHAL PREM
Published: December 2011

A subwavelength aperture-microbolometer sensor was simulated using a finite-difference time domain (FDTD) numerical method. The system consisted of a focusing bullseye grating with a central subwavelength aperture. A thin vanadium oxide sensing layer was suspended behind the aperture for sensing purposes, backed by a thin layer of silicon dioxide. The maximum electric field across the vanadium oxide was measured as a function of incident field. Total noise equivalent power (NEP) was estimated to be 180 pW/√Hz at a frequency of 0.665 THz, comparable to similar current micro sensors. The formation of surface plasmonics greatly increases its sensitivity to particular incident wavelengths. This fact, along with its compact size, make this system a promising candidate for numerous low-cost, small-scale terahertz sensing applications.
APPLICATION OF 25 NM QUANTUM DOT GATE FETs TO THE DESIGN OF ADC AND DAC CIRCUITS
Authors: KARMAKAR SUPRIYA , CHANDY JOHN A , JAIN FAQUIR C.
Published: December 2011

This paper describes design of analog-to-digital converters (ADCs) and digital-to-analog onverters (DACs) using field-effect transistors that exhibit three states in their transfer characteristics. An intermediate state " i " has been observed in the transfer characteristics (drain current-gate voltage) of FETs when two layers of cladded quantum dots (e.g. SiO x - Si and GeO x - Ge ) are introduced in the gate region above the tunnel insulator between the source and drain regions. Three states in such a transistor, defined as quantum dot gate field-effect transistor (QDG-FET) include two stable states (ON and OFF) and a low-current saturation state " i " in its transfer characteristics. QDG-FETs are quite different in construction than nanodot based nonvolatile memories, reported in the literature, where the quantum dots are sandwiched between a tunnel gate insulator and a relatively thick control gate dielectric.

In this paper we present analog-to-digital converters (ADCs) using comparators based on QDG-FETs. A comparator is designed with fewer three-state QDG-FETs. Designs of 3-bit ADC, using 25 nm QDG-FETs, are simulated showing a signal-to-noise ratio (SNR) of ~18. In addition, the R-2R ladder problem, encountered in conventional analog-to digital converters (ADCs), is absent in QDG-FET based architecture.
Automatic Assessment of Document Quality in Web Collaborative Digital Libraries
Authors: Dalip Daniel Hasan , Gonçalves Marcos André , Cristo Marco , Calado Pável
Published: December 2011

The old dream of a universal repository containing all of human knowledge and culture is becoming possible through the Internet and the Web. Moreover, this is happening with the direct collaborative participation of people. Wikipedia is a great example. It is an enormous repository of information with free access and open edition, created by the community in a collaborative manner. However, this large amount of information, made available democratically and virtually without any control, raises questions about its quality. In this work, we explore a significant number of quality indicators and study their capability to assess the quality of articles from three Web collaborative digital libraries. Furthermore, we explore machine learning techniques to combine these quality indicators into one single assessment. Through experiments, we show that the most important quality indicators are those which are also the easiest to extract, namely, the textual features related to the structure of the article. Moreover, to the best of our knowledge, this work is the first that shows an empirical comparison between Web collaborative digital libraries regarding the task of assessing article quality.
Pancreatic β-cells depend on basal expression of active ATF6α-p50 for cell survival even under nonstress conditions
Authors: Teodoro Tracy , Odisho Tanya , Sidorova Elena , Volchuk Allen
Published: December 2011

Activating transcription factor 6 (ATF6) is one of three principle endoplasmic reticulum (ER) stress response proteins and becomes activated when ER homeostasis is perturbed. ATF6 functions to increase ER capacity by stimulating transcription of ER-resident chaperone genes such as GRP78. Using an antibody that recognizes active ATF6α-p50, we found that active ATF6α was detected in insulinoma cells and rodent islets even under basal conditions and the levels were further increased by ER stress. To examine the function of ATF6α-p50, we depleted endogenous ATF6α-p50 levels using small interfering RNA in insulinoma cells. Knockdown of endogenous ATF6α-p50 levels by ∼60% resulted in a reduction in the steady-state levels of GRP78 mRNA and protein levels in nonstressed cells. Furthermore, ATF6α knockdown resulted in an apoptotic phenotype. We hypothesized that removal of the ATF6α branch of the unfolded protein response (UPR) would result in ER stress. However, neither the PKR-like endoplasmic reticulum kinase (PERK), nor the inositol requiring enzyme 1 (IRE1) pathways of the UPR were significantly activated in ATF6α knockdown cells, although these cells were more sensitive to ER stress-inducing compounds. Interestingly, phosphorylation of JNK, p38, and c-Jun were elevated in ATF6α knockdown cells and inhibition of JNK or p38 kinases prevented apoptosis. These results suggest that ATF6α may have a role in maintaining β-cell survival even in the absence of ER stress.
Opioid-induced hypernociception is associated with hyperexcitability and altered tetrodotoxin-resistant Na+ channel function of dorsal root ganglia
Authors: Ross Gracious R. , Gade Aravind R. , Dewey William L. , Akbarali Hamid I.
Published: December 2011

Opiates are potent analgesics for moderate to severe pain. Paradoxically, patients under chronic opiates have reported hypernociception, the mechanisms of which are unknown. Using standard patch-clamp technique, we examined the excitability, biophysical properties of tetrodotoxin-resistant (TTX-R) Na+ and transient receptor potential vanilloid 1 (TRPV1) channels of dorsal root ganglia neurons (DRG) (L5–S1) from mice pelleted with morphine (75 mg) or placebo (7 days). Hypernociception was confirmed by acetic acid-writhing test following 7-day morphine. Chronic morphine enhanced the neuronal excitability, since the rheobase for action potential (AP) firing was significantly ( P < 0.01) lower (38 ± 7 vs. 100 ± 15 pA) while the number of APs at 2× rheobase was higher (4.4 ± 0.8 vs. 2 ± 0.5) than placebo ( n = 13–20). The potential of half-maximum activation ( V1/2) of TTX-R Na+ currents was shifted to more hyperpolarized potential in the chronic morphine group (−37 ± 1 mV) vs. placebo (−28 ± 1 mV) without altering the V1/2 of inactivation (−41 ± 1 vs. −33 ± 1 mV) ( n = 8–11). Recovery rate from inactivation of TTX-R Na+ channels or the mRNA level of any Na+ channel subtypes did not change after chronic morphine. Also, chronic morphine significantly ( P < 0.05) enhanced the magnitude of TRPV1 currents (−64 ± 11 pA/pF) vs. placebo (−18 ± 6 pA/pF). The increased excitability of sensory neurons by chronic morphine may be due to the shift in the voltage threshold of activation of TTX-R Na+ currents. Enhanced TRPV1 currents may have a complementary effect, with TTX-R Na+ currents on opiate-induced hyperexcitability of sensory neurons causing hypernociception. In conclusion, chronic morphine-induced hypernociception is associated with hyperexcitability and functional remodeling of TTX-R Na+ and TRPV1 channels of sensory neurons.