bluuebunny/crossref_metadata_2025 huggingface dataset:
Two Cases of Ruminococcus gnavus Bacteremia Associated with Diverticulitis
Authors: Hansen Sanne G. K. , Skov Marianne N. , Justesen Ulrik S.
Published: January 2013

We report two cases of bacteremia with the anaerobic bacterium
Ruminococcus gnavus
. In both cases, the bacteremia was associated with diverticular disease. Preliminary conventional identification suggested peptostreptococci, and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis did not produce scores high enough for species identification. Finally, the bacteria were identified by 16S rRNA gene sequencing.
The Human Papillomavirus Type 8 E6 Protein Interferes with NOTCH Activation during Keratinocyte Differentiation
Authors: Meyers Jordan M. , Spangle Jennifer M. , Munger Karl
Published: January 2013

Cutaneous β-human papillomavirus (β-HPV) E6 proteins inhibit NOTCH signaling by associating with the transcriptional coactivator MAML1. NOTCH has tumor suppressor activities in epithelial cells and is activated during keratinocyte differentiation. Here we report that HPV type 8 (HPV8) E6 subverts NOTCH activation during keratinocyte differentiation by inhibiting RBPJ/MAML1 transcriptional activator complexes at NOTCH target DNA. NOTCH inhibition impairs epithelial differentiation and may thus contribute to β-HPV replication and viral oncogenesis.
Infection of the Upper Respiratory Tract with Seasonal Influenza A(H3N2) Virus Induces Protective Immunity in Ferrets against Infection with A(H1N1)pdm09 Virus after Intranasal, but Not Intratracheal, Inoculation
Authors: Bodewes Rogier , Kreijtz Joost H. C. M. , van Amerongen Geert , Hillaire Marine L. B. , Vogelzang-van Trierum Stella E. , Nieuwkoop Nella J. , van Run Peter , Kuiken Thijs , Fouchier Ron A. M. , Osterhaus Albert D. M. E. , Rimmelzwaan Guus F.
Published: January 2013

The clinical symptoms caused by infection with influenza A virus vary widely and depend on the strain causing the infection, the dose and route of inoculation, and the presence of preexisting immunity. In most cases, seasonal influenza A viruses cause relatively mild upper respiratory tract disease, while sometimes patients develop an acute severe pneumonia. Heterosubtypic immunity induced by previous infections with influenza A viruses may dampen the development of clinical symptoms caused by infection with influenza A viruses of another subtype, as is the case during influenza pandemics. Here we show that ferrets acquire protective immunity after infection of the upper respiratory tract with a seasonal influenza A(H3N2) virus against subsequent infection with influenza A(H1N1)pdm09 virus inoculated by the intranasal route. However, protective heterosubtypic immunity was afforded locally, since the prior infection with the A(H3N2) virus did not provide protection against the development of pneumonia induced after intratracheal inoculation with the A(H1N1)pdm09 virus. Interestingly, some of these animals developed more severe disease than that observed in naïve control animals. These findings are of interest in light of the development of so-called universal influenza vaccines that aim at the induction of cross-reactive T cell responses.
Structural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus
Authors: Muhaxhiri Zana , Deng Lisheng , Shanker Sreejesh , Sankaran Banumathi , Estes Mary K. , Palzkill Timothy , Song Yongcheng , Prasad B. V. Venkataram
Published: January 2013

Norwalk virus (NV), the prototype human calicivirus, is the leading cause of nonbacterial acute gastroenteritis. The NV protease cleaves the polyprotein encoded by open reading frame 1 of the viral genome at five nonhomologous sites, releasing six nonstructural proteins that are essential for viral replication. The structural details of how NV protease recognizes multiple substrates are unclear. In our X-ray structure of an NV protease construct, we observed that the C-terminal tail, representing the native substrate positions P5 to P1, is inserted into the active site cleft of the neighboring protease molecule, providing atomic details of how NV protease recognizes a substrate. The crystallographic structure of NV protease with the C-terminal tail redesigned to mimic P4 to P1 of another substrate site provided further structural details on how the active site accommodates sequence variations in the substrates. Based on these structural analyses, substrate-based aldehyde inhibitors were synthesized and screened for inhibition potency. Crystallographic structures of the protease in complex with each of the three most potent inhibitors were determined. These structures showed concerted conformational changes in the S4 and S2 pockets of the protease to accommodate variations in the P4 and P2 residues of the substrate/inhibitor, which could be a mechanism for how the NV protease recognizes multiple sites in the polyprotein with differential affinities during virus replication. These structures further indicate that the mechanism of inhibition by these inhibitors involves covalent bond formation with the side chain of the conserved cysteine in the active site by nucleophilic addition, and such substrate-based aldehydes could be effective protease inhibitors.
Inhibition of the Host Translation Shutoff Response by Herpes Simplex Virus 1 Triggers Nuclear Envelope-Derived Autophagy
Authors: Radtke Kerstin , English Luc , Rondeau Christiane , Leib David , Lippé Roger , Desjardins Michel
Published: January 2013

Macroautophagy is a cellular pathway that degrades intracellular pathogens and contributes to antigen presentation. Herpes simplex virus 1 (HSV-1) infection triggers both macroautophagy and an additional form of autophagy that uses the nuclear envelope as a source of membrane. The present study constitutes the first in-depth analysis of nuclear envelope-derived autophagy (NEDA). We established LC3a as a marker that allowed us to distinguish between NEDA and macroautophagy in both immunofluorescence and flow cytometry. NEDA was observed in many different cell types, indicating that it is a general response to HSV-1 infection. This autophagic pathway is known to depend on the viral protein γ34.5, which can inhibit macroautophagy via binding to beclin-1. Using mutant viruses, we were able to show that binding of beclin-1 by γ34.5 had no effect on NEDA, demonstrating that NEDA is regulated differently than macroautophagy. Instead, NEDA was triggered in response to γ34.5 binding to protein phosphatase 1α, an interaction used by the virus to prevent host cells from shutting off protein translation. NEDA was not triggered when late viral protein production was inhibited with acyclovir or hippuristanol, indicating that the accumulation of these proteins might stress infected cells. Interestingly, expression of the late viral protein gH was sufficient to rescue NEDA in the context of infection with a virus that otherwise does not support strong late viral protein expression. We argue that NEDA is a cellular stress response triggered late during HSV-1 infection and might compensate for the viral alteration of the macroautophagic response.
Structural and Functional Analysis of Coxsackievirus A9 Integrin α
v
β
6
Binding and Uncoating
Authors: Shakeel Shabih , Seitsonen Jani J. T. , Kajander Tommi , Laurinmäki Pasi , Hyypiä Timo , Susi Petri , Butcher Sarah J.
Published: January 2013

Coxsackievirus A9 (CVA9) is an important pathogen of the
Picornaviridae
family. It utilizes cellular receptors from the integrin α
v
family for binding to its host cells prior to entry and genome release. Among the integrins tested, it has the highest affinity for α
v
β
6
, which recognizes the arginine-glycine-aspartic acid (RGD) loop present on the C terminus of viral capsid protein, VP1. As the atomic model of CVA9 lacks the RGD loop, we used surface plasmon resonance, electron cryo-microscopy, and image reconstruction to characterize the capsid-integrin interactions and the conformational changes on genome release. We show that the integrin binds to the capsid with nanomolar affinity and that the binding of integrin to the virion does not induce uncoating, thereby implying that further steps are required for release of the genome. Electron cryo-tomography and single-particle image reconstruction revealed variation in the number and conformation of the integrins bound to the capsid, with the integrin footprint mapping close to the predicted site for the exposed RGD loop on VP1. Comparison of empty and RNA-filled capsid reconstructions showed that the capsid undergoes conformational changes when the genome is released, so that the RNA-capsid interactions in the N termini of VP1 and VP4 are lost, VP4 is removed, and the capsid becomes more porous, as has been reported for poliovirus 1, human rhinovirus 2, enterovirus 71, and coxsackievirus A7. These results are important for understanding the structural basis of integrin binding to CVA9 and the molecular events leading to CVA9 cell entry and uncoating.
Ribosomal Protein P0 Promotes
Potato Virus A
Infection and Functions in Viral Translation Together with VPg and eIF(iso)4E
Authors: Hafrén Anders , Eskelin Katri , Mäkinen Kristiina
Published: January 2013

We report here that the acidic ribosomal protein P0 is a component of the membrane-associated
Potato virus A
(PVA) ribonucleoprotein complex. As a constituent of the ribosomal stalk, P0 functions in translation. Although the ribosomal stalk proteins P0, P1, P2, and P3 are all important for PVA infection, P0 appears to have a distinct role from those of the other stalk proteins in infection. Our results indicate that P0 also regulates viral RNA functions as an extraribosomal protein. We reported previously that PVA RNA can be targeted by VPg to a specific gene expression pathway that protects the viral RNA from degradation and facilitates its translation. Here, we show that P0 is essential for this activity of VPg, similar to eIF4E/eIF(iso)4E. We also demonstrate that VPg, P0, and eIF(iso)4E synergistically enhance viral translation. Interestingly, the positive effects of VPg and P0 on viral translation were negatively correlated with the cell-to-cell spread of infection, suggesting that these processes may compete for viral RNA.
ComprehensiveIn VitroAnalysis of Simian Retrovirus Type 4 Susceptibility to Antiretroviral Agents
Authors: Togami Hiroaki , Shimura Kazuya , Okamoto Munehiro , Yoshikawa Rokusuke , Miyazawa Takayuki , Matsuoka Masao
Published: January 2013

Simian retrovirus type 4 (SRV-4), a simian type D retrovirus, naturally infects cynomolgus monkeys, usually without apparent symptoms. However, some infected monkeys presented with an immunosuppressive syndrome resembling that induced by simian immunodeficiency virus infection. Antiretrovirals with inhibitory activity against SRV-4 are considered to be promising agents to combat SRV-4 infection. However, although some antiretrovirals have been reported to have inhibitory activity against SRV-1 and SRV-2, inhibitors with anti-SRV-4 activity have not yet been studied. In this study, we identified antiretroviral agents with anti-SRV-4 activity from a panel of anti-human immunodeficiency virus (HIV) drugs using a robustin vitroluciferase reporter assay. Among these, two HIV reverse transcriptase inhibitors, zidovudine (AZT) and tenofovir disoproxil fumarate (TDF), potently inhibited SRV-4 infection within a submicromolar to nanomolar range, which was similar to or higher than the activities against HIV-1, Moloney murine leukemia virus, and feline immunodeficiency virus. In contrast, nonnucleoside reverse transcriptase inhibitors and protease inhibitors did not exhibit any activities against SRV-4. Although both AZT and TDF effectively inhibited cell-free SRV-4 transmission, they exhibited only partial inhibitory activities against cell-to-cell transmission. Importantly, one HIV integrase strand transfer inhibitor, raltegravir (RAL), potently inhibited single-round infection as well as cell-free and cell-to-cell SRV-4 transmission. These findings indicate that viral expansion routes impact the inhibitory activity of antiretrovirals against SRV-4, while only RAL is effective in suppressing both the initial SRV-4 infection and subsequent SRV-4 replication.
RNA Transfer from Poliovirus 135S Particles across Membranes Is Mediated by Long Umbilical Connectors
Authors: Strauss Mike , Levy Hazel C. , Bostina Mihnea , Filman David J. , Hogle James M.
Published: January 2013

During infection, the binding of poliovirus to its cell surface receptor at 37°C triggers an expansion of the virus in which internal polypeptides that bind to membranes are externalized. Subsequently, in a poorly understood process, the viral RNA genome is transferred directly across an endosomal membrane, and into the host cell cytoplasm, to initiate infection. Here, cryoelectron tomography demonstrates the results of 37°C warming of a poliovirus-receptor-liposome model complex that was produced using Ni-nitrilotriacetic acid lipids and His-tagged receptor ectodomains. In total, 651 subtomographic volumes were aligned, classified, and averaged to obtain detailed pictures, showing both the conversion of virus into its expanded form and the passage of RNA into intact liposomes. Unexpectedly, the virus and membrane surfaces were located ∼50 Å apart, with the 5-fold axis tilted away from the perpendicular, and the solvent spaces between them were spanned by either one or two long “umbilical” density features that lie at an angle to the virus and membrane. The thinner connector, which sometimes appears alone, is 28 to 30 Å in diameter and has a footprint on the virus surface located close to either a 5-fold or a 3-fold axis. The broader connector has a footprint near the quasi-3-fold hole that opens upon virus expansion and is hypothesized to include RNA, shielded from enzymatic degradation by polypeptides that include the N-terminal extension of VP1 and capsid protein VP4. The implications of these observations for the mechanism of RNase-protected RNA transfer in picornaviruses are discussed.
An Antiviral Role for Antimicrobial Peptides during the Arthropod Response to Alphavirus Replication
Authors: Huang Zhijing , Kingsolver Megan B. , Avadhanula Vasanthi , Hardy Richard W.
Published: January 2013

Alphaviruses establish a persistent infection in arthropod vectors which is essential for the effective transmission of the virus to vertebrate hosts. The development of persistence in insects is not well understood, although it is thought to involve the innate immune response. Using a transgenic fly system expressing a self-replicating viral RNA genome analog, we have previously demonstrated antiviral roles of the
Drosophila
Imd (immune deficiency) and Jak-STAT innate immunity pathways in response to alphavirus replication. In the present study, comparative microarray analysis of flies harboring an alphavirus replicon and control green fluorescent protein flies identified 95 SINrep-sensitive genes. Furthermore, a subset of these genes is regulated by Rel or STAT transcription factors of the Imd and Jak-STAT pathways, respectively. We identified two antimicrobial peptide genes,
attC
and
dptB
, which are SINrep sensitive and regulated by STAT and Rel, respectively. SINrep flies heterozygous for
attC
had an increased viral RNA level, while knocking down
dptB
in SINrep flies resulted in impaired development. When injected with whole virus, the double-stranded RNA knockdowns of either
attC
or
dptB
showed a significant increase in virus titers. Our data demonstrate an antiviral response involving the Imd and Jak-STAT mediated expression of
dptB
and
attC
.
Chromatin Immunoprecipitation and Microarray Analysis Suggest Functional Cooperation between Kaposi's Sarcoma-Associated Herpesvirus ORF57 and K-bZIP
Authors: Hunter Olga V. , Sei Emi , Richardson R. Blake , Conrad Nicholas K.
Published: January 2013

The Kaposi's sarcoma-associated herpesvirus (KSHV) open reading frame 57 (ORF57)-encoded protein (Mta) is a multifunctional regulator of viral gene expression. ORF57 is essential for viral replication, so elucidation of its molecular mechanisms is important for understanding KSHV infection. ORF57 has been implicated in nearly every aspect of viral gene expression, including transcription, RNA stability, splicing, export, and translation. Here we demonstrate that ORF57 interacts with the KSHV K-bZIP protein
in vitro
and in cell extracts from lytically reactivated infected cells. To further test the biological relevance of the interaction, we performed a chromatin immunoprecipitation and microarray (ChIP-chip) analysis using anti-ORF57 antibodies and a KSHV tiling array. The results revealed four specific areas of enrichment, including the ORF4 and K8 (K-bZIP) promoters, as well as oriLyt, all of which interact with K-bZIP. In addition, ORF57 associated with DNA corresponding to the PAN RNA transcribed region, a known posttranscriptional target of ORF57. All of the peaks were RNase insensitive, demonstrating that ORF57 association with the viral genome is unlikely to be mediated exclusively by an RNA tether. Our data demonstrate that ORF57 associates with the viral genome by using at least two modes of recruitment, and they suggest that ORF57 and K-bZIP coregulate viral gene expression during lytic infection.
Structural and Thermodynamic Basis of Amprenavir/Darunavir and Atazanavir Resistance in HIV-1 Protease with Mutations at Residue 50
Authors: Mittal Seema , Bandaranayake Rajinthna M. , King Nancy M. , Prabu-Jeyabalan Moses , Nalam Madhavi N. L. , Nalivaika Ellen A. , Kurt Yilmaz Nese , Schiffer Celia A.
Published: January 2013

Drug resistance occurs through a series of subtle changes that maintain substrate recognition but no longer permit inhibitor binding. In HIV-1 protease, mutations at I50 are associated with such subtle changes that confer differential resistance to specific inhibitors. Residue I50 is located at the protease flap tips, closing the active site upon ligand binding. Under selective drug pressure, I50V/L substitutions emerge in patients, compromising drug susceptibility and leading to treatment failure. The I50V substitution is often associated with amprenavir (APV) and darunavir (DRV) resistance, while the I50L substitution is observed in patients failing atazanavir (ATV) therapy. To explain how APV, DRV, and ATV susceptibility are influenced by mutations at residue 50 in HIV-1 protease, structural and binding thermodynamics studies were carried out on I50V/L-substituted protease variants in the compensatory mutation A71V background. Reduced affinity to both I50V/A71V and I50L/A71V double mutants is largely due to decreased binding entropy, which is compensated for by enhanced enthalpy for ATV binding to I50V variants and APV binding to I50L variants, leading to hypersusceptibility in these two cases. Analysis of the crystal structures showed that the substitutions at residue 50 affect how APV, DRV, and ATV bind the protease with altered van der Waals interactions and that the selection of I50V versus I50L is greatly influenced by the chemical moieties at the P1 position for APV/DRV and the P2 position for ATV. Thus, the varied inhibitor susceptibilities of I50V/L protease variants are largely a direct consequence of the interdependent changes in protease inhibitor interactions.
The Myeloid Transcription Factor GATA-2 Regulates the Viral UL144 Gene during Human Cytomegalovirus Latency in an Isolate-Specific Manner
Authors: Poole Emma , Walther Anett , Raven Kathy , Benedict Christopher A. , Mason Gavin M. , Sinclair John
Published: January 2013

It is generally accepted that, following primary infection, human cytomegalovirus (HCMV) establishes lifelong latency in CD34+progenitor cells and other derivative cells of the myeloid lineage. In this study, we show that the viral UL144 gene is expressed during latent infection in two cell types of the myeloid lineage, CD34+and CD14+monocytes, and that the UL144 protein is functional in latently infected monocytes. However, this latency-associated expression of UL144 occurs only in certain isolates of HCMV and depends on the presence of functional GATA-2 transcription factor binding sites in theUL144promoter, in contrast to the viral latency-associated geneLUNA, which we also show is regulated by GATA-2 but expressed uniformly during latent infection independent of the virus isolate. Taken together, these data suggest that the HCMV latency-associated transcriptome may be virus isolate specific and dependent on the repertoire of transcription factor binding sites in the promoters of latency-associated genes.
Large B cell lymphoma of the subtalar and talonavicular joint synovium
Authors: George David Alexander , Afsharpad Arash , Chifu Mihai Daniel , Ray Pinak
Published: January 2013

We present the unique case of a 68-year-old man with a background of rheumatoid arthritis, who underwent left subtalar and talonavicular arthrodesis due to degenerative changes and chronic pain. Histology of the synovium demonstrated large B cell lymphoma. The patient subsequently underwent R-CHOP chemotherapy and radiotherapy to the affected area. This is the first described case of a primary large B cell lymphoma of the subtalar and talonavicular joints, without bony involvement.
Primary Ewing's sarcoma of the skull
Authors: Rahman Asifur , Bhandari Paawan Bahadur , Hoque Saif Ul , Wakiluddin Abu Naim Md
Published: January 2013

Ewing's sarcoma, a highly malignant bone tumour, typically affects the pelvis and the long bones of the lower extremities in children and young adults and primary involvement of the skull is rare. Here, we present a case of primary Ewing's sarcoma of the skull with localised swelling in a young adult that involved the frontoparietal region of the skull and was very aggressive in nature. Even with aggressive surgery, the patient had multiple recurrences within 1 month of surgery and ultimately the patient died.
Pseudohypoaldosteronism without nephropathy masking salt-wasting congenital adrenal hyperplasia genetically confirmed
Authors: Balcells Carla , Gili Teresa , Pérez Jacobo , Corripio Raquel
Published: January 2013

Salt-losing crisis with hypoglycaemia and shock are the main manifestations of congenital adrenal hyperplasia (CAH) during the first weeks of life, while hyponatremia and hyperpotassemia alone are seen on mineralocorticoid deficiency or resistance. During the neonatal period, high blood levels of adrenal steroids may lead to confusing laboratory tests not being able to identify the real level of each hormone. A 33-day-old male baby was admitted at the emergency department with severe salt-losing crisis (Na+99 mEq/l and K+9.4 mEq/l) and mild acidosis. No hypoglycaemia or hypotension was seen. Urinary tract infection was excluded. Despite treatment with hydrocortisone and fludrocortisone, hyperpotassemia was hard to control. Laboratory tests could not differentiate between pseudohypoaldosteronism and CAH as both the aldosterone (2454 pg/ml) and 17-OH-progesterone (656.6 ng/ml) levels were high. Diagnosis was made, thanks to the genetic study that proved classical mutations in both alleles of the 21-hydroxylase gene.
Survival from profound metabolic acidosis due to hypovolaemic shock. A world record?
Authors: Di Rollo Nicola , Caesar David , Ferenbach David A , Dunn Mark J G
Published: January 2013

This case describes the unexpected survival of an adult man who presented to the emergency department with hypovolaemic shock secondary to a splenic haemorrhage. Before surgery he had a pH 6.527, base excess (BE) −34.2 mmol/l and lactate 15.6 mmol/l. He underwent a splenectomy after which his condition stabilised. He was managed in the intensive care unit postoperatively where he required organ support including renal replacement therapy but was subsequently discharged home with no neurological or renal deficit. Although there are case reports of patients surviving such profound metabolic acidosis these have mainly been cases of near drowning or toxic alcohol ingestion. To the best of our knowledge this is the first reported case of survival after a pH of 6.5 secondary to hypovolaemic shock.
Effect of pelvic floor muscle training during pregnancy and after childbirth on prevention and treatment of urinary incontinence: a systematic review
Authors: Mørkved Siv , Bø Kari
Published: January 2013

Background

Urinary incontinence (UI) is a common condition in women causing reduced quality of life and withdrawal from fitness and exercise activities. Pregnancy and childbirth are established risk factors. Current guidelines for exercise during pregnancy have no or limited focus on the evidence for the effect of pelvic floor muscle training (PFMT) in the prevention and treatment of UI.

Aims

Systematic review to address the effect of PFMT during pregnancy and after delivery in the prevention and treatment of UI.

Data sources

PubMed, CENTRAL, Cochrane Library, EMBASE and PEDro databases and hand search of available reference lists and conference abstracts (June 2012).

Methods

Study eligibility criteria: Randomised controlled trials (RCTs) and quasiexperimental trials published in the English language. Participants: Primiparous or multiparous pregnant or postpartum women. Interventions: PFMT with or without biofeedback, vaginal cones or electrical stimulation. Study appraisal and synthesis methods: Both authors independently reviewed, grouped and qualitatively synthesised the trials.

Results

22 randomised or quasiexperimental trials were found. There is a very large heterogeneity in the populations studied, inclusion and exclusion criteria, outcome measures and content of PFMT interventions. Based on the studies with relevant sample size, high adherence to a strength-training protocol and close follow-up, we found that PFMT during pregnancy and after delivery can prevent and treat UI. A supervised training protocol following strength-training principles, emphasising close to maximum contractions and lasting at least 8 weeks is recommended.

Conclusions

PFMT is effective when supervised training is conducted. Further high-quality RCTs are needed especially after delivery. Given the prevalence of female UI and its impact on exercise participation, PFMT should be incorporated as a routine part of women's exercise programmes in general.
Statistical process control charts for attribute data involving very large sample sizes: a review of problems and solutions
Authors: Mohammed Mohammed A , Panesar Jagdeep S , Laney David B , Wilson Richard
Published: January 2013

The use of statistical process control (SPC) charts in healthcare is increasing. The primary purpose of SPC is to distinguish between common-cause variation which is attributable to the underlying process, and special-cause variation which is extrinsic to the underlying process. This is important because improvement under common-cause variation requires action on the process, whereas special-cause variation merits an investigation to first find the cause. Nonetheless, when dealing with attribute or count data (eg, number of emergency admissions) involving very large sample sizes, traditional SPC charts often produce tight control limits with most of the data points appearing outside the control limits. This can give a false impression of common and special-cause variation, and potentially misguide the user into taking the wrong actions. Given the growing availability of large datasets from routinely collected databases in healthcare, there is a need to present a review of this problem (which arises because traditional attribute charts only consider within-subgroup variation) and its solutions (which consider within and between-subgroup variation), which involve the use of the well-established measurements chart and the more recently developed attribute charts based on Laney's innovative approach. We close by making some suggestions for practice.
Assessing inter-rater agreement of environmental audit data in a matched case-control study on bicycling injuries
Authors: Romanow Nicole T R , Couperthwaite Amy B , McCormack Gavin R , Nettel-Aguirre Alberto , Rowe Brian H , Hagel Brent E
Published: January 2013

Background

Environmental audit tools must be reliable in order to accurately estimate the association between built environmental characteristics and bicycling injury risk.

Objective

To examine the inter-rater agreement of a built environment audit tool within a case-control study on the environmental determinants of bicycling injuries.

Methods

Auditor pairs visited locations where bicycling injuries occurred and independently recorded location characteristics using the Systematic Pedestrian and Cyclist Environmental Scan (SPACES). Two case groups were defined: (1) where a bicyclist was struck by a motor-vehicle (MV) and (2) where the bicyclist's injuries required hospitalisation. The two corresponding control groups were (1) where non-MV bicycle-related injuries occurred and (2) where minor bicycle-related injuries occurred. Inter-rater reliability of each item on the tool was assessed using observed agreement and κ with 95% CI.

Results

Ninety-seven locations were audited. Inter-observer agreement was generally high (≥95%); most items had a 1–2% difference in responses. Items with ≥5% differences between raters included path condition, slope and obstructions. For land use, path and roadway characteristics, κ ranged from 0.3 for presence of offices and cleanliness to 0.9 for schools and number of lanes; overall, 78% of items had at least substantial agreement (κ≥0.61). For bicyclists struck by a MV the proportion of items with substantial agreement was 60%, compared with 73% for non-MV related injuries. For hospitalisations and minor bicycle-related injuries, 76% of items had substantial agreement.

Conclusions

Agreement was substantial for most, but not all SPACES items. The SPACES provides reliable quantitative descriptions of built environmental characteristics at bicycling injury locations.
The association between recreational parks, facilities and childhood obesity: a cross-sectional study of the 2007 National Survey of Children's Health
Authors: Alexander Dayna S , Huber Larissa R Brunner , Piper Crystal R , Tanner Amanda E
Published: January 2013

Background

Despite the rising childhood obesity rates, few studies have examined the association between access to recreational parks and facilities and obesity.

Methods

A cross-sectional study was performed among 42 278 US children who participated in the 2007 National Survey of Children's Health. Access to parks and recreational facilities was self-reported by parents, and body mass index was calculated from parents’ self-report of the child's height and weight. Logistic regression was used to obtain ORs and 95% CIs. Since obesity was not a rare occurrence, an OR correction method was used to provide a more reliable estimate of the prevalence ratio (PR).

Results

Children with access to parks and facilities had decreased prevalence of obesity as compared to children without access (PR=0.79, 95% CI 0.69 to 0.91). After adjustment for covariates, the magnitude of the association remained unchanged; however, results were no longer statistically significant (PR=0.77, 95% CI 0.55 to 1.07). Race/ethnicity was an effect modifier of the access–obesity relationship (p<0.0001). Among Non-Hispanic White children, there was no strong association (PR=0.89, 95% CI 0.64 to 1.23). However, among Non-Hispanic Black children, those who had access to recreational parks and facilities had 0.40 times the prevalence of obesity as compared to those without access, and this result was statistically significant (95% CI 0.17 to 0.90).

Conclusions

This research highlights potential health disparities in childhood obesity due to limited access to recreational parks and facilities. Additional studies are needed to further investigate this association. If confirmed, providing safe, accessible parks and facilities may be one way to combat childhood obesity, particularly among minority children.
Prescribing for weight loss in primary care: evidence from a population based study
Authors: Patterson Lynsey , Patterson Chris , Kee Frank , Hughes Carmel , Donnelly Michael , O'Reilly Dermot
Published: January 2013

Background

Taking antiobesity medication can be a cost effective way to lose weight. Uptake is determined in part by a General Practitioner's decision to prescribe weight loss medication and, in part, by patient preference. It is probable that the latter may indicate a patient's readiness to lose weight.

Methods

Analysis of cross-sectional data (from February 2003 to March 2011) from a population based prescribing database (∼1.75 million people) using an adjusted Poisson regression.

Results

The number of antiobesity medications increased from 23.4 per 1000 population in 2004 to 30.7 per 1000 population in 2010 and was three times higher in female than in male subjects. Against this background, a marked seasonal variation in the number of antiobesity medications dispensed was evident (p<0.001), peaking in June/July with a trough in December/January (±8.0% peak to trough). The seasonal component was stronger in female subjects, ±11.2% peak to trough, compared with ±3.5% for male subjects.

Conclusions

Obese patients, particularly women, increase their uptake of weight loss medication in the months leading up to the summer holiday period. The period prior to the summer may represent a time that health professionals could promote increased participation of obese patients in weight loss programmes.
Reconsidering residency: characterization and conservation implications of complex migratory patterns of shortnose sturgeon (Acispenser brevirostrum)
Authors: Dionne Phillip E. , Zydlewski Gayle B. , Kinnison Michael T. , Zydlewski Joseph , Wippelhauser Gail S.
Published: January 2013

Efforts to conserve endangered species usually involve attempts to define and manage threats at the appropriate scale of population processes. In some species that scale is localized; in others, dispersal and migration link demic units within larger metapopulations. Current conservation strategies for endangered shortnose sturgeon (Acipenser brevirostrum) assume the species is river resident, with little to no movement between rivers. However we have found that shortnose sturgeon travel more than 130 km through coastal waters between the largest rivers in Maine. Indeed, acoustic telemetry shows that shortnose sturgeon enter six out of the seven acoustically monitored rivers we have monitored, with over 70% of tagged individuals undertaking coastal migrations between river systems. Four migration patterns were identified for shortnose sturgeon inhabiting the Penobscot River, Maine: river resident (28%), spring coastal emigrant (24%), fall coastal emigrant (33%), and summer coastal emigrant (15%). No shortnose sturgeon classified as maturing female exhibited a resident pattern, indicating differential migration. Traditional river-specific assessment and management of shortnose sturgeon could be better characterized using a broader metapopulation scale, at least in the Gulf of Maine, that accounts for diverse migratory strategies and the importance of migratory corridors as critical habitat.
PHASE TRANSITIONS AND THE KORTEWEG-DE VRIES EQUATION IN THE DENSITY DIFFERENCE LATTICE HYDRODYNAMIC MODEL OF TRAFFIC FLOW
Authors: TIAN JUN-FANG , YUAN ZHEN-ZHOU , JIA BIN , FAN HONG-QIANG
Published: January 2013

We investigate the phase transitions and the Korteweg-de Vries (KdV) equation in the density difference lattice hydrodynamic (DDLM) model, which shows a close connection with the gas-kinetic-based model and the microscopic car following model. The KdV equation near the neutral stability line is derived and the corresponding soliton solution describing the density waves is obtained. Numerical simulations are conducted in two aspects. On the one hand, under periodic conditions perturbations are applied to demonstrate the nonlinear analysis result. On the other hand, the open boundary condition with random fluctuations is designed to explore the empirical congested traffic patterns. The phase transitions among the free traffic (FT), widening synchronized flow pattern (WSP), moving localized cluster (MLC), oscillatory congested traffic (OCT) and homogeneous congested traffic (HCT) occur by varying the amplitude of the fluctuations. To our knowledge, it is the first research showing that the lattice hydrodynamic model could reproduce so many congested traffic patterns.
ON PLANAR MEDIANOID COMPETITIVE LOCATION PROBLEMS WITH MANHATTAN DISTANCE
Authors: FU KE , MIAO ZHAOWEI , XU JIAYAN
Published: January 2013

A medianoid problem is a competitive location problem that determines the locations of a number of new service facilities that are competing with existing facilities for service to customers. This paper studies the medianoid problem on the plane with Manhattan distance. For the medianoid problem with binary customer preferences, i.e., a case where customers choose the closest facility to satisfy their entire demand, we show that the general problem is NP-hard and present solution methods to solve various special cases in polynomial time. We also show that the problem with partially binary customer preferences can be solved with a similar approach we develop for the model with binary customer preferences.
ADDITIVE DECOMPOSABILITY OF FUNCTIONS OVER ABELIAN GROUPS
Authors: COUCEIRO MIGUEL , LEHTONEN ERKKO , WALDHAUSER TAMÁS
Published: January 2013

Abelian groups are classified by the existence of certain additive decompositions of group-valued functions of several variables.
SIMULATION AND EXPERIMENTAL STUDIES ON SUBSTRATE TEMPERATURE AND GAS DENSITY FIELD IN HFCVD DIAMOND FILMS GROWTH ON WC–Co DRILL TOOLS
Authors: ZHANG JIANGUO , ZHANG TAO , WANG XINCHANG , SHEN BIN , SUN FANGHONG
Published: January 2013

Uniform temperature and gas density field inside the reactor play an important role on synthesis of high-quality diamond films using hot filament chemical vapor deposition (HFCVD) method. In the present study, the finite volume method (FVM) is adopted to simulate the temperature and gas density distribution during the deposition process. Temperature–measuring experiments are conducted to verify the correctness of the simulation results. Thereafter, the deposition parameters are optimized using this model as D (filament separation) = 35 mm, H (filament–substrate distance) = -10 mm and N (number of gas inlet) = 3. Finally, experiments of depositing diamond films on WC– Co drill tools are carried out with the optimal deposition parameters. The results of the characterization by SEM and Raman spectrum exhibit that as-fabricated diamond-coated tools present a layer of high-quality diamond films with homogeneous surface and uniform thickness, further validating the accuracy of the parameter optimization using the simulation method.
An Empirical Analysis of the Relationship between Chinese RMB Fluctuation and Overall Unemployment Rates in US
Authors: Li Ziran , Bao Qin , Wang Shouyang , Cheng Siwei
Published: January 2013

The relation between China's RMB exchange rate and US real economy has recently become a hotly debated issue among scholars, researchers, and policymakers. Using monthly data from Nov. 2001–Nov. 2010, this paper employs the cointegration test and VECM model to capture the relationships among the Chinese RMB exchange rate, US–China bilateral trade, and the US unemployment rate. Results indicate that the US unemployment rate is negatively correlated with the RMB exchange rate. Impulse response analysis discloses the transmission mechanism of RMB appreciation: an appreciation of the RMB leads to a drop in US–China bilateral trade, which associates with a slight rise in the US unemployment rate. A potential explanation for these unconventional results lie in the complementary industrial structures between the two countries. Some policy suggestions are made at the end.
STRUCTURES AND ELECTRONIC PROPERTIES OF FOUR CRYSTAL GeO2 AND TWO RARE-EARTH ELEMENT OXIDES La2O3 AND CeO2: FIRST PRINCIPLES CALCULATION
Authors: LIU CHONG , FAN XIAO-LI , AHMED SABEEH
Published: January 2013

This paper presents a first principles calculation of the structure and electronic properties of four crystal GeO2 structures and two rare-earth element oxides CeO2 and La2O3 . A GGA was used to optimize structures and calculate band structure and density of states (DOS). It is found that La2O3 has the largest band gap (4.19 eV) among all the six structures, which also means it is the best insulator among them. When it comes to four crystal GeO2 structures, which were calculated to make a comparison with two insulators CeO2 and La2O3 , we found the q- GeO2 and b- GeO2 are more likely to work as the dielectrics used in MOS devices than the other two crystalline forms. Three of the four GeO2 forms have larger band gap than that of CeO2 (2.09 eV), which indicates CeO2 is not a wise choice when deposited directly on the surface of Ge substrate.
MOLECULAR ACIDITY OF BUILDING BLOCKS OF BIOLOGICAL SYSTEMS: A DENSITY FUNCTIONAL REACTIVITY THEORY STUDY
Authors: ZHAO DONGBO , RONG CHUNYING , YIN DULIN , LIU SHUBIN
Published: January 2013

An accurate prediction of the molecular acidity by employing ab initio or density functional approaches for typical molecular systems is still challenging. Recently, we proposed to utilize two quantum descriptors, molecular electrostatic potential (MEP) and the sum of valence natural atomic orbital (NAO) energies on the nucleus of both the acidic atom and leaving proton, to quantitatively evaluate the pKa values. This new approach has been validated by a number of organic and inorganic systems and justified within the framework of density functional reactivity theory (DFRT). In this work, we apply the approach to building blocks of biological systems, namely, 20 natural α-amino acids and 5 DNA/RNA bases, together with a few other biologically relevant species. Our results show that there exists a strong linear correlation between MEP on the nucleus of the N atom and the sum of N 2p NAO energies, with the correlation coefficient R2 = 0.99. Also, we observe that both MEP on the nitrogen nucleus and the sum of N 2p NAO energies correlate well with experimental pKa values, with the correlation coefficient equal to 0.91. Using this established model, we predicted the trend of pKa changes of amino acids in proteins with different dielectric constants. We also applied the model to predict pKa values for dipeptides. Implications of these linear relationships to understand functions and reactivity of biological systems are discussed as well.
MODEL-BASED CLUSTERING WITH GENE RANKING USING PENALIZED MIXTURES OF HEAVY-TAILED DISTRIBUTIONS
Authors: COZZINI ALBERTO , JASRA AJAY , MONTANA GIOVANNI
Published: January 2013

Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have been proposed in which the distribution of gene expression values within each sub-group is assumed to be Gaussian. In the presence of noise and extreme observations, a mixture of Gaussian densities may over-fit and overestimate the true number of clusters. Moreover, commonly used model-based clustering algorithms do not generally provide a mechanism to quantify the relative contribution of each gene to the final partitioning of the data. We propose a penalized mixture of Student's t distributions for model-based clustering and gene ranking. Together with a resampling procedure, the proposed approach provides a means for ranking genes according to their contributions to the clustering process. Experimental results show that the algorithm performs well comparably to traditional Gaussian mixtures in the presence of outliers and longer tailed distributions. The algorithm also identifies the true informative genes with high sensitivity, and achieves improved model selection. An illustrative application to breast cancer data is also presented which confirms established tumor sub-classes.
CLASSIFICATION OF ENTANGLEMENT IN SYMMETRIC STATES
Authors: AULBACH MARTIN
Published: January 2013

Quantum states that are symmetric with respect to permutations of their subsystems appear in a wide range of physical settings, and they have a variety of promising applications in quantum information science. In this thesis, the entanglement of symmetric multipartite states is categorized, with a particular focus on the pure multi-qubit case and the geometric measure of entanglement. An essential tool for this analysis is the Majorana representation, a generalization of the single-qubit Bloch sphere representation, which allows for a unique representation of symmetric n-qubit states by n points on the surface of a sphere. Here this representation is employed to search for the maximally entangled symmetric states of up to 12 qubits in terms of the geometric measure, and an intuitive visual understanding of the upper bound on the maximal symmetric entanglement is given. Furthermore, it will be seen that the Majorana representation facilitates the characterization of entanglement equivalence classes such as stochastic local operations and classical communication (SLOCC) and the degeneracy configuration (DC). It is found that SLOCC operations between symmetric states can be described by the Möbius transformations of complex analysis, which allows for a clear visualization of the SLOCC freedoms and facilitates the understanding of SLOCC invariants and equivalence classes. In particular, explicit forms of representative states for all symmetric SLOCC classes of up to five qubits are derived. Well-known entanglement classification schemes such as the four qubit entanglement families or polynomial invariants are reviewed in the light of the results gathered here, which leads to sometimes surprising connections. Some interesting links and applications of the Majorana representation to related fields of mathematics and physics are also discussed.
SMOOTHED FINITE ELEMENT METHODS FOR THERMO-MECHANICAL IMPACT PROBLEMS
Authors: KUMAR V.
Published: January 2013

We present a Smoothed Finite Element Methods (SFEM) for thermo-mechanical impact problems. The smoothing is applied to the strains and the standard finite element approach is used for the temperature field. The SFEM allows for highly accurate results and large deformations. No isoparametric mapping is needed; the shape functions are computed in the physical domain. Moreover, no derivatives of the shape functions must be computed. We implemented a visco-plastic constitutive model and validate the method by comparing numerical results to experimental data.
DISCRETE-TIME EPIDEMIC DYNAMICS WITH AWARENESS IN RANDOM NETWORKS
Authors: SHANG YILUN
Published: January 2013

Human behavioral responses fundamentally influence the spread of infectious disease. In this paper, we study a discrete-time SIS epidemic process in random networks. Three forms of individual awareness, namely, local awareness, global awareness and contact awareness, are considered. The effect of awareness is to reduce the risk of infection. Based on the stability theory of matrix difference equation, we derive analytically the epidemic threshold. It is found that both local and contact awareness can raise the epidemic threshold, while the global awareness only decreases the epidemic prevalence. Our results are in line with a recent result using differential equation-based methods.