bluuebunny/crossref_metadata_2025 huggingface dataset:
Humidity Control and Dew Point Management
Authors: Klein Levente J. , Hamann Hendrik F.
Published: February 2012

Humidity control in buildings is important for several reasons ranging from ensuring comfort of the occupants to mold control. While the optimum humidity range can be different depending on the function of a particular facility, data centers require especially tight control of humidity and dew point. For example, at low humidity (electro-static discharge) ESD might impose a significant risk to the computing equipment while at high humidity levels hardware failures are more probable due to the growth of conductive filaments or corrosion of circuit boards. In this paper we present a detailed comparison of data centers from several geographical locations, where we have measured humidity and temperature distributions over extended periods of time. The data are analyzed in terms of spatial and temporal dew point variations. We derive detailed dew point “maps” of the respective data center and the impact on reliability and energy efficiency is being discussed.
A Numerical Technique for the Approximation of Thermal Zones
Authors: Lo´pez Vanessa , Hamann Hendrik F.
Published: February 2012

The concept of thermal zones has been proposed in recent years as a means for providing operational information regarding which physical areas (or zones) in a data center are being supplied by the different air conditioning units, in order to gain insights as to optimal use of cooling equipment [1, 2]. One methodology for computing such thermal zones consists of explicit tracing of streamlines of an air velocity field [2]. In the present work, we propose an alternative technique which does not require explicit tracing of streamlines. Specifically, the problem of identifying thermal zones is being formulated as a boundary value problem for convective transport. Using a numerical method capable of solving convection-dominated problems accurately leads to identification of the zones by a simple postprocessing of the numerical solution of the boundary value problem, making the procedure convenient to apply, especially in three-dimensional domains.
Reliability Studies for Package-on-Package Components in Drop and Shock Environments
Authors: Lall Pradeep , Angral Arjun , Suhling Jeff
Published: February 2012

The consumer electronics industry stands at a critical juncture where manufacturers strive to incorporate more functionality in smaller packages. In the highly competitive consumer electronics market, a continued demand for products with smallest possible form-factor yet high functionality has led to the proliferation of 3D packaging technologies. Package-on-Package (PoP) architectures, in particular have attracted a lot of interest, especially in portable electronics industry. The advantages of these stacked 3D architectures include simplified and compact design, savings of board space allowing for more package landings, reduced pin counts and optimized production costs. While a lot of recent research, in the field of PoP architectures has been focused on development of optimum process flows and warpage control during reflow, the effects of reflow parameters on the quality of PoP build and the associated reflow defects including warpage have not been extensively researched. Additionally, studies on reliability issues associated with PoP assemblies in drop and shock environments are scarce. Since PoP architectures find their applications mainly in portable electronics, which are susceptible to frequent drops and careless handling at the hand of the consumer, the reliability of PoP architectures in environments representative of the real world is critical to their success in the industry. In this study, Single component PoP test vehicles have been fabricated as per JEDEC standards for quantifying the reliability of PoP packages in drop and shock. Daisy chained double-stack PoP components have been used to identify failure for subsequent drop/shock performance analysis. Experimental strain data acquired using Digital Image Correlation and high speed continuity data- for identifying failure has been used in conjunction with validated FE simulations of drop test events; for development of life prediction models for PoP architectures. Validated node based global-local FE simulations are used to predict strains in critical solder balls in both layers of the PoP stack. The drop/shock reliability studies and life prediction models presented in this work, present an insight into PoP failures and eliminate the need for exhaustive testing procedures.
Modeling Fracture in Dielectric Stacks due to Chip-Package Interaction: Impact of Dielectric Material Selection
Authors: Tambat Abhishek , Lin Hung-Yun , Claydon Ian , Subbarayan Ganesh , Jung Dae-Young , Sammakia Bahgat
Published: February 2012

The trend towards decreasing dielectric constant of Interlayer Dielectric (ILD) materials has required significant trade-off between electrical performance and mechanical integrity of the die stack. Fracture caused by thermal stresses due to large coefficient of thermal expansion (CTE) mismatch between these materials arising during fabrication or testing are often the main driving force for failure. In this paper, we use CAD-inspired hierarchical field compositions [1] to carry out Isogeometric (meshfree) fracture simulations. We model cracks as arbitrary curves/surfaces and the crack propagation criterion is based on the evolving energy release rate (ERR) of the system. We simulate the solder reflow process to assess the impact of chip-package interaction on the reliability of ILD stacks. We use multi-level modeling to extract displacement boundary conditions for the local model of the ILD stack. Eight layers of metallization are considered in the ILD stack. We study the relative risks of replacing stronger dielectric (SiO2) with weaker dielectrics (SiCOH, ULK) on the criticality of preexisting flaws in the structure. Further, we study the impact of varying interfacial toughness values on the crack growth patterns in ILD stacks. Crack patterns reflect the propensity towards predominantly bulk failure with increasing interfacial toughness.
An Accurate and Efficient Link Analysis Methodology for High Speed I/O Design
Authors: Mazumder Mohiuddin , Jaussi James , Iyer Sitaraman , Spagna Fulvio , Wu Zuoguo , Lee Beomtaek , Kumar Arvind
Published: February 2012

This paper describes an accurate and efficient analysis methodology that enables circuit optimization directly guided by platform-level metric such as link eye margin. Prior to this work, such analysis was not feasible due to significant compute time required by complex circuit simulations. A new method of developing highly abstracted behavioral models of complex circuit blocks is a critical element of this analysis methodology. The method uses statistical signaling analysis and optimization capabilities coupled with behavioral modeling of I/O clocking, transmitter and receiver circuitry that are based on accurate circuit simulations. We also present measured data from products and test chips that show correlation between measured and modeled data within 10–15%. Finally, we describe how the methodology was used to optimize the design of a high speed serial link and achieve approximately 70% improvement in eye margins with limited design iterations.
Approaches to Establish PV System Reliability
Authors: Feng Jie , Gaston Ryan S. , Ramesh Narayan
Published: February 2012

Reliability has been studied in the PV industry using a variety of experimental and modeling techniques, to probe specific aspects of design and performance. In this paper, a methodology that integrates experimental and modeling techniques to enable risk mitigation in the development cycle and reliability estimation is presented.
Power Allocation Towards Hermetic Solder Joint Health of High Powered MEMS Chip for Harsh Environment Applications
Authors: Bhopte Siddharth , Arunasalam Parthiban , Alsaleem Fadi , Rao Arvind , Hariharan Nataraj
Published: February 2012

Solders have been utilized extensively in the MEMS packaging industry to create vacuum or hermetic seals in a variety of applications. MEMS technology is finding applications in wide range of products like pressure sensors, actuators, flow control devices etc. For many harsh low temperature environment applications, like commercial refrigeration systems, MEMS based pressure sensors and flow actuators are directly mounted on to metal substrates using solders to create hermetic sealing. Solders attaching silicon devices directly to metal substrates may be subjected to very high thermal stresses due to significant difference in thermal expansion coefficients during chip operation or environment temperatures. In this paper, case study of a high powered MEMS chip (referred in the paper as die) operating in a commercial refrigeration system is presented. Accelerated test method for qualifying solder joint for high pressure applications is briefly discussed. Lab experiments showing typical refrigeration cycle thermal load on solder joint are presented. Based on the study, concepts of die power toggling and power allocation towards enhancing hermetic solder joint reliability are discussed. Detailed numerical case studies are presented to quantify the improvement in solder joint reliability due to the proposed concept.
Adding Aliphatic C–H Bond Oxidations to Synthesis
Authors: White M. Christina
Published: February 2012

Oxidations of aliphatic C–H bonds, known since the 1800s, have only recently been considered for use in organic synthesis.
Survival Analysis of Faculty Retention in Science and Engineering by Gender
Authors: Kaminski Deborah , Geisler Cheryl
Published: February 2012

Faculty Fates

Academic careers in STEM (science, technology, engineering, and math) include challenges that may differ depending on gender.Kaminski and Geisler(p.864) analyzed the retention rates for tenure-track faculty at 14 U.S. universities in various disciplines. College catalogs, departmental Web sites, and other public sources of information were used to follow the academic careers of nearly 3000 STEM faculty. Except in mathematics faculties—where women left a couple of years earlier than men—generally, women and men were retained and promoted at the same rate.
Crystal Structure of a Lipid G Protein–Coupled Receptor
Authors: Hanson Michael A. , Roth Christopher B. , Jo Euijung , Griffith Mark T. , Scott Fiona L. , Reinhart Greg , Desale Hans , Clemons Bryan , Cahalan Stuart M. , Schuerer Stephan C. , Sanna M. Germana , Han Gye Won , Kuhn Peter , Rosen Hugh , Stevens Raymond C.
Published: February 2012

A Lipid-Sensing GPCR

Sphingosine 1-phosphate (S1P) is a sphingolipid that binds to the G protein–coupled receptor subtype 1 (S1P
1
) to activate signaling pathways involved in regulation of the vascular and immune systems.

Hanson
et al.

(p.
851
) determined the crystal structure of S1PR in complex with an antagonist sphingolipid mimic. Ligand access to the receptor from the extracellular milieu is occluded, and a gap between helices I and VII may provide ligand access from within the membrane. The structural information, together with mutagenesis and structure activity relationship data, provides insight into the molecular recognition events that modulate signaling.
Learning Ecological Ethics from Plato
Plato's Revenge
Politics in the Age of Ecology

by William Ophuls

MIT Press, Cambridge, MA, 2011. 270 pp. $27.95, £19.95. ISBN 9780262015905.
Eco-Republic
What the Ancients Can Teach Us About Ethics, Virtue, and Sustainable Living

by Melissa Lane

Princeton University Press, Princeton, NJ, 2012. 255 pp. $29.95. £19.95. ISBN 9780691151243.
Authors: Ali Saleem H.
Published: February 2012

The books by Ophuls and Lane offer two perspectives on how Plato might help us develop an ecologically sustainable society.
Hard Times for OSTP
Authors: Mervis Jeffrey
Published: February 2012

The Office of Science and Technology Policy is facing its own tough budget choices this year as it tries to coordinate research activities across the government.
Marriage Decision Highlights Same-Sex Studies
Authors: Malakoff David
Published: February 2012

The legal jousting over California's Proposition 8 has helped highlight a growing body of research on the psychological and socioeconomic aspects of same-sex relationships.
A Tiny Window Opens Into Lake Vostok, While a Vast Continent Awaits
Authors: Gramling Carolyn
Published: February 2012

On 8 February, the Russian Arctic and Antarctic Research Institute announced that a team of its engineers and scientists had drilled through nearly 4 kilometers of Antarctic ice to Lake Vostok.
Uncovering Civilization's Roots
Authors: Lawler Andrew
Published: February 2012

What sparked the first cities? Digs in Kuwait and Syria are reshaping how archaeologists see the first stirrings of urban life.
Cross-Reactivity of Antipneumococcal Surface Protein C (PspC) Antibodies with Different Strains and Evaluation of Inhibition of Human Complement Factor H and Secretory IgA Binding via PspC
Authors: Moreno Adriana T. , Oliveira Maria Leonor S. , Ho Paulo L. , Vadesilho Cintia F. M. , Palma Giovana M. P. , Ferreira Jorge M. C. , Ferreira Daniela M. , Santos Silvia R. , Martinez Marina B. , Miyaji Eliane N.
Published: February 2012

Pneumococcal surface protein C (PspC) is an important candidate for a cost-effective vaccine with broad coverage against pneumococcal diseases. Previous studies have shown thatStreptococcus pneumoniaeis able to bind to both human factor H (FH), an inhibitor of complement alternative pathway, and human secretory IgA (sIgA) via PspC. PspC was classified into 11 groups based on variations of the gene. In this work, we used three PspC fragments from different groups (PspC3, PspC5, and PspC8) to immunize mice for the production of antibodies. Immunization with PspC3 induced antibodies that recognized the majority of the clinical isolates as analyzed by Western blotting of whole-cell extracts and flow cytometry of intact bacteria, while anti-PspC5 antibodies showed cross-reactivity with the paralogue pneumococcal surface protein A (PspA), and anti-PspC8 antibodies reacted only with the PspC8-expressing strain. Most of the isolates tested showed strong binding to FH and weaker interaction with sIgA. Preincubation with anti-PspC3 and anti-PspC5 IgG led to some inhibition of binding of FH, and preincubation with anti-PspC3 partially inhibited sIgA binding in Western blotting. The analysis of intact bacteria through flow cytometry showed only a small decrease in FH binding after incubation of strain D39 with anti-PspC3 IgG, and one clinical isolate showed inhibition of sIgA binding by anti-PspC3 IgG. We conclude that although anti-PspC3 antibodies were able to recognize PspC variants from the majority of the strains tested, partial inhibition of FH and sIgA binding through anti-PspC3 antibodiesin vitrocould be observed for only a restricted number of isolates.
Identification of Clinically Relevant Corynebacterium spp., Arcanobacterium haemolyticum, and Rhodococcus equi by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Vila Jordi , Juiz Pedro , Salas Carlos , Almela Manel , de la Fuente Celia García , Zboromyrska Yuliya , Navas Jesús , Bosch Jordi , Agüero Jesús , de la Bellacasa Jorge Puig , Martínez-Martínez Luis
Published: February 2012

The identification of 83
Corynebacterium
, 13
Arcanobacterium haemolyticum
, and 10
Rhodococcus equi
strains by conventional methods (API Coryne complemented with 16S rRNA gene sequence analysis) was compared with matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry identification. The correlation between API and MALDI-TOF results was 89%. MALDI-TOF is a rapid and accurate system for identification of the above-mentioned microorganisms.
Comparison of the GenoFlow Human Papillomavirus (HPV) Test and the Linear Array Assay for HPV Screening in an Asian Population
Authors: Wong Oscar Gee-Wan , Lo C. K. , Chow Joanne N. K. , Tsun Obe K. L. , Szeto Elaine , Liu Stephanie S. , Ngan Hextan Y. S. , Cheung Annie N. Y.
Published: February 2012

High-risk human papillomavirus (HR-HPV) DNA detection in cervical cytology samples is useful for primary screening of cervical cancer and for triage of patients with equivocal cytological findings. The GenoFlow HPV array test (GF assay; Diagcor Bioscience Inc., Hong Kong) was recently developed to detect 33 HPV genotypes by a “flowthrough” hybridization technology. In this study, we assessed the analytical sensitivity and reproducibility of the GF assay and compared its genotyping results with those of the Linear Array (LA) assay (Roche Molecular Diagnostics, Indianapolis, IN), using 400 archived liquid-based cytology samples representing the full range of cytology findings. Genotyping findings of the GF and LA assays were concordant or compatible for 93.44% of tested samples, with a good (κ = 0.797) to very good (κ = 0.812) strength of agreement for assay-common and oncogenic HPV types, respectively. The two assays showed good (κ = 0.635) agreement in detecting infections with multiple HPV genotypes. The lowest detection limits of the GF assay for HPV16 and HPV18 were 25 copies and 20 copies, respectively. Repeat testing of 60 samples by use of two different lots of the GF assay revealed no discordant results, suggesting good reproducibility of the assay. Both assays achieved approximately 80% and 100% sensitivity for identifying cases of atypical squamous cells of undetermined significance (ASC-US) and low-grade squamous intraepithelial lesions (LSIL) with subsequent detection of LSIL+ and high-grade squamous intraepithelial lesions or higher (HSIL+) in 2 years, respectively. Among ASC-US samples, the GF assay achieved the highest specificity (23.08%) for indicating subsequent identification of HSIL compared with the LA (19.23%) and Hybrid Capture 2 (HC2) (8.97%) assays. The GF and LA assays showed significant discrepancy in detecting HPV genotypes 11, 26, 39, 52, and 66. More sensitive detection of HPV52 by GF assay offers an advantage in regions where HPV52 is more prevalent. The sensitivity of the GF assay for detecting patients with HSIL+ was noninferior to that of the LA assay.
Sequence Typing Confirms that a Predominant Listeria monocytogenes Clone Caused Human Listeriosis Cases and Outbreaks in Canada from 1988 to 2010
Authors: Knabel Stephen J. , Reimer Aleisha , Verghese Bindhu , Lok Mei , Ziegler Jennifer , Farber Jeffrey , Pagotto Franco , Graham Morag , Nadon Celine A. , Gilmour Matthew W.
Published: February 2012

Human listeriosis outbreaks in Canada have been predominantly caused by serotype 1/2a isolates with highly similar pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MVLST) each identified a diverse population of
Listeria monocytogenes
isolates, and within that, both methods had congruent subtypes that substantiated a predominant clone (clonal complex 8; virulence type 59; proposed epidemic clone 5 [ECV]) that has been causing human illness across Canada for more than 2 decades.
Molecular Characterization of Human Enteroviruses in the Central African Republic: Uncovering Wide Diversity and Identification of a New Human Enterovirus A71 Genogroup
Authors: Bessaud Maël , Pillet Sylvie , Ibrahim Wafa , Joffret Marie-Line , Pozzetto Bruno , Delpeyroux Francis , Gouandjika-Vasilache Ionela
Published: February 2012

Human enteroviruses (HEV) are among the most common viruses infecting humans. Their circulation has been widely studied in most parts of the world but not in sub-Saharan Africa, where poliomyelitis remains prevalent. We report here the molecular characterization of 98 nonpoliovirus (non-PV) HEV strains isolated from 93 randomly selected cell culture-positive supernatants from stool samples collected from 1997 through 2006 from children with acute flaccid paralysis living in the Central African Republic (CAR). The isolates were typed by sequencing the VP1 coding region and sequenced further in the VP2 coding region, and phylogenetic studies were carried out. Among the 98 VP1 sequences, 3, 74, 18, and 3 were found to belong to the HEV-A, -B, -C, and -D species, respectively. Overall, 42 types were detected. In most cases, the VP2 type was correlated with that of the VP1 region. Some of the isolates belonged to lineages that also contain viruses isolated in distant countries, while others belonged to lineages containing viruses isolated only in Africa. In particular, one isolate (type EV-A71) did not fall into any of the genogroups already described, indicating the existence of a previously unknown genogroup for this type. These results illustrate the considerable diversity of HEV isolates from the stools of paralyzed children in the CAR. The presence of diverse HEV-C types makes recombination between poliovirus and other HEV-C species possible and could promote the emergence of recombinant vaccine-derived polioviruses similar to those that have been implicated in repeated poliomyelitis outbreaks in several developing countries.
Detection of a Possible Bioterrorism Agent, Francisella sp., in a Clinical Specimen by Use of Next-Generation Direct DNA Sequencing
Authors: Kuroda Makoto , Sekizuka Tsuyoshi , Shinya Fumiaki , Takeuchi Fumihiko , Kanno Takayuki , Sata Tetsutaro , Asano Shigeyuki
Published: February 2012

Deep sequencing detected a potential bioterrorism agent,
Francisella tularensis
, in a human abscess sample (Iwaki-08) of unknown etiology. Identified single-nucleotide variations suggest that the Iwaki-08 case was associated with
Francisella tularensis
subsp.
holarctica
(biovar
japonica
) but not the highly virulent type A (
Francisella tularensis
subsp.
tularensis
).
The Immune Response to a Vesicular Stomatitis Virus Vaccine Vector Is Independent of Particulate Antigen Secretion and Protein Turnover Rate
Authors: Cobleigh Melissa A. , Bradfield Clinton , Liu Yuanjie , Mehta Anand , Robek Michael D.
Published: February 2012

Vesicular stomatitis virus (VSV) is a highly cytopathic virus being developed as a vaccine vector due to its ability to induce strong protective T cell and antibody responses after a single dose. However, little is known regarding the mechanisms underlying the potent immune responses elicited by VSV. We previously generated a VSV vector expressing the hepatitis B virus middle envelope surface glycoprotein (MS) that induces strong MS-specific T cell and antibody responses in mice. After synthesis in the cytoplasm, the MS protein translocates to the endoplasmic reticulum, where it forms subviral particles that are secreted from the cell. To better understand the contributions of secreted and intracellular protein to the VSV-induced immune response, we produced a vector expressing a secretion-deficient MS mutant (MSC69A) and compared the immunogenicity of this vector to that of the wild-type VSV-MS vector in mice. As expected, the MSC69Aprotein was not secreted from VSV-infected cells and displayed enhanced proteasome-mediated degradation. Surprisingly, despite these differences in intracellular protein processing, the T cell and antibody responses generated to MSC69Awere comparable to those elicited by virus expressing wild-type MS protein. Therefore, when it is expressed from VSV, the immune responses to MS are independent of particulate antigen secretion and the turnover rate of cytoplasmic protein. These results are consistent with a model in which the immune responses to VSV are strongly influenced by the replication cycle of the vector and demonstrate that characteristics of the vector have the capacity to affect vaccine efficacy more than do the properties of the antigen itself.
Level of Gene Expression Is a Major Determinant of Protein Evolution in the Viral Order Mononegavirales
Authors: Pagán Israel , Holmes Edward C. , Simon-Loriere Etienne
Published: February 2012

Although the rate at which proteins change is a key parameter in molecular evolution, its determinants are poorly understood in viruses. A variety of factors, including gene length, codon usage bias, protein abundance, protein function, and gene expression level, have been shown to affect the rate of protein evolution in a diverse array of organisms. However, the role of these factors in viral evolution has yet to be addressed. The polar 3′-5′ stepwise attenuation of transcription in theMononegavirales, a group of single-strand negative-sense RNA viruses, provides a unique system to explore the determinants of protein evolution in viruses. We analyzed the relative importance of a variety of factors in shaping patterns of sequence variation in full-length genomes from 13Mononegaviralesspecies. Our analysis suggests that the level of gene expression, and by extension the relative genomic position of each gene, is a key determinant of the protein evolution in these viruses. This appears to be the consequence of selection for translational robustness, but not for translational accuracy, in highly expressed genes. The small genome size and number of proteins encoded by these viruses allowed us to identify other protein-specific factors that may also play a role in virus evolution, such as host-virus interactions and functional constraints. Finally, we explored the evolutionary pressures acting on noncoding regions inMononegaviralesgenomes and observed that, despite being less constrained than coding regions, their evolutionary rates are also associated with genomic position.
A Conserved Tandem Cyclophilin-Binding Site in Hepatitis C Virus Nonstructural Protein 5A Regulates Alisporivir Susceptibility
Authors: Grisé Henry , Frausto Stephen , Logan Timothy , Tang Hengli
Published: February 2012

Cyclophilin A (CyPA) and its peptidyl-prolyl isomerase (PPIase) activity play an essential role in hepatitis C virus (HCV) replication, and mounting evidence indicates that nonstructural protein 5A (NS5A) is the major target of CyPA. However, neither a consensus CyPA-binding motif nor specific proline substrates that regulate CyPA dependence and sensitivity to cyclophilin inhibitors (CPIs) have been defined to date. We systematically characterized all proline residues in NS5A domain II, low-complexity sequence II (LCS-II), and domain III with both biochemical binding and functional replication assays. A tandem cyclophilin-binding site spanning domain II and LCS-II was identified. The first site contains a consensus sequence motif of AØPXW (where Ø is a hydrophobic residue) that is highly conserved in the majority of the genotypes of HCV (six of seven; the remaining genotype has VØPXW). The second tandem site contains a similar motif, and the ØP sequence is again conserved in six of the seven genotypes. Consistent with the similarity of their sequences, peptides representing the two binding motifs competed for CyPA binding in a spot-binding assay and induced similar chemical shifts when bound to the active site of CyPA. The two prolines (P310 and P341 of Japanese fulminant hepatitis 1 [JFH-1]) contained in these motifs, as well as a conserved tryptophan in the spacer region, were required for CyPA binding, HCV replication, and CPI resistance. Together, these data provide a high-resolution mapping of proline residues important for CyPA binding and identify critical amino acids modulating HCV susceptibility to the clinical CPI Alisporivir.
Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China
Authors: Ge Xingyi , Li Yan , Yang Xinglou , Zhang Huajun , Zhou Peng , Zhang Yunzhi , Shi Zhengli
Published: February 2012

Increasing data indicate that bats harbor diverse viruses, some of which cause severe human diseases. In this study, sequence-independent amplification and high-throughput sequencing (Solexa) were applied to the metagenomic analysis of viruses in bat fecal samples collected from 6 locations in China. A total of 8,746,417 reads with a length of 306,124,595 bp were obtained. Among these reads, 13,541 (0.15%) had similarity to phage sequences and 9,170 (0.1%) had similarity to eukaryotic virus sequences. A total of 129 assembled contigs (>100 nucleotides) were constructed and compared with GenBank: 32 contigs were related to phages, and 97 were related to eukaryotic viruses. The most frequent reads and contigs related to eukaryotic viruses were homologous to densoviruses, dicistroviruses, coronaviruses, parvoviruses, and tobamoviruses, a range that includes viruses from invertebrates, vertebrates, and plants. Most of the contigs had low identities to known viral genomic or protein sequences, suggesting that a large number of novel and genetically diverse insect viruses as well as putative mammalian viruses are transmitted by bats in China. This study provides the first preliminary understanding of the virome of some bat populations in China, which may guide the discovery and isolation of novel viruses in the future.
Sensing Adenovirus Infection: Activation of Interferon Regulatory Factor 3 in RAW 264.7 Cells
Authors: Stein Saskia C. , Falck-Pedersen Erik
Published: February 2012

We have used the RAW 264.7 murine macrophage-like cell line as a platform to characterize the recognition and early signaling response to recombinant adenoviral vectors (rAdV). Infection of RAW 264.7 cells triggers an early response (2 to 6 h postinfection) that includes phosphorylation of the interferon (IFN) response factor 3 (IRF3) transcription factor, upregulation of IRF3 primary response genes (interferon-stimulated gene 56 [ISG56], beta IFN [IFN-β]), and subsequent type I IFN secondary signaling (STAT1/2 phosphorylation). Using short hairpin RNA (shRNA) lentiviral vectors, we show an essential role for Tank binding kinase 1 (TBK1) in this pathway. Data also support a role for STING (MITA) as an adaptor functioning in response to rAdV infection. Using UV/psoralen (Ps)-inactivated virus to block viral transcription, Ps-inactivated virus stimulated primary (IRF3) and secondary (STAT1/2) activation events to the same degree as untreated virus. IRF3 phosphorylation was not blocked in RAW 264.7 cells pretreated with the RNA polymerase III inhibitor ML60218. However, they were compromised in the type I IFN-dependent secondary response (phosphorylation of STAT1/STAT2). At 24 h postinfection, ML60218-treated cells were compromised in the overall antiviral response. Therefore, initial sensing of rAdV or viral DNA (vDNA) does not depend on viral template transcription, but ML60218 treatment influences cellular cascades required for an antiviral response to rAdV. Using overexpression or knockdown assays, we examined how four DNA sensors influence the antiviral response. Knockdown of DNA Activator of Interferon (DAI) and p204, the murine ortholog to IFI16, had minimal influence on IRF3 phosphorylation. However, knockdown of absent in melanoma 2 (AIM2) and the helicase DDX41 resulted in diminished levels of
pser388
IRF3 following rAdV infection. Based on these data, multiple DNA sensors contribute to an antiviral DNA recognition response, leading to TBK1-dependent IRF3 phosphorylation in RAW 264.7 cells.
Qualitative cross-sectional study of the perceived causes of depression in South Asian origin women in Toronto: Table 1
Authors: Ekanayake Samanthika , Ahmad Farah , McKenzie Kwame
Published: February 2012

Objective

To explore how South Asian origin women in Toronto, Canada, understand and explain the causes of their depression.

Design

Cross-sectional in-depth qualitative interviews.

Setting

Outpatient service in Toronto, Ontario.

Participants

Ten women with symptoms of depression aged between 22 and 65 years of age. Seven were from India, two from Sri Lanka and one from Pakistan. Four were Muslim, three Hindu and three Catholic. Two participants had university degrees, one a high school diploma and seven had completed less than a high school education. Eight were married, one was unmarried and one a widow.

Results

Three main factors emerged from the participant narratives as the causes of depression: family and relationships, culture and migration and socioeconomic. The majority of the participants identified domestic abuse, marital problems and interpersonal problems in the family as the cause of their depression. Culture and migration and socioeconomic factors were considered contributory. None of our study participants reported spiritual, supernatural or religious factors as causes of depression.

Conclusion

A personal–social–cultural model emerged as the aetiological paradigm for depression. Given the perceived causation, psycho-social treatment methods may be more acceptable for South Asian origin women.
The role of the general practitioner in the Australian approach to HIV care: interviews with ‘key informants’ from government, non-government and professional organisations
Authors: Newman Christy E , de Wit John B F , Kippax Susan C , Reynolds Robert H , Canavan Peter G , Kidd Michael R
Published: February 2012

Objectives

HIV care is provided in a range of settings in Australia, but advances in HIV treatment and demographic and geographic changes in the affected population and general practitioner (GP) workforce are testing the sustainability of the special role for GPs. This paper explores how a group of ‘key informants’ described the role of the GP in the Australian approach to HIV care, and conceptualised the challenges currently inspiring debate around future models of care.

Methods

A thematic analysis was conducted of semistructured interviews carried out in 2010 with 24 professionals holding senior roles in government, non-government and professional organisations that influence Australian HIV care policy.

Results

The strengths of the role of the GP were described as their community setting, collaborative partnership with other medical and health professions, and focus on patient needs. A number of associated challenges were also identified including the different needs of GPs with high and low HIV caseloads, the changing expectations of professional roles in general practice, and barriers to service accessibility for people living with HIV.

Conclusions

While there are many advantages to delivering HIV services in primary care, GPs need flexible models of training and accreditation, support in strengthening relationships with other health and medical professionals, and assistance in achieving service accessibility. Consideration of how to support the GP workforce so that care can be made available in the broadest range of geographical and service settings is also critical if systems of HIV care delivery are to be realistic and cost-effective and meet consumer needs.
Hopes interrupted: accessing and experiences of antiretroviral therapy in South Africa
Authors: Fried Jana , Harris Bronwyn , Eyles John
Published: February 2012

Objectives

Using the example of South Africa, this study aimed to examine and obtain a better understanding of the experiences and challenges of urban and rural patients on antiretroviral therapy (ART) in accessing this complex treatment in a resource-limited setting.

Methods

Following a narrative approach, in-depth interviews were conducted with 20 patients successfully and unsuccessfully (ie, with interruptions) receiving ART in urban Johannesburg and rural Bushbuckridge, using a detailed interview guide structured to illuminate interviewees' life circumstances and contextualise illness and treatment trajectories. Participants were interviewed by trained fieldworkers in their local languages. The translated and transcribed interviews were coded by several team members. Codes were cross-examined and showed good congruence.

Results

All interviewees emphasised the positive aspects of receiving ART, the lifeline and hope it provided by improving health, increasing their ability to live actively and reducing visible signs of (stigmatised) illness. Important factors supporting continuing adherence included social and economic support by individuals, role models and networks as well as positive experiences within the healthcare system and of the treatment itself. The main challenges were linked to patients' difficult life circumstances, especially those related to poverty (eg, transport and food costs) and health system constraints, including perceived lack of compassion and flexibility by healthcare workers.

Conclusions

While there are many challenges for the sustainability of ART on an individual and health system level, this study emphasised the need for a patient-centric focus to continue to provide and increase the number of HIV-positive people receiving this lifeline, receiving hope.
Is there a role for primary care clinicians in providing shared care in HIV treatment? A systematic literature review
Authors: Wong W C W , Luk C W , Kidd M R
Published: February 2012

Background

Despite HIV being increasingly considered as a chronic illness, there is as yet no consensus about how primary care should be integrated with specialty care to provide optimal clinical management for people living with HIV.

Objective

To examine the effectiveness of shared care models of HIV between primary care and specialty care and how primary care providers can assist in improving the care of people with HIV.

Methods

Three databases, PubMed, Medline and EMBase, were searched for relevant terms from studies published in the period from 1996 to 2011. Studies that integrated primary care in HIV management and included highly active antiretroviral therapy (HAART) as part of the treatment modality were included.

Results

Eleven studies that met the inclusion criteria were included in this review. Primary care was found to be at least as effective in HIV counselling, testing and treatment and, to a lesser degree, prevention, when compared with specialty care alone. Screening for HIV at a primary care level was cost-effective, especially in a high HIV prevalence and high-risk community. There were no significant adverse clinical outcomes reported in a primary care approach. Effectiveness of various interventions using a primary care approach was demonstrated in the review, including HAART adherence programmes, home care, the involvement of peer health workers and perinatal use of HAART.

Conclusions

Primary care has an important role in the shared care of the diagnosis and management of people with HIV. Some improvements with current guidelines on the management in primary care of people with HIV in developing countries should be considered.
Indicators of political commitment to respond to HIV
Authors: Goldberg Allison B , Fox Ashley M , Gore Radhika J , Bärnighausen Till
Published: February 2012

Objectives

National political commitment is likely to become particularly crucial to sustaining antiretroviral treatment programmes in the coming decade, as donor contributions to HIV funding decreases. The objective of this study is to synthesise information on existing indicators of political commitment to respond to national HIV epidemics.

Methods

The authors describe and critically evaluate the existing indicators and propose studies to validate them.

Results

Several indicators have been developed to measure governments' political commitment to respond to national HIV epidemics—theAIDS Program Effort Index, theUnited Nations General Assembly Special Session on HIV/AIDS Declaration of Commitment Indicatorsand theAIDS Policy Aggressiveness Indicators—but the validity of these measures has not been systematically assessed. The indicators differ in their intended use, collection methods, content categories, data coverage, and strengths and limitations. Several types of studies could be used to test indicator validity (based on indicator content, comparisons of the same indicator using different elicitation methods, relationship patterns between indicators, relations between indicators and other variables and the consequences of using the indicators).

Conclusions

The existing indicators of political commitment to respond to national HIV epidemics are useful for many purposes, including research, policymaking and advocacy. A range of studies could improve the understanding of indicator validity. New data collection and measurement approaches offer opportunities to improve how actors in the HIV community capture the complicated, multidimensional concept of political commitment.
HODGKIN–HUXLEY AXON IS MADE OF MEMRISTORS
Authors: CHUA LEON , SBITNEV VALERY , KIM HYONGSUK
Published: February 2012

This paper presents a rigorous and comprehensive nonlinear circuit-theoretic foundation for the memristive Hodgkin–Huxley Axon Circuit model. We show that the Hodgkin–Huxley Axon comprises a potassium ion-channel memristor and a sodium ion-channel memristor, along with some mundane circuit elements. From this new perspective, many hitherto unresolved anomalous phenomena and paradoxes reported in the literature are explained and clarified. The yet unknown nonlinear dynamical mechanisms which give birth to the action potentials remain hidden within the memristors, and the race is on for uncovering the ultimate truth.
NONLINEAR TIME SERIES ANALYSIS OF ELECTROENCEPHALOGRAM TRACINGS OF CHILDREN WITH AUTISM
Authors: KEH LANCE ONG-SIONG CO TING , CHUPUNGCO ANA MARIA AQUINO , ESGUERRA JOSE PERICO
Published: February 2012

Three methods of nonlinear time series analysis, Lempel–Ziv complexity, prediction error and covariance complexity were employed to distinguish between the electroencephalograms (EEGs) of normal children, children with mild autism, and children with severe autism. Five EEG tracings per cluster of children aged three to seven medically diagnosed with mild, severe and no autism were used in the analysis. A general trend seen was that the EEGs of children with mild autism were significantly different from those with severe or no autism. No significant difference was observed between normal children and children with severe autism. Among the three methods used, the method that was best able to distinguish between EEG tracings of children with mild and severe autism was found to be the prediction error, with a t-Test confidence level of above 98%.
ONE-DIMENSIONAL DISCONTINUOUS MAP ANALYSIS OF DC–DC CONVERTERS UNDER VOLTAGE CONTROLLED PULSE SKIPPING MODULATION
Authors: KAPAT SANTANU , BANERJEE SOUMITRO , PATRA AMIT
Published: February 2012

A pulse skipping modulation (PSM) technique is useful for improving the efficiency of a dc–dc converter under light load conditions. Under such condition, the discrete-time model of the converter could be modeled as a discontinuous map, comprising either 1D functions only or a combination of 1D and 2D functions. Using the PSM mechanism, efficiency and spectral composition could be further improved by incorporating a voltage feedback loop. In this paper we show that, in a converter under voltage controlled PSM, the entire map can be restricted to one dimension for a wide range of parameters, by properly designing the controller. As a parameter is varied, the periodicity of the output waveform may change either monotonically or non-monotonically depending on the character of the voltage mode control loop. Technically it is desirable to operate the converter in such a way that a variation of a parameter can cause only incremental change in the periodicity and hence in the spectral composition. In the nonlinear dynamics literature, such a bifurcation scenario is known as pure period incrementing cascade. Using the theory for 1D discontinuous maps, we obtain the conditions on the converter's parameters such that such a cascade is obtained, and the variation of a parameter does not cause large variation of the periodicity. The results have been experimentally validated.
EFFECTS OF SHORT-CUT IN A DELAYED RING NETWORK
Authors: MAN JUANJUAN , GUO SHANGJIANG , HE YIGANG
Published: February 2012

This paper presents a detailed analysis on the dynamics of a ring network with short-cut. We first investigate the absolute synchronization on the basis of Lyapunov stability approach, and then discuss the linear stability of the trivial solution by analyzing the distribution of zeros of the characteristic equation. Based on the equivariant branching lemma, we not only obtain the existence of primary steady state bifurcation but also analyze the patterns and stability of the bifurcated nontrivial equilibria. Moreover, by means of the equivariant Hopf bifurcation theorem, we not only investigate the effect of connection strength on the spatio-temporal patterns of periodic solutions emanating from the trivial equilibrium, but also derive the formula to determine the direction and stability of Hopf bifurcation. In particular, we further consider the secondary bifurcation of the nontrivial equilibria. These studies show that short-cut may be used as a simple but efficient switch to control the dynamics of a system.
EXTENSION OF CHICONE'S METHOD FOR PERTURBATION SYSTEMS OF THREE PARAMETERS WITH APPLICATION TO THE LIENARD SYSTEM
Authors: AFSHARNEZHAD Z. , AMALEH M. KARIMI
Published: February 2012

In this paper, Chicone's method has been extended for perturbation systems with three parameters. By applying Diliberto's theorem and variational lemma, some conditions for continuation of periodic solutions of a three-parametric autonomous perturbation system has been introduced. Also, the continuation region in the parameter space has been found. As an application of this extension, we applied it to the Lienard system.
UNIVERSALITY IN THE GRAVITATIONAL STRETCHING OF CLOCKS, WAVES AND QUANTUM STATES
Authors: UNNIKRISHNAN C. S. , GILLIES G. T.
Published: February 2012

There are discernible and fundamental differences between clocks, waves and physical states in classical physics. These fundamental concepts find a common expression in the context of quantum physics in gravitational fields; matter and light waves, quantum states and oscillator clocks become quantum synonymous through the Planck–Einstein–de Broglie relations and the equivalence principle. With this insight, gravitational effects on quantum systems can be simply and accurately analyzed. Apart from providing a transparent framework for conceptual and quantitative thinking on matter waves and quantum states in a gravitational field, we address and resolve with clarity the recent controversial discussions on the important issue of the relation and the crucial difference between gravimetery using atom interferometers and the measurement of gravitational time dilation.
SUBTLE IS THE LORD: ON THE DIFFERENCE BETWEEN NEWTONIAN (LYAPUNOV) STABILITY ANALYSIS AND GEOMETRICAL STABILITY ANALYSIS OF GRAVITATIONAL ORBITS
Authors: HORWITZ L. P. , YAHALOM A. , LEWKOWICZ M. , LEVITAN J.
Published: February 2012

In this essay we discuss the geometrical embedding method (GEM) for the analysis of the stability of Hamiltonian systems using geometrical techniques familiar from general relativity. This method has proven to be very effective. In particular, we show that although the application of standard Lyapunov analysis predicts that completely integrable Kepler motion is unstable, this geometrical analysis predicts the observed stability. Moreover, we apply this approach to the three body problem in which the third body is restricted to move on a circle of large radius which induces an adiabatic time dependent potential on the second body. This causes the second body to move in a very intricate but periodic trajectory. The geometric approach predicts the correct stable motion in this case as well.