bluuebunny/crossref_metadata_2025 huggingface dataset:
Comment on “Global Resilience of Tropical Forest and Savanna to Critical Transitions”
Authors: Ratajczak Zak , Nippert Jesse B.
Published: May 2012

Hirota
et al
. (Reports, 14 October 2011, p. 232) used spatial data to show that grasslands, savannas, and forests represent opposing stable states. Reanalyzing their data and drawing from temporal studies, we argue that spatial analyses underestimate the bistability of grasslands and savannas due to limitations of substituting space for time. We propose that temporal and spatial data are needed to predict critical transitions between grasslands and savannas.
Response to Comment on “Global Resilience of Tropical Forest and Savanna to Critical Transitions”
Authors: Van Nes Egbert H. , Holmgren Milena , Hirota Marina , Scheffer Marten
Published: May 2012

Ratajczak and Nippert note that transient states between treeless and savanna states are more common than between savanna and forest, and suggest that this can be explained by a slower rate of change in the intermediate conditions at drier sites. We show that probability distributions of tree cover rather reflect the interplay between intrinsic rates of change and perturbation regimes.
The Impact of Ionic Frustration on Electronic Order
Authors: Balents Leon
Published: May 2012

The frustrated ordering of dipoles created by copper and antimony ions in an oxide material may help to create an exotic quantum electronic state.
Empowering Science Teachers
Authors: Tobias Sheila , Baffert Anne
Published: May 2012

At any one time, there are thousands of U.S. Graduate Students with strong Science expertise and an interest in education who would be more than qualified to stem the critical shortage of secondary chemistry, physics, earth sciences, and biology teachers, but who will most likely never set foot in a high-school (precollege) classroom. Instead, nearly all of them are choosing to pursue research rather than to teach the science that fascinates them to young people. To change this situation, and the widespread lack of understanding and appreciation for science in the United States, it is critical to pinpoint the major source of the problem.
Complexities of the Uniquely Human Vagina
Authors: Witkin Steven S. , Ledger William J.
Published: May 2012

The vaginal microbiome in healthy women changes over short periods of time, differs among individuals, and varies in its response to sexual intercourse.
Improvement of Detection of Bacterial Pathogens in Normally Sterile Body Sites with a Focus on Orthopedic Samples by Use of a Commercial 16S rRNA Broad-Range PCR and Sequence Analysis
Authors: Grif K. , Heller I. , Prodinger W. M. , Lechleitner K. , Lass-Flörl C. , Orth D.
Published: May 2012

A new commercially available universal 16S and 18S rRNA gene PCR test, which is followed by sequence analysis of amplicons (SepsiTest), was evaluated for rapid identification of pathogens in the diagnosis of bone and joint infections. Eighty-three orthopedic samples and 21 specimens from other normally sterile body sites collected from 84 patients were analyzed in parallel by culture and PCR for detection of bacteria and fungi. Compared to culture, the diagnostic sensitivity and specificity of PCR were 88.5% and 83.5%, respectively. The detection rate of PCR (34.6%) was higher than that of bacterial culture (25.0%) as a consequence of the presence of fastidious and noncultivable species in samples and antibiotic treatment of patients. Thirteen culture-negative infections were identified by PCR, and PCR was able to detect culture-proven polymicrobial infections. On the other hand, three samples were culture positive but PCR negative. SepsiTest was demonstrated to be a valuable supplemental tool in the rapid detection of bacteria, especially for fastidious and noncultivable organisms, allowing earlier initiation of pathogen-adapted therapy in patients with bone and joint infections.
Molecular Identification and Antifungal Susceptibility Testing of Clinical Isolates of the Candida rugosa Species Complex and Proposal of the New Species Candida neorugosa
Authors: Paredes Katihuska , Sutton Deanna A. , Cano Josep , Fothergill Annette W. , Lawhon Sara D. , Zhang Sean , Watkins Jeffrey P. , Guarro Josep
Published: May 2012

Candida rugosa
is a poorly known fungal species occasionally involved in human infections. A molecular analysis of the sequences of the D1/D2 domains and the internal transcribed spacer (ITS) region of the ribosomal genes of 24 clinical isolates phenotypically identified as
C. rugosa
demonstrated that only 10 (41.6%) isolates belonged to that species. The other isolates were identified as
Candida pararugosa
(41.6%) and
Candida pseudorugosa
(8.3%). The remaining two isolates, from human and equine infections, respectively, were clearly different from the others and represent a new species proposed here as
Candida neorugosa
. The closest species by D1/D2 sequences was the type strain of
C. rugosa
, with only 92.3% similarity.
C. neorugosa
can also be differentiated from all other species of the
C. rugosa
complex by phenotypic features. The eight antifungal drugs tested showed high
in vitro
activity against the 24 isolates included in the study.
Can a Simple Flotation Method Lower the Limit of Detection of Mycobacterium tuberculosis in Extrapulmonary Samples Analyzed by the GeneXpert MTB/RIF Assay?
Authors: Taylor Nathan , Gaur Rajiv L. , Baron Ellen J. , Banaei Niaz
Published: May 2012

The rapid and accurate diagnosis of tuberculosis (TB) in children and extrapulmonary TB in adults continues to be a challenge. In this study, we determined the lower limit of detection (LOD) of the GeneXpert MTB/RIF assay with nonrespiratory specimens and investigated the utility of flotation procedures for concentrating the bacilli. Clinical specimens (9 cerebrospinal fluid [CSF], 13 gastric aspirate, 8 tissue, and 17 stool) were spiked with single-celled
Mycobacterium tuberculosis
, and the LOD of the GeneXpert assay was determined. Flotation studies were conducted with sucrose and NaCl, and the cycle thresholds of the MTB/RIF assay were compared between treated and untreated samples. There was no significant difference between the LODs of the GeneXpert assay with saline solution (median, 33 CFU/ml) and CSF (median, 25 CFU/ml) (
P
> 0.05) or gastric aspirate samples (median, 58 CFU/ml) (
P
> 0.05). The LOD with spiked tissue (median, 1,525 CFU/ml) and stool samples (median, 6,800 CFU/ml) was significantly elevated compared to that determined with saline solution (
P
≤ 0.05 and ≤ 0.0005, respectively). Flotation studies with sucrose or NaCl did not consistently result in lowered cycle thresholds in stool or gastric aspirates, but a cycle reduction of >10 was achieved in two of the three pooled CSF samples. Unlike the results seen with tissue and stool samples, there was no significant PCR inhibition in the MTB/RIF assay with CSF and gastric aspirates. Although preconcentration of CSF samples with sucrose and NaCl may enhance detection of
M. tuberculosis
by PCR, further advances are needed to concentrate the bacilli and eliminate PCR inhibitors in paucibacillary nonrespiratory samples.
Sequetyping: Serotyping Streptococcus pneumoniae by a Single PCR Sequencing Strategy
Authors: Leung Marcus H. , Bryson Kevin , Freystatter Kathrin , Pichon Bruno , Edwards Giles , Charalambous Bambos M. , Gillespie Stephen H.
Published: May 2012

The introduction of pneumococcal conjugate vaccines necessitates continued monitoring of circulating strains to assess vaccine efficacy and replacement serotypes. Conventional serological methods are costly, labor-intensive, and prone to misidentification, while current DNA-based methods have limited serotype coverage requiring multiple PCR primers. In this study, a computer algorithm was developed to interrogate the capsulation locus (cps) of vaccine serotypes to locate primer pairs in conserved regions that border variable regions and could differentiate between serotypes.In silicoanalysis ofcpsfrom 92 serotypes indicated that a primer pair spanning the regulatory genecpsBcould putatively amplify 84 serotypes and differentiate 46. This primer set was specific toStreptococcus pneumoniae, with no amplification observed for other species, includingS. mitis,S. oralis, andS. pseudopneumoniae. One hundred thirty-eight pneumococcal strains covering 48 serotypes were tested. Of 23 vaccine serotypes included in the study, most (19/22, 86%) were identified correctly at least to the serogroup level, including all of the 13-valent conjugate vaccine and other replacement serotypes. Reproducibility was demonstrated by the correct sequetyping of different strains of a serotype. This novel sequence-based method employing a single PCR primer pair is cost-effective and simple. Furthermore, it has the potential to identify new serotypes that may evolve in the future.
High-Risk Human Papillomavirus (hrHPV) E6/E7 mRNA Testing by PreTect HPV-Proofer for Detection of Cervical High-Grade Intraepithelial Neoplasia and Cancer among hrHPV DNA-Positive Women with Normal Cytology
Authors: Rijkaart D. C. , Heideman D. A. M. , Coupe V. M. H. , Brink A. A. T. P. , Verheijen R. H. M. , Skomedal H. , Karlsen F. , Morland E. , Snijders P. J. F. , Meijer C. J. L. M.
Published: May 2012

Our aim was to investigate whether high-risk HPV (hrHPV) mRNA detection by PreTect HPV-Proofer can be used to stratify hrHPV DNA-positive women of different cytology classes for risk of high-grade cervical intraepithelial neoplasia or worse (cervical precancer or cancer, i.e., cervical intraepithelial neoplasia grade 2 or higher [≥CIN2]). A total of 375 women participating in population-based screening, with a GP5+/6+-PCR hrHPV DNA-positive cervical scrape with normal cytology (
n
= 202), borderline or mild dyskaryosis (BMD) (
n
= 88), or moderate dyskaryosis or worse (>BMD) (
n
= 85), were enrolled. Cervical scrapes were additionally subjected to HPV16/18/31/33/45 E6/E7 mRNA analysis by PreTect HPV-Proofer (mRNA test). Referral and follow-up policies were based on cytology, hrHPV DNA, and mRNA testing. The primary study endpoint was the number of ≥CIN2 detected within 3 years of follow-up. The mRNA positivity increased with the severity of cytological abnormality, ranging from 32% (64/202) in hrHPV DNA-positive women with normal cytology to 47% (41/88) in BMD and 68% (58/85) in >BMD groups (
P
< 0.01). Women with ≥CIN2 were more likely to test positive by mRNA test (63%) than women without evidence of ≥CIN2 (32%;
P
< 0.01). A positive mRNA test result conferred an increased ≥CIN2 risk in hrHPV DNA-positive women with normal cytology, i.e., 0.55 (95% confidence interval [95% CI], 0.34 to 0.76) in mRNA-positive versus 0.20 (95% CI, 0.07 to 0.33) in mRNA-negative women. In hrHPV DNA-positive women with BMD or >BMD, the result of the mRNA test did not influence the ≥CIN2 risk. In conclusion, mRNA testing by PreTect HPV-Proofer might be of value to select hrHPV DNA-positive women with normal cytology in need of immediate referral for colposcopy.
Functional Cooperation between Human Adenovirus Type 5 Early Region 4, Open Reading Frame 6 Protein, and Cellular Homeobox Protein HoxB7
Authors: Müller Daniela , Schreiner Sabrina , Schmid Melanie , Groitl Peter , Winkler Michael , Dobner Thomas
Published: May 2012

Human adenovirus type 5 (HAdV5) E4orf6 (early region 4 open reading frame 6 protein) is a multifunctional early viral protein promoting efficient replication and progeny production. E4orf6 complexes with E1B-55K to assemble cellular proteins into a functional E3 ubiquitin ligase complex that not only mediates proteasomal degradation of host cell substrates but also facilitates export of viral late mRNA to promote efficient viral protein expression and host cell shutoff. Recent findings defined the role of E4orf6 in RNA splicing independent of E1B-55K binding. To reveal further functions of the early viral protein in infected cells, we used a yeast two-hybrid system and identified the homeobox transcription factor HoxB7 as a novel E4orf6-associated protein. Using a HoxB7 knockdown cell line, we observed a positive role of HoxB7 in adenoviral replication. Our experiments demonstrate that the absence of HoxB7 leads to inefficient viral progeny production, as HAdV5 gene expression is highly regulated by HoxB7-mediated activation of various adenoviral promoters. We have thus identified a novel role of E4orf6 in HAdV5 gene transcription via regulation of homeobox protein-dependent modulation of viral promoter activity.
A Human Coronavirus Responsible for the Common Cold Massively Kills Dendritic Cells but Not Monocytes
Authors: Mesel-Lemoine Mariana , Millet Jean , Vidalain Pierre-Olivier , Law Helen , Vabret Astrid , Lorin Valérie , Escriou Nicolas , Albert Matthew L. , Nal Béatrice , Tangy Frédéric
Published: May 2012

Human coronaviruses are associated with upper respiratory tract infections that occasionally spread to the lungs and other organs. Although airway epithelial cells represent an important target for infection, the respiratory epithelium is also composed of an elaborate network of dendritic cells (DCs) that are essential sentinels of the immune system, sensing pathogens and presenting foreign antigens to T lymphocytes. In this report, we show thatin vitroinfection by human coronavirus 229E (HCoV-229E) induces massive cytopathic effects in DCs, including the formation of large syncytia and cell death within only few hours. In contrast, monocytes are much more resistant to infection and cytopathic effects despite similar expression levels of CD13, the membrane receptor for HCoV-229E. While the differentiation of monocytes into DCs in the presence of granulocyte-macrophage colony-stimulating factor and interleukin-4 requires 5 days, only 24 h are sufficient for these cytokines to sensitize monocytes to cell death and cytopathic effects when infected by HCoV-229E. Cell death induced by HCoV-229E is independent of TRAIL, FasL, tumor necrosis factor alpha, and caspase activity, indicating that viral replication is directly responsible for the observed cytopathic effects. The consequence of DC death at the early stage of HCoV-229E infection may have an impact on the early control of viral dissemination and on the establishment of long-lasting immune memory, since people can be reinfected multiple times by HCoV-229E.
HIV-1 gp120 Vaccine Induces Affinity Maturation in both New and Persistent Antibody Clonal Lineages
Authors: Moody M. Anthony , Yates Nicole L. , Amos Joshua D. , Drinker Mark S. , Eudailey Joshua A. , Gurley Thaddeus C. , Marshall Dawn J. , Whitesides John F. , Chen Xi , Foulger Andrew , Yu Jae-Sung , Zhang Ruijun , Meyerhoff R. Ryan , Parks Robert , Scull Julia Cavanaugh , Wang Lu , Vandergrift Nathan A. , Pickeral Joy , Pollara Justin , Kelsoe Garnett , Alam S. Munir , Ferrari Guido , Montefiori David C. , Voss Gerald , Liao Hua-Xin , Tomaras Georgia D. , Haynes Barton F.
Published: May 2012

Most antibodies that broadly neutralize HIV-1 are highly somatically mutated in antibody clonal lineages that persist over time. Here, we describe the analysis of human antibodies induced during an HIV-1 vaccine trial (GSK PRO HIV-002) that used the clade B envelope (Env) gp120 of clone W6.1D (gp120
W6.1D
). Using dual-color antigen-specific sorting, we isolated Env-specific human monoclonal antibodies (MAbs) and studied the clonal persistence of antibodies in the setting of HIV-1 Env vaccination. We found evidence of V
H
somatic mutation induced by the vaccine but only to a modest level (3.8% ± 0.5%; range 0 to 8.2%). Analysis of 34 HIV-1-reactive MAbs recovered over four immunizations revealed evidence of both sequential recruitment of naïve B cells and restimulation of previously recruited memory B cells. These recombinant antibodies recapitulated the anti-HIV-1 activity of participant serum including pseudovirus neutralization and antibody-dependent cell-mediated cytotoxicity (ADCC). One antibody (3491) demonstrated a change in specificity following somatic mutation with binding of the inferred unmutated ancestor to a linear C2 peptide while the mutated antibody reacted only with a conformational epitope in gp120 Env. Thus, gp120
W6.1D
was strongly immunogenic but over four immunizations induced levels of affinity maturation below that of broadly neutralizing MAbs. Improved vaccination strategies will be needed to drive persistent stimulation of antibody clonal lineages to induce affinity maturation that results in highly mutated HIV-1 Env-reactive antibodies.
Activation of Cap-Dependent Translation by Mucosal Human Papillomavirus E6 Proteins Is Dependent on the Integrity of the LXXLL Binding Motif
Authors: Spangle Jennifer M. , Ghosh-Choudhury Nayana , Munger Karl
Published: May 2012

The human papillomavirus (HPV) type 16 (HPV16) E6 protein can stimulate mechanistic target of rapamycin complex 1 (mTORC1) signaling and cap-dependent translation through activation of the PDK1 and mTORC2 kinases. Here we report that HPV18 E6 also enhances cap-dependent translation. The integrity of LXXLL and PDZ protein binding domains is important for activation of cap-dependent translation by high-risk mucosal HPV E6 proteins. Consistent with this model, low-risk mucosal HPV6b and HPV11 E6 proteins, which do not contain a PDZ protein binding motif, also activate cap-dependent translation and mTORC1, albeit at a lower efficiency than high-risk HPV E6 proteins. In contrast, cutaneous HPV5 and HPV8 E6 proteins, which lack LXXLL and PDZ motif protein binding, do not enhance cap-dependent translation. Mutagenic analyses of low-risk HPV E6 proteins revealed that association with the LXXLL motif containing ubiquitin ligase E6AP (UBE3A) correlates with activation of cap-dependent translation. Hence, activation of mTORC1 and cap-dependent translation may be important for the viral life cycle in specific epithelial tissue types and contribute to cellular transformation in cooperation with other biological activities of high-risk HPV E6-containing proteins.
The Human T-Lymphotropic Virus Type 1 Tax Protein Inhibits Nonsense-Mediated mRNA Decay by Interacting with INT6/EIF3E and UPF1
Authors: Mocquet Vincent , Neusiedler Julia , Rende Francesca , Cluet David , Robin Jean-Philippe , Terme Jean-Michel , Duc Dodon Madeleine , Wittmann Jürgen , Morris Christelle , Le Hir Hervé , Ciminale Vincenzo , Jalinot Pierre
Published: May 2012

In this report, we analyzed whether the degradation of mRNAs by the nonsense-mediated mRNA decay (NMD) pathway was affected in human T-lymphotropic virus type 1 (HTLV-1)-infected cells. This pathway was indeed strongly inhibited in C91PL, HUT102, and MT2 cells, and such an effect was also observed by the sole expression of the Tax protein in Jurkat and HeLa cells. In line with this activity, Tax binds INT6/EIF3E (here called INT6), which is a subunit of the translation initiation factor eukaryotic initiation factor 3 (eIF3) required for efficient NMD, as well as the NMD core factor upstream frameshift protein 1 (UPF1). It was also observed that Tax expression alters the morphology of processing bodies (P-bodies), the cytoplasmic structures which concentrate RNA degradation factors. The presence of UPF1 in these subcellular compartments was increased by Tax, whereas that of INT6 was decreased. In line with these effects, the level of the phosphorylated form of UPF1 was increased in the presence of Tax. Analysis of several mutants of the viral protein showed that the interaction with INT6 is necessary for NMD inhibition. The alteration of mRNA stability was observed to affect viral transcripts, such as that coding for the HTLV-1 basic leucine zipper factor (HBZ), and also several cellular mRNAs sensitive to the NMD pathway. Our data indicate that the effect of Tax on viral and cellular gene expression is not restricted to transcriptional control but can also involve posttranscriptional regulation.
A dedicated inflammatory bowel disease service quantitatively and qualitatively improves outcomes in less than 18 months: a prospective cohort study in a large metropolitan centre
Authors: Phan Vinh-An Huu , van Langenberg Daniel R , Grafton Rachel , Andrews Jane M
Published: May 2012

Introduction

Maintaining high efficacy and quality of care in inflammatory bowel disease (IBD) management is a priority. The authors examined whether the introduction of a formal IBD Service (IBDS) positively influenced outcomes for their patients.

Methods

In 2007-2008, all IBD patients attending the Royal Adelaide Hospital were surveyed regarding clinical/demographic data, IBD knowledge, quality of life, mental health and satisfaction. Survey responders were re-surveyed ≥15 months later.

Results

162 responded to survey 1 and 81 again responded to survey 2. Within the responders, 61% had Crohn's disease and 48% were men. Compared with survey 1, the proportions of patients with improved knowledge, adherence, satisfaction with care, QoL (≥5 points), anxiety and depression scores were 63% (95% CI 51 to 73), 62% (95% CI 50 to 72), 65% (95% CI 54 to 76), 42% (95% CI 31 to 54), 52% (95% CI 40 to 63) and 43% (95% CI 32 to 55), respectively. When comparing survey 2 with survey 1, reductions in hospitalisation (48% vs 30%, p=0.02), courses of corticosteroids and opiates (mean 1.63 vs 0.91 and 1.00 vs 0.61, both p<0.05) and overall medications (5.63 vs 4.65, p<0.05), were seen. Fewer 2009 non-responders required hospitalisation (53% vs 21%, p<0.001), suggesting a `cohort' rather than `responder-specific' effect.

Conclusions

The introduction of an IBDS resulted in improved patient outcomes with significant reductions in negative markers for IBD morbidity including: hospitalisations, polypharmacy, steroid and opiate use. Despite increased costs in additional staff, these measures are likely to be cost effective.
The ERCP quality network benchmarking project: a preliminary comparison of practice in UK and USA
Authors: Oppong Kofi W , Romagnuolo Joseph , Cotton Peter B
Published: May 2012

Objective

The Endoscopic retrograde cholangiopancreatography (ERCP) Quality Network is a voluntary system for submission of data to generate individual report cards and benchmarking. The aim of this study was to compare aspects of ERCP practice between USA and UK participants.

Design

Analysis was limited to USA and UK based endoscopists who had each entered more than 30 cases. A number of practice and performance measures were studied including, rates of deep biliary cannulation, sedation use and success in bile duct stone removal.

Setting and patients

Patients attending for routine and emergency ERCP in participating tertiary and secondary care units in the UK and USA.

Results

61 US endoscopists performed 18 182 procedures and 16 UK endoscopists 3172, respectively. The UK participants performed less complex procedures as judged by the accepted complexity grading system, 8% versus 35% at grade 3, p<0.001. There was a significantly greater use of sedation as opposed to anaesthesia in the UK 97% versus 34%, p<0.001. UK deep biliary cannulation rate was 93% versus 97%, p<0.001. For small bile duct stones (<10 mm) the UK success rate was 96% compared with 99%, p<0.001.

Conclusion

The present data, while not purporting to be an accurate representation of practice in either country, documents good technical success in both cohorts, albeit significantly better in the USA. The inexorable drive to greater accountability and transparency of outcomes in endoscopic practice is likely to lead to increased participation in subsequent benchmarking projects.
ONYX versus n-BCA for embolization of cranial dural arteriovenous fistulas
Authors: Rabinov James David , Yoo Albert J , Ogilvy Christopher S , Carter Bob S , Hirsch Joshua A
Published: May 2012

Purpose

To evaluate the efficacy of n-butyl-2-cyanoacrylate (Trufill n-BCA) versus ethylene vinyl alcohol copolymer (ONYX) for the embolization of cranial dural arteriovenous fistulas (DAVF).

Methods

Fifty-three consecutive patients with cranial dural AVF were treated with liquid embolic agents from November, 2003 to November, 2008. These 53 patients had 56 lesions treated with arterial embolization. Patients embolized to completion underwent follow-up angiography at 3 months to assess for durable occlusion.

Results

Twenty-one lesions were treated with n-BCA. Seven patients treated with n-BCA had initial angiographic occlusion of their DAVF, which were durable at 3 months. Six patients had adjunctive treatment with coils and/or polyvinyl alcohol particles, but none of these were occluded by endovascular treatment alone. Eleven patients underwent post-embolization surgery for closure of their DAVF. There was one death related to intractable status epilepticus at presentation. One patient developed a major stroke from venous sinus thrombosis after embolization. Thirty-five lesions were treated with ONYX in 34 patients. Twenty-nine patients treated with ONYX had initial angiographic occlusion of their DAVF by embolization alone. One patient had recurrence at 3 months and was re-treated out of 27 total follow-ups. Four patients underwent post-embolization surgical obliteration of their lesions. No deaths or major strokes occurred in this cohort.

Conclusion

Initial angiographic occlusion (p=0.0004) and durable angiographic occlusion (p=0.0018) rates for embolization of cranial DAVF show a statistically significant higher efficacy with ONYX compared with n-BCA. Patients embolized with ONYX underwent surgery less frequently compared with those treated with n-BCA (p=0.0015).
Polarized continuum model study of bond dissociation energies of the O–NO2 bond — A density functional theory study and natural bond order analysis
Authors: Ruizhou Zhang , Zhumu Fu , Xiaohong Li , Xianzhou Zhang
Published: May 2012

Density functional methods (B3LYP, B3PW91, B3P86, and MPWB95) with 6–31G** basis sets and complete basis methods are employed to investigate the bond dissociation energies (BDEs) of the O–NO2 bond for seven O-nitroalcohol compounds in acetonitrile solution. B3LYP/6–31+G**, (RO)B3LYP/6–311++G(2df,2p), and B3LYP/6–311G(d,p) methods are also used. By comparing the calculated results with the experimental values, B3LYP/6–31+G** is the most accurate method to compute the reliable BDEs for the studied compounds. The substituent effects on the O–NO2 BDEs are analyzed. It is found that electron-withdrawing groups increase the BDE of the parent compound, whereas electron-donating groups decrease the BDE of the parent compound. Further, the natural bond orbital analysis shows that there exist good linear correlations between E(2) and Hammett constants, the BDE, and the difference of the second-order stabilization energies E(2) of lpO3 → BD*(O1–N1) and lpO3 → BD*(O2–N1).
Highly efficient solvent-free acetylation of alcohols with acetic anhydride catalyzed by recyclable sulfonic acid catalyst (SBA-15–Ph–Pr–SO3H) — An environmentally benign method
Authors: Zareyee Daryoush , Ghadikolaee Abdollah Razaghi , Khalilzadeh Mohammad A.
Published: May 2012

The catalytic activity of highly thermal stable, hydrophobic, and complete heterogeneous propylsulfonic acid functionalized nanostructured SBA-15 for excellent acetylation of alcohols and phenols with acetic anhydride at ambient temperature in solvent-free conditions was examined under environmentally benign reaction conditions. The salient features of this protocol are the absence of solvent, a green experimental procedure, and simple reusability of the catalyst (at least five reaction cycles).
Factors governing the regulation ofSclerotinia sclerotiorumcutinase A and polygalacturonase 1 during different stages of infection
Authors: Bashi Zafer Dallal , Rimmer S. Roger , Khachatourians George G. , Hegedus Dwayne D.
Published: May 2012

Sclerotinia sclerotiorum releases hydrolytic enzymes that sequentially degrade the plant cuticle, middle lamellae, and primary and secondary cell walls. The cuticle was found to be a barrier to S. sclerotiorum infection, as leaves stripped of epicuticular wax were more rapidly colonized. Consequently, the factors affecting the regulation of genes encoding polygalacturonase 1 (SsPG1) and a newly identified cutinase (SsCUTA) were examined. In vitro, SsCutA transcripts were detected within 1 h postinoculation of leaves, and expression was primarily governed by contact of mycelia with solid surfaces. Expression of SsPg1 was moderately induced by contact with solid surfaces including the leaf, and expression was restricted to the expanding margin of the lesion as the infection progressed. SsPg1 expression was induced by carbohydrate starvation but repressed by galacturonic acid. Glucose supported a basal level of SsPg1 expression but accentuated expression when provided to mycelia used to inoculate leaves. These observations were contrary to earlier reports indicating that glucose repressed SsPg1 expression while galacturonic acid induced expression. Pharmacological studies showed that disruption of calcium signalling affected SsCutA and SsPg1 expression and decreased S. sclerotiorum virulence, whereas elevated cAMP levels reduced virulence without affecting gene expression. The mechanisms involved in coordinating the expression of S. sclerotiorum hydrolytic enzymes throughout the various stages of the infection are discussed.
Characterization of an endophytic whorl-forming Streptomyces from Catharanthus roseus stems producing polyene macrolide antibiotic
Authors: Rakotoniriana Erick Francisco , Chataigné Gabrielle , Raoelison Guy , Rabemanantsoa Christian , Munaut Françoise , El Jaziri Mondher , Urveg-Ratsimamanga Suzanne , Marchand-Brynaert Jacqueline , Corbisier Anne-Marie , Declerck Stéphane , Quetin-Leclercq Joëlle
Published: May 2012

An endophytic whorl-forming Streptomyces sp. designated as TS3RO having antifungal activity against a large number of fungal pathogens, including Sclerotinia sclerotiorum , Rhizoctonia solani , Colletotrichum gloeosporioides , Cryphonectria parasitica , Fusarium oxysporum , Pyrenophora tritici-repentis , Epidermophyton floccosum , and Trichophyton rubrum , was isolated from surface-sterilized Catharanthus roseus stems. Preliminary identification showed that Streptomyces cinnamoneus subsp. sparsus was its closest related species. However, strain TS3RO could readily be distinguished from this species using a combination of phenotypic properties, 16S rDNA sequence similarity, and phylogenetic analyses. Thus, the whorl-forming Streptomyces sp. strain TS3RO is likely a new subspecies within the Streptomyces cinnamoneus group. Direct bioautography on a thin-layer chromatography plate with Cladosporium cucumerinum was conducted throughout the purification steps for bioassay-guided isolation of the active antifungal compounds from the crude extract. Structural elucidation of the isolated bioactive compound was obtained via LC–MS spectrometry, UV-visible spectra, and nuclear magnetic resonance data. It revealed that fungichromin, a known methylpentaene macrolide antibiotic, was the main antifungal component of TS3RO strain, as shown by thin-layer chromatography bioautography. This is the first report of an endophytic whorl-forming Streptomyces isolated from the medically important plant Catharanthus roseus.
Poly-β-hydroxybutyrate accumulation in bacterial consortia from different environments
Authors: Carpa Rahela , Butiuc-Keul Anca , Lupan Iulia , Barbu-Tudoran Lucian , Muntean Vasile , Dobrotă Cristina
Published: May 2012

The aim of the present study was to examine soil samples from various vegetation zones in terms of physicochemical properties, microbial communities, and isolation and identification (by polymerase chain reaction and transmission electron microscopy) of bacteria producing poly-β-hydroxybutyrates (PHBs). Soil samples were analysed originating from zones with heterogeneous environmental conditions from the Romanian Carpathian Mountains (mountain zone with alpine meadow, karstic zone with limestone meadow, hill zone with xerophilous meadow, and flood plain zone with hygrophilic meadow). Different bacterial groups involved in the nitrogen cycle (aerobic mesophilic heterotrophs, ammonifiers, denitrifiers, nitrifiers, and free nitrogen-fixing bacteria from Azotobacter genus) were analysed. Soil biological quality was assessed by the bacterial indicator of soil quality, which varied between 4.3 and 4.7. A colony polymerase chain reaction technique was used for screening PHB producers. With different primers, specific bands were obtained in all the soil samples. Some wild types of Azotobacter species were isolated from the 4 studied sites. Biodegradable polymers of PHB were assessed by negative staining in transmission electron microscopy. The maximum PHB granules density was obtained in the strains isolated from the xerophilous meadow (10–18 granules/cell), which was the most stressful environment from all the studied sites, as the physicochemical and microbiological tests proved.
Bacterial contamination of tile drainage water and shallow groundwater under different application methods of liquid swine manure
Authors: Samarajeewa A.D. , Glasauer S.M. , Lauzon J.D. , O’Halloran I.P. , Parkin Gary W. , Dunfield K.E.
Published: May 2012

A 2 year field experiment evaluated liquid manure application methods on the movement of manure-borne pathogens ( Salmonella sp.) and indicator bacteria ( Escherichia coli and Clostridium perfringens ) to subsurface water. A combination of application methods including surface application, pre-application tillage, and post-application incorporation were applied in a randomized complete block design on an instrumented field site in spring 2007 and 2008. Tile and shallow groundwater were sampled immediately after manure application and after rainfall events. Bacterial enumeration from water samples showed that the surface-applied manure resulted in the highest concentration of E. coli in tile drainage water. Pre-tillage significantly (p < 0.05) reduced the movement of manure-based E. coli and C. perfringens to tile water and to shallow groundwater within 3 days after manure application (DAM) in 2008 and within 10 DAM in 2007. Pre-tillage also decreased the occurrence of Salmonella sp. in tile water samples. Indicator bacteria and pathogens reached nondetectable levels within 50 DAM. The results suggest that tillage before application of liquid swine manure can minimize the movement of bacteria to tile and groundwater, but is effective only for the drainage events immediately after manure application or initial rainfall-associated drainage flows. Furthermore, the study highlights the strong association between bacterial concentrations in subsurface waters and rainfall timing and volume after manure application.
Introducing an interface between FeynRules and WHIZARD
Authors: Christensen Neil D. , Duhr Claude , Fuks Benjamin , Reuter Jürgen , Speckner Christian
Published: May 2012

While Monte Carlo event generators like Whizard have become indispensable tools in studying the impact of new physics on collider observables over the last decades, the implementation of new models in such packages has remained a rather awkward and error-prone process. Recently, the FeynRules package was introduced which greatly simplifies this process by providing a single unified model format from which model implementations for many different Monte Carlo codes can be derived automatically. In this note, we present an interface which extends FeynRules to provide this functionality also for the Whizard package, thus making Whizard’s strengths and performance easily available to model builders.
FINDING COMMUNITY STRUCTURE IN SPATIAL MARITIME SHIPPING NETWORKS
Authors: SUN ZHUO , ZHENG JIANFENG , HU HONGTAO
Published: May 2012

This study explores the community structure in spatial maritime shipping networks. As compared with air transportation networks and urban road networks, ports in spatial maritime shipping networks have smaller connections due to the physical confinement. A new divisive algorithm is proposed for detecting community structure in spatial maritime shipping networks. At each iteration for modularity optimization, the length of each edge is successively updated, instead of edge removal used in the conventional divisive method. Finally, numerical experiments based on the global maritime shipping network are carried out to account for the properties of community structure in spatial maritime shipping networks.
GENERALIZED VAN HOVE FORMULA FOR SCATTERING OF NEUTRONS BY THE NONEQUILIBRIUM STATISTICAL MEDIUM
Authors: KUZEMSKY A. L.
Published: May 2012

The theory of scattering of particles (e.g., neutrons) by statistical medium was recast for the nonequilibrium statistical medium. The correlation scattering function of the relevant variables give rise to a very compact and entirely general expression for the scattering cross-section of interest. The formula obtained by Van Hove provides a convenient method of analyzing the properties of slow neutron and light scattering by systems of particles such as gas, liquid or solid in the equilibrium state. In this paper the theory of scattering of particles by many-body system was reformulated and generalized for the case of nonequilibrium statistical medium. A new method of quantum-statistical derivation for the space and time Fourier transforms of the Van Hove correlation function was formulated. Thus in place of the usual Van Hove scattering function, a generalized one was deduced and the result was shown to be of greater potential utility than those previously given in the literature. This expression gives a natural extension of the familiar Van Hove formula for scattering of slow neutrons for the case in which the system under consideration is in a nonequilibrium state. The feasibility of light- and neutron-scattering experiments to investigate the appropriate problems in real physical systems was discussed briefly.
UV AND IR QUANTUM-SPACETIME EFFECTS FOR THE CHANDRASEKHAR MODEL
Authors: AMELINO-CAMELIA GIOVANNI , LORET NICCOLÒ , MANDANICI GIANLUCA , MERCATI FLAVIO
Published: May 2012

We modify the Chandrasekhar model of white dwarfs by introducing some of the momentum-space features which have been considered in the quantum-gravity literature. We find that when the new effects are confined to high energies, one only finds significant corrections to the Chandrasekhar model in regimes where the model anyway lacks any contact with observations. But these high-energy effects could play an important role in cases where ultra-high densities are present, even when the relevant star is still gigantic in Planck-length units. If the effects are not confined to high energies, as a result of "ultraviolet/infrared mixing", there could be significant implications for white dwarfs whose mass is roughly half the mass of the Sun, some of which are described in the literature as "strange white dwarfs".
Computational Nano-Materials Design of Low Cost and High Efficiency Cu2ZnSn[Se1-xSx]4 Photovoltaic Solar Cells by Self-Organized Two-Dimensional Spinodal Nanodecomposition
Authors: Tani Yoshimasa , Sato Kazunori , Katayama-Yoshida Hiroshi
Published: May 2012

We propose the possibility of spinodal nanodecomposition in Cu2ZnSn[Se1-x
S
x
]4 (CZTSeS) for high efficiency photovoltaic solar cells, based on the first-principles calculations within the self-interaction-corrected local density approximation. By using the Korringa–Kohn–Rostoker coherent potential approximation method, electronic structures of CZTSeS are calculated. Due to the calculated positive mixing energy and type II band alignment between Cu2ZnSnSe4 and Cu2ZnSnS4, we can expect that the efficiency of CZTSeS becomes higher by spinodal nano-decomposition. Then we simulate the self-organized two-dimensional spinodal nanodecomposition by Monte Carlo method using the Ising model with chemical pair interactions calculated from the first principles.
Fabrication and Characterization of Bragg Reflector Slow-Light Waveguide with Oxide Lateral Confinement
Authors: Fuchida Ayumi , Matsutani Akihiro , Koyama Fumio
Published: May 2012

Slowing light in Bragg reflector waveguides enables us to miniaturize optical devices. A platform of low-loss slow-light waveguides with lateral optical confinement is required. We propose and fabricate a slow-light waveguide with lateral oxide confinement using an equivalent index difference in a lateral direction. The coupling and propagation losses are evaluated from the waveguide length dependence of insertion losses. The propagation loss is in the range of 0.1 dB/µm for transverse magnetic (TM) modes. Also, it is predicted that the propagation loss can be reduced if we replace a top Au/distributed Bragg reflector (DBR) hybrid mirror with a Si/SiO2 DBR.
Ultrasensitive Far-Infrared Phototransistors Fabricated in Superlattice Structures
Authors: Ueda Takeji , Nagai Naomi , Komiyama Susumu
Published: May 2012

Charge sensitive infrared phototransistors (CSIPs), ultrasensitive detectors in the wavelength range of 10–50 µm, are fabricated in GaAs/AlGaAs superlattice structures. The superlattice structures consist of alternately grown 2-nm-thick Al0.3Ga0.7As tunnel barriers and thickness-modulated GaAs layers from 2 to 10 nm. The tilted miniband formed in a superlattice structure serves as a potential slope similar to formally used compositionally graded barriers. The utilization of the superlattice in a CSIP is expected to give advantages of easier design, less impurities, and better repeatability in crystal growth, and therefore provides more reliable device performance. The novel structure paves the way for the future mass production of CSIPs.
Translation from Schottky Barrier to Atomic Bridging-Type Surface Photovoltages in Cr-Aqueous-Solution-Rinsed Si(001) Wafers
Authors: Shimizu Hirofumi , Sanada Yuji
Published: May 2012

The Cr(OH)3/n-Si Schottky-barrier-type AC surface photovoltage (SPV) in n-type Si(001) wafers fades away during long air exposure at room temperature and/or thermal oxidation at 100 °C for a short time (10 min), indicating a collapse of the Schottky barrier. At 100 °C, the AC SPV reappears with a longer duration time in n-type Si wafers, explaining the occurrence and growth of a negative oxide charge because of the formation of an atomic bridging (CrOSi)-or CrO2-network reported previously. At 200 °C, the AC SPV approaches a strong inversion state in n-type Si. In contrast, in p-type Si(001) wafers, the AC SPV decreases with oxidation duration time at 100 °C. At 200 °C, the AC SPV completely disappears in p-type Si. This result explains why a positive fixed oxide charge in p-type Si was compensated for by the growth of a Cr-induced negative charge [(CrOSi)-or CrO2-network]. This reverse interrelation gives evidence that the translation occurs from the Schottky barrier to the atomic bridging AC SPV, and thus the Cr-induced negative charge can be proved to be described as (CrOSi)-and/or CrO2-networks as well as (AlOSi)-or (FeOSi)-networks that were demonstrated previously.
Thresholds of Etchable Track Formation and Chemical Damage Parameters in Poly(ethylene terephthalate), Bisphenol A polycarbonate, and Poly(allyl diglycol carbonate) Films at the Stopping Powers Ranging from 10 to 12,000 keV/µm
Authors: Yamauchi Tomoya , Mori Yutaka , Morimoto Akira , Kanasaki Masato , Oda Keiji , Kodaira Satoshi , Konishi Teruaki , Yasuda Nakahiro , Tojo Sachiko , Honda Yoshihide , Barillon Rémi
Published: May 2012

The damage structure of latent tracks in poly(ethylene terephthalate) (PET) has been examined by Fourier transform infrared (FT-IR) measurements. Results are compared with those from previous studies on bisphenol A polycarbonate (PC) and poly(allyl diglycol carbonate) (PADC). These polymers are exposed to protons and heavy ions (He, C, Ne, Si, Ar, Fe, Kr, and Xe) in air with energies less than 6 MeV/n, as well as gamma rays from an intense Co-60 source. Chemical damage parameters, namely, damage density, which is the number of losses of considered functional groups per unit length of tracks, radial size of the track core, in which the considered chemical groups are lost, and radiation chemical yields (G values) for each group are evaluated as a function of the stopping power. It has been confirmed that latent tracks will be etchable when the radial track core size is larger than the distance between two adjacent breaking points of polymer chains. The predominant breaking points are the C–O bonds in ether, ester, and carbonate ester bonds.
Quantitative Imaging with Fluorescent Biosensors
Authors: Okumoto Sakiko , Jones Alexander , Frommer Wolf B.
Published: May 2012

Molecular activities are highly dynamic and can occur locally in subcellular domains or compartments. Neighboring cells in the same tissue can exist in different states. Therefore, quantitative information on the cellular and subcellular dynamics of ions, signaling molecules, and metabolites is critical for functional understanding of organisms. Mass spectrometry is generally used for monitoring ions and metabolites; however, its temporal and spatial resolution are limited. Fluorescent proteins have revolutionized many areas of biology—e.g., fluorescent proteins can report on gene expression or protein localization in real time—yet promoter-based reporters are often slow to report physiologically relevant changes such as calcium oscillations. Therefore, novel tools are required that can be deployed in specific cells and targeted to subcellular compartments in order to quantify target molecule dynamics directly. We require tools that can measure enzyme activities, protein dynamics, and biophysical processes (e.g., membrane potential or molecular tension) with subcellular resolution. Today, we have an extensive suite of tools at our disposal to address these challenges, including translocation sensors, fluorescence-intensity sensors, and Förster resonance energy transfer sensors. This review summarizes sensor design principles, provides a database of sensors for more than 70 different analytes/processes, and gives examples of applications in quantitative live cell imaging.
Plant Innate Immunity: Perception of Conserved Microbial Signatures
Authors: Schwessinger Benjamin , Ronald Pamela C.
Published: May 2012

Plants and animals sense conserved microbial signatures through receptors localized to the plasma membrane and cytoplasm. These receptors typically carry or associate with non-arginine-aspartate (non-RD) kinases that initiate complex signaling networks cumulating in robust defense responses. In plants, coregulatory receptor kinases have been identified that not only are critical for the innate immune response but also serve an essential function in other regulatory signaling pathways.
A New Development: Evolving Concepts in Leaf Ontogeny
Authors: Townsley Brad T. , Sinha Neelima R.
Published: May 2012

Elucidation of gene regulatory networks (GRNs) underlying aspects of leaf development in multiple model species has uncovered surprisingly plastic regulatory architecture. The meticulously mapped network interactions in one model species cannot now be assumed to map directly onto a different species. Despite these overall differences, however, many modules do appear to be almost universal. Extrapolating findings across different model systems will demand great care but promises to reveal a rich tapestry of themes in GRN architecture and regulation. The purpose of this review is to approach the field of leaf development from the perspectives of the evolution of developmental systems that orchestrate leaf development.
Titan's Methane Weather
Authors: Roe Henry G.
Published: May 2012

Conditions in Titan's troposphere are near the triple point of methane, the second most abundant component of its atmosphere. Our understanding of Titan's lower atmosphere has shifted considerably in the past decade. Ground-based observations, Hubble Space Telescope images, and data returned from the Cassini and Huygens spacecraft show that Titan's troposphere hosts a methane-based meteorology in direct analogy to the water-based meteorology of Earth. What once was thought to be a quiescent place, lacking in clouds or localized weather and changing only subtly on long seasonal timescales, is now understood to be a dynamic system with significant weather events regularly occurring against the backdrop of dramatic seasonal changes. Although the observational record of Titan's weather covers only a third of its 30-year seasonal cycle, Titan's atmospheric processes appear to be more closely analogous to those of Earth than to those of any other object in our solar system.