bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron/phonon coupling in group-IV transition-metal and rare-earth nitrides
Authors: Mei A. B. , Rockett A. , Hultman L. , Petrov I. , Greene J. E.
Published: November 2013

Transport electron/phonon coupling parameters and Eliashberg spectral functions αtr2F(ℏω) are determined for group-IV transition-metal (TM) nitrides TiN, ZrN, and HfN, and the rare-earth (RE) nitride CeN using an inversion procedure based upon temperature-dependent (4 < T < 300 K) resistivity measurements of high-crystalline-quality stoichiometric epitaxial films grown on MgO(001) by magnetically-unbalanced reactive magnetron sputtering. Transport electron/phonon coupling parameters λtr vary from 1.11 for ZrN to 0.82 for HfN, 0.73 for TiN, and 0.44 for CeN. The small variation in λtr among the TM nitrides and the weak coupling in CeN are consistent with measured superconducting transition temperatures 10.4 (ZrN), 9.18 (HfN), 5.35 (TiN), and <4 K for CeN. The Eliashberg spectral function describes the strength and energy spectrum of electron/phonon coupling in conventional superconductors. Spectral peaks in α2F(ℏω), corresponding to regions in energy-space for which electrons couple to acoustic ℏωac and optical ℏωop phonon modes, are centered at ℏωac = 33 and ℏωop = 57 meV for TiN, 25 and 60 meV for ZrN, 18 and 64 meV for HfN, and 21 and 39 meV for CeN. The acoustic modes soften with increasing cation mass; optical mode energies remain approximately constant for the TM nitrides, but are significantly lower for the RE nitride due to a lower interatomic force constant. Optical/acoustic peak-intensity ratios are 1.15 ± 0.1 for all four nitrides, indicating similar electron/phonon coupling strengths αtr(ℏω) for both modes.
Spin transport and spin polarization properties in double-stranded DNA
Authors: Simchi Hamidreza , Esmaeilzadeh Mahdi , Mazidabadi Hossein
Published: November 2013

We study the spin-dependent electron transport through a double-stranded DNA (dsDNA) using the Bogoliubov-de Gennes equations and non-equilibrium Green's function method. We calculate the spin-dependent electron conductance and spin-polarization for different lengths, helix angles, twist angles of dsDNA, the environment-induced dephasing factors, and hopping integral. It is shown that the conductance decreases by increasing the length and dephasing factor. Also, we show that the spin-polarization depends on the helical symmetry and the length of DNA. It is shown that the double-stranded DNA can act as a perfect spin filter. Finally, we show that the sign of spin polarization can be inverted from +1 (−1) to −1 (+1) for some values of hopping integral.
A transition from localized shear banding to homogeneous superplastic flow in nanoglass
Authors: Adibi Sara , Sha Zhen-Dong , Branicio Paulo S. , Joshi Shailendra P. , Liu Zi-Shun , Zhang Yong-Wei
Published: November 2013

A promising remedy to the failure of metallic glasses (MGs) by shear banding is the use of a dense network of glass-glass interfaces, i.e., a nanoglass (NG). Here we investigate the effect of grain size (d) on the failure of NG by performing molecular dynamics simulations of tensile-loading on Cu50Zr50 NG with d = 5 to 15 nm. Our results reveal a drastic change in deformation mode from a single shear band (d ∼ 15 to 10 nm), to cooperative shear failure (d ∼ 10 to 5 nm), to homogeneous superplastic flow (d ≤ 5 nm). Our results suggest that grain size can be an effective design parameter to tune the mechanical properties of MGs.
Low repetition rate and broad frequency tuning from a grating-coupled passively mode-locked quantum dot laser
Authors: Cheng H. C. , Wu Q. Y. , Pan C. H. , Lee C. P. , Lin G.
Published: November 2013

Passively mode-locked quantum dot lasers with a grating-coupled external cavity arrangement are investigated. A broad repetition-rate tuning range of fundamental mode-locking from 2 GHz to a record-low frequency of 79.3 MHz is achieved with selecting the wavelength at 1.28 μm. A narrow RF linewidth of ∼25 Hz and an intrinsic linewidth as low as 0.15 Hz are also obtained.
First demonstration of an asymmetric kinetic equilibrium for a thin current sheet
Authors: Aunai Nicolas , Belmont Gerard , Smets Roch
Published: November 2013

The modeling of steady state collisionless asymmetric tangential current layers is a challenging and poorly understood problem. For decades now, this difficulty has been limiting numerical models to approximate equilibria built with locally Maxwellian current layers and theoretical analyses to the very restricted Harris equilibrium. We show how the use of any distribution functions depending only on local macroscopic quantities results in a strong alteration of the current layer internal structure, which converges toward an unpredictable quasi-steady state with emission of ion scale perturbations. This transient can be explained in terms of ion kinetic and electron fluid physics. We demonstrate, for the first time, the validity of an asymmetric kinetic equilibrium model as well as its usability as an initial condition of hybrid kinetic simulations. This offers broad perspectives for the current sheet modeling, for which the early phase of instabilities can be studied within the kinetic formalism.
Role of social environment and social clustering in spread of opinions in coevolving networks
Authors: Malik Nishant , Mucha Peter J.
Published: November 2013

Taking a pragmatic approach to the processes involved in the phenomena of collective opinion formation, we investigate two specific modifications to the coevolving network voter model of opinion formation studied by Holme and Newman [Phys. Rev. E 74, 056108 (2006)]. First, we replace the rewiring probability parameter by a distribution of probability of accepting or rejecting opinions between individuals, accounting for heterogeneity and asymmetric influences in relationships between individuals. Second, we modify the rewiring step by a path-length-based preference for rewiring that reinforces local clustering. We have investigated the influences of these modifications on the outcomes of simulations of this model. We found that varying the shape of the distribution of probability of accepting or rejecting opinions can lead to the emergence of two qualitatively distinct final states, one having several isolated connected components each in internal consensus, allowing for the existence of diverse opinions, and the other having a single dominant connected component with each node within that dominant component having the same opinion. Furthermore, more importantly, we found that the initial clustering in the network can also induce similar transitions. Our investigation also indicates that these transitions are governed by a weak and complex dependence on system size. We found that the networks in the final states of the model have rich structural properties including the small world property for some parameter regimes.
11. Prevalence of anal high risk human papilloma virus (hr-HPV) infection and cytological
Authors: Gandra Sumanth , Azar Aline , Kini Nisha , Barton Bruce , Wessolossky Mireya
Published: November 2013

Background
Although anal HPV infection and cytological abnormalities are highly prevalent among HIV-infected MSM patients, there is limited data on HIV-infected heterosexual men and women. Since November 2010 at our clinic, anal cancer screening with both hr-HPV and cytology was routinely performed in all HIV-infected patients. The purpose of the study was to evaluate the prevalence of anal hr-HPV infection and cytological abnormalities among our cohort of HIV-infected MSM, heterosexual men and women. We also evaluated the performance of hr-HPV and abnormal cytology in detecting high-grade dysplasia (AIN2+). Methods: A retrospective cohort study was conducted in HIV patients who underwent routine screening for anal cancer from January 2011 to January 2013. The hr-HPV test is done concomitantly on an anal cytology specimen using the Hybrid Capture 2 assay (Digene Corporation). Medical records of patients who underwent high-resolution anoscopy (HRA) because of abnormal cytology (ASCUS and above) or positive hr-HPV were reviewed. Results: A total of 221 HIV patients underwent screening with both hr-HPV and anal cytology. Among them, 67% were men (73% MSM vs 27% heterosexual). hr-HPV was positive in 43% (54% MSM, 28% non-MSM and 27% women). Anal cytology was abnormal in 39% (48% MSM, 28% non-MSM and 34% of women). Among 117 (53%) patients with an abnormal screening test, 27% had both hr-HPV infection and abnormal cytology, 14% had only hr-HPV infection and 13% had only abnormal cytology. Cytology results were normal in 50%, non-diagnostic in 10%, ASCUS in 23%, LSIL in 14% and HSIL in 2%. Among 68 HIV patients who underwent HRA because of either abnormal anal cytology or hr-HPV infection, 22 patients had AIN2+ (17 were MSM) and all had hr-HPV. None of 14 patients with negative hr-HPV who underwent HRA for abnormal cytology had AIN2+. Paired results of cytology and biopsy did not correlate (rs = –0.13). Conclusions: Anal hr-HPV infection, cytological abnormalities and AIN2+ are prevalent among our cohort of HIV-infected heterosexual men and women. We suggest anal cancer screening for all HIV-infected patients. In our limited sample, hr-HPV performed better than anal cytology in detecting and ruling out AIN2+.
31. Lifetime prevalence of anal intercourse among sexually active female youth and young female sex workers: a comparative systematic review and meta-analysis
Authors: Owen Branwen Nia , Brock Paddy M. , Shubber Zara , Baggaley Rebecca F. , Butler Ailsa R. , Pickles Michael , Brisson Marc , Drolet Melanie , Boily Marie-Claude
Published: November 2013

Background
Anal cancer incidence has increased over the past twenty years. Heterosexual anal intercourse (AI) is a risk factor for HPV and HIV infection but is under-researched and ill-understood. We compare AI practices among young, sexually active general population females and female sex workers (FSW). Methods: We searched PubMed for heterosexual AI studies among young females, including FSWs (mean age <25 years), to December 2012. Study estimates were pooled using a random-effects model. Results: Fifty-four studies (42 average-risk, 6 higher-risk, 6 FSWs) were included. Most studies among general population youth were conducted in North America using self-administered questionnaires. All FSW studies were conducted in Africa and Asia using face-to-face interviews (FTFI). Pooled estimates of lifetime AI prevalence were larger among average-risk (23.6%, 95% CI 20.4–26.7) and higher-risk youth (25.5%, 95% CI 11.7–39.2) than FSWs (12.8%, 95% CI 8.4–17.3), but highly heterogeneous (I2 >90%). However, pooled AI estimates by continent of average-risk youth (Asia = 13.9%, 95% CI = 1.7–29.5; Africa = 18.4%, 95% CI 0.9–35.8) were more similar to those of FSWs (Asia = 16.0%, 95% CI 10.3–21.6; Africa = 9.7%, 95% CI 3.8–15.7). Estimates of average-risk youth reporting via FTFI (12.1%, 95% CI 0.7–23.5) were likewise similar to those among FSWs (12.8%, 95% CI 8.4–17.3). Pooled AI prevalence estimates among FSWs were higher in studies conducted after 2001 than in earlier studies. Conclusions: AI is common among sexually active females and may be increasing; it could therefore be an important determinant of HPV transmission and anal cancers. AI is as or more common among the general population youth than young FSWs but this may be confounded by continent, interview method and other unmeasured variables.
32. HPV type and strain variant concordance between anal cancers and their preceding high-grade squamous intraepithelial lesions
Authors: Palefsky Joel , Da Costa Maria , Darragh Teresa M. , Jay Naomi , Berry J. Michael
Published: November 2013

Background
Anal high-grade squamous intraepithelial lesions (HSIL) are frequently found overlying anal cancer on histology, and anal cancer has been observed to develop in the same location as previously diagnosed anal HSIL. These observations support the role of HSIL as the direct precursor lesion to anal cancer. To further investigate a direct pathogenetic relationship between anal HSIL and cancer, we typed and sequenced HPV DNA in anal HSIL and the cancers that subsequently developed in the same location. Methods: Tissues samples were analysed from 15 HIV-infected men followed at UCSF in whom anal cancer developed at a previously biopsied site of HSIL. Formalin-fixed paraffin-embedded pairs of HSIL and cancer were typed for HPV DNA using L1 PCR. HPV 16-positive samples underwent E6-based strain variant analysis. Results: Nine matched pairs for which DNA from both HSIL and cancer were available were analysed. Eight pairs (89%) contained HPV 16 DNA. One (11%) contained both HPV 18 and 51 in both samples. Of the eight HPV 16-positive pairs, each pair contained the same HPV 16 strain variant. Four contained the Eur-350T variant alone, and one contained Eur-350T in both the HSIL and cancer, with an additional 426T variant in the cancer. One pair contained both Eur-350T and 457C in both the HSIL and the cancer. Two pairs contained the Eur-350G variant alone. Conclusions: Concordance of both the HPV type and strain variant in anal cancers and their site-matched preceding HSIL further supports the role of anal HSIL as an anal cancer precursor.
34. One lesion, one virus: individual components of high-grade anal intraepithelial neoplasia in HIV+ men contain a single HPV type
Authors: Richel O. , Quint K. D. , Lindeman J. , Van Noesel C. M. , De Koning M. N. C. , Van den Munckhof H. A. M. , De Vries H. J. C. , Prins J. M. , Quint W. G. V.
Published: November 2013

Background
Anal intraepithelial neoplasia (AIN) is present in the majority of HIV+ men who have sex with men (MSM). The main aetiological factor is human papilloma virus (HPV). We analysed whether HPV PCR genotyping of whole tissue sections (WTS) and subsequent laser capture microdissection (LCM) detects type-specific HPV DNA in individual areas of HGAIN, and compared these lesional HPV genotypes with HPV types in anal swabs. Methods: DNA was isolated from anal swabs and WTS of 31 HGAIN biopsies obtained from 21 HIV+ MSM and analysed by the SPF10 PCR/LiPA25 HPV genotyping system. In case of multiple HPV types per WTS, PCR was repeated in selected areas of AIN obtained by LCM. Results: A single HPV type was observed in 15 (48%) of 31 WTS. In the 16 WTS with multiple HPV types, LCM-isolated dysplastic areas were studied. In 14 of the 16 WTS, one single HPV type was demonstrated within each discrete area of the lesion, resulting in a total of 29 (15+14) biopsies in which a single HPV type was found in (all components of) the lesion. HPV 16 was found in 14 of 31 biopsies (45%). In almost half the biopsies, lesional HPV types were not detected in the anal swabs. Conclusions: WTS PCR and subsequent LCM PCR is accurate in detecting lesion-specific HPV types in HGAIN and in 94% of the biopsies a single HPV was found in (each component of) the HGAIN lesion. In the majority, HPV16 was not the causative type and HPV genotyping of anal swabs was not useful in detecting the lesion-specific type.
37. ADXS11-001, mitomycin, 5-FU and radiation for anal cancera A phase I/II study
Authors: Safran Howard , Perez Kimberly , Klipfel Adam , Shah Nishit , Vrees Matthew , Dipetrillo Thomas , Austin T. , Jean Maureen , Luppe Denise , Rosati Kayla
Published: November 2013

Background
Human papillomavirus (HPV) DNA is present in the majority of squamous cell cancers of the anus. ADXS11–001 immunotherapy is a live attenuated Listeria monocytogenes (Lm) bioengineered to secrete an HPV-16-E7 fusion protein targeting HPV-transformed cells. The Lm vector infects antigen-presenting cells, stimulating both MHC class 1 and 2 pathways resulting in specific T-cell immunity to tumours. The Brown University Oncology Research Group has initiated a phase I/II study evaluating two treatment schedules of ADXS11–001 with standard chemoradiation for anal cancer. Methods: Patients with newly diagnosed anal cancer with a primary tumour >4 cm or lymph node involvement, without distant metastases, are eligible. All patients receive two courses of mitomycin, 5-FU with concurrent radiation (54 Gy in 30 fractions by IMRT). Patients receive four treatments of ADXS11–001, 1 × 109 colony-forming units intravenously once approximately every 28 days. In treatment schedule 1, the first dose is given before chemoradiation and the second to fourth doses are given every 28 days after completion of radiation. In treatment schedule 2, the second dose of ADXS11–001 is administered during chemoradiation. Results: Three patients have been treated with ADXS11–001 and chemoradiation on treatment schedule 1. One patient developed grade 3 chills and one patient experienced grade 2 flu-like symptoms post-infusion, both resolved with symptomatic treatment. Conclusions: ADXS11–001 is a highly novel form of immunotherapy designed to generate an immune response against HPV transformed cells. Accrual is continuing to evaluate safety and efficacy for patients with anal cancer.
45. Is there potential for use of the quadrivalent HPV vaccine as a post-treatment adjuvant?
Authors: Swedish Kristin A. , Goldstone Stephen E.
Published: November 2013

Background
The quadrivalent HPV (qHPV) vaccine (Gardasil®; Merck and Co., Whitehouse Station, NJ) is licensed to prevent anorectal HPV related disease in men and women through age 26 years. We demonstrated previously that qHPV was associated with decreased risk of recurrent HSIL among men who have sex with men (MSM; HR 0.50, 95% CI 0.26–0.98; P = 0.04). We endeavoured to determine if qHPV was effective in preventing condyloma development and recurrence in older MSM patients. Methods: A non-concurrent cohort study of patients vaccinated with qHPV compared with non-vaccinated patients. Those with a history of condyloma were disease free for 1 year. Results: 313 patients with a mean age of 42 years were followed for a median of 981 days. During 773.6 person-years follow-up, condyloma developed in 10 (8.6%) vaccinated patients (incidence 3.7 per 100 person-years) and 37 (18.8%) unvaccinated patients (incidence 7.3 per 100 person-years; P = 0.05). Multivariable hazards ratio showed that qHPV was associated with decreased risk of anal condyloma development (HR 0.45; 95% CI 0.22–0.92; P = 0.03). Kaplan–Meier (KM) survival analysis showed significantly reduced recurrence out to 4 years (cumulative incidence vaccinated 0.1 vs unvaccinated 0.25; P = 0.04). In the smaller subset of 103 patients with a history of condyloma, KM survival analysis showed striking separation of curves in the vaccinated vs unvaccinated with the cumulative incidence of recurrence (0.15, 0.35, respectively) but it did not reach significance (P = 0.12). Conclusions: The qHPV vaccine appears to prevent incident and recurrent condyloma in patients older than 26 years and might be a useful post treatment adjuvant.
9. Cellular immune response to anal dysplasia in HIV-positive men on highly active antiretroviral therapy
Authors: Farhat Nada , Laver Nora , Caro José
Published: November 2013

Background
The role of the cellular immune response to anal dysplasia progression is poorly understood. Extrapolated from the cervical model, CD4+ (killed by HIV) and CD8+ cells may have crucial anti-tumour activity. We report pilot data on key immune responses in HIV+ patients on HAART with anal dysplasia. Methods: High-resolution anoscopy and biopsies were performed. Ten tissue biopsies with high-grade anal intraepithelial neoplasia (HGAIN) were stained with immunohistochemistry for CD4+, CD8+, CXCL12+ and FOXP3+, and compared with 10 samples with low-grade anal intraepithelial neoplasia (LGAIN). Serum CD4+ and CD8+ counts were available. Tissue photographs were obtained and analysed utilising MetaXpress software. Results: In all dysplastic tissue, we found a higher number of CD4+, CD8+ and FOXP3+ cells in the subepithelium than epithelium. In HGAIN, the number of FOXP3+, intraepithelial CD4+ cells, and the ratio of intraepithelial to serum CD4+ were higher than in LGAIN. CXCL12+ staining was more abundant in HGAIN. CD4+ cells outnumbered CD8+ cells in all dysplastic tissue. Conclusions: The higher CD4+ to CD8+ ratio in HGAIN may be explained by the excess demand for antitumour activity, which is known to be a function of CD4+ cells against HPV-dysplasia in the analogous cervical dysplasia model. Cytotoxic CD8 cells, although known to have an important anti-tumour role, were less abundant in our study. The pro-tumour FOXP3+ cells, being more abundant in HGAIN, may have a key role in the progression of anal dysplasia. Strategies to block CXCL12+ may be useful in the treatment of HPV-related dysplasia.
Evolutionary mix-and-match with MFS transporters II
Authors: Madej M. Gregor , Kaback H. Ronald
Published: November 2013

Significance

The Major Facilitator Superfamily (MFS), the largest family of secondary transport proteins, catalyzes transport of a wide range of substrates. Difficulty discerning underlying mechanistic principles is due to low sequence conservation. However, a common structural feature of MFS members, suggesting that they may have arisen by intragenic multiplication, is a repeat of four three-helix bundles organized in two pseudosymmetrical domains. An alignment of these triple-helix motifs in combinatorial fashion allows detection of functionally homologous positions. Thus, substrate and H
+
-binding sites in distantly related symporters are located at the same relative positions. The structural organization also suggests that an ordered kinetic mechanism similar to that determined for lactose permease may be operative in other MFS symporters.
Effect of separate sampling on classification accuracy
Authors: Shahrokh Esfahani Mohammad , Dougherty Edward R.
Published: November 2013

Motivation: Measurements are commonly taken from two phenotypes to build a classifier, where the number of data points from each class is predetermined, not random. In this ‘separate sampling’ scenario, the data cannot be used to estimate the class prior probabilities. Moreover, predetermined class sizes can severely degrade classifier performance, even for large samples.

Results: We employ simulations using both synthetic and real data to show the detrimental effect of separate sampling on a variety of classification rules. We establish propositions related to the effect on the expected classifier error owing to a sampling ratio different from the population class ratio. From these we derive a sample-based minimax sampling ratio and provide an algorithm for approximating it from the data. We also extend to arbitrary distributions the classical population-based Anderson linear discriminant analysis minimax sampling ratio derived from the discriminant form of the Bayes classifier.

Availability: All the codes for synthetic data and real data examples are written in MATLAB. A function called mmratio, whose output is an approximation of the minimax sampling ratio of a given dataset, is also written in MATLAB. All the codes are available at: http://gsp.tamu.edu/Publications/supplementary/shahrokh13b.

Contact:  edward@ece.tamu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
FastPros: screening of reaction knockout strategies for metabolic engineering
Authors: Ohno Satoshi , Shimizu Hiroshi , Furusawa Chikara
Published: November 2013

Motivation: Although constraint-based flux analysis of knockout strains has facilitated the production of desirable metabolites in microbes, current screening methods have placed a limitation on the number knockouts that can be simultaneously analyzed.

Results: Here, we propose a novel screening method named FastPros. In this method, the potential of a given reaction knockout for production of a specific metabolite is evaluated by shadow pricing of the constraint in the flux balance analysis, which generates a screening score to obtain candidate knockout sets. To evaluate the performance of FastPros, we screened knockout sets to produce each metabolite in the entire Escherichia coli metabolic network. We found that 75% of these metabolites could be produced under biomass maximization conditions by adding up to 25 reaction knockouts. Furthermore, we demonstrated that using FastPros in tandem with another screening method, OptKnock, could further improve target metabolite productivity.

Availability and implementation: Source code is freely available at http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FastPros/, implemented in MATLAB and COBRA toolbox.

Contact:  chikara.furusawa@riken.jp or shimizu@ist.osaka-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria
Authors: Valach Matus , Moreira Sandrine , Kiethega Georgette N. , Burger Gertraud
Published: November 2013

Mitochondrial ribosomal RNAs (rRNAs) often display reduced size and deviant secondary structure, and sometimes are fragmented, as are their corresponding genes. Here we report a mitochondrial large subunit rRNA (mt-LSU rRNA) with unprecedented features. In the protist Diplonema, the rnl gene is split into two pieces (modules 1 and 2, 534- and 352-nt long) that are encoded by distinct mitochondrial chromosomes, yet the rRNA is continuous. To reconstruct the post-transcriptional maturation pathway of this rRNA, we have catalogued transcript intermediates by deep RNA sequencing and RT-PCR. Gene modules are transcribed separately. Subsequently, transcripts are end-processed, the module-1 transcript is polyuridylated and the module-2 transcript is polyadenylated. The two modules are joined via trans-splicing that retains at the junction ∼26 uridines, resulting in an extent of insertion RNA editing not observed before in any system. The A-tail of trans-spliced molecules is shorter than that of mono-module 2, and completely absent from mitoribosome-associated mt-LSU rRNA. We also characterize putative antisense transcripts. Antisense-mono-modules corroborate bi-directional transcription of chromosomes. Antisense-mt-LSU rRNA, if functional, has the potential of guiding concomitantly trans-splicing and editing of this rRNA. Together, these findings open a window on the investigation of complex regulatory networks that orchestrate multiple and biochemically diverse post-transcriptional events.
The Effect of Bioprocessing on the Phenolic Acid Composition and Antioxidant Activity of Wheat Bran
Authors: Zhang Lixia , Gao Wenyuan , Chen Xuetao , Wang Haiyang
Published: November 2013

In the present study, bioprocessing with eight microbial strains including Bacillus species, yeasts, and filamentous fungi was evaluated for its potential to improve the phenolic acid composition and antioxidant activity of wheat bran. The soluble free and soluble conjugated fractions of ethanolic extracts of the treated bran samples were compared for their total phenolic contents, phenolic acid composition, and in vitro antioxidant activities. In general, total phenolic content in the soluble free fraction increased significantly, accounting for 241.11 ± 1.25 μg of gallic acid equivalents (GE)/g (Rhizopus oryzae), 230.50 ± 1.05 μg of GE/g (Mucor circinelloides), and 230.19 ± 1.02 μg of GE/g (Saccharomycopsis fibuligera). The phenolic acid composition, especially of the soluble free fraction, was improved most by S. fibuligera (hydroxybenzoic, vanillic, syringic, and trans‐ferulic acids), M. circinelloides (chlorogenic acid), and R. oryzae (protocatechuic, trans‐coumaric, and benzoic acids). Comparatively, bioprocessing exhibited less effectiveness on conjugated phenolic acid composition. Fermented wheat bran displayed enhanced reducing capacity, superoxide anion radical scavenging activity, and 1,1‐diphenyl‐2‐picrylhydrazyl radical scavenging activity in comparison with the nonfermented sample. The antioxidant activity was significantly correlated to the total phenolic content.
Characterization of Staphylococcus epidermidis and Staphyloccocus warneri small-colony variants associated with prosthetic-joint infections
Authors: Bogut Agnieszka , Niedźwiadek Justyna , Kozioł-Montewka Maria , Strzelec-Nowak Dagmara , Blacha Jan , Mazurkiewicz Tomasz , Marczyński Wojciech , Plewik Dorota
Published: November 2013

We determined the frequency of isolation of staphylococcal small-colony variants (SCVs) from 31 culture-positive patients undergoing revision of total hip prosthesis for aseptic loosening or presumed prosthetic-joint infection (PJI). We analysed auxotrophy of cultured SCVs, their antimicrobial susceptibility profiles and their biofilm-forming capacity. Eight SCV strains were cultivated from six (19 %) patients. All SCVs were coagulase-negative staphylococci (CNS) with Staphylococcus epidermidis as the predominant species; there was also one Staphylococcus warneri SCV. The SCVs were auxotrophic for haemin, with one strain additionally auxotrophic for menadione. We noted the presence of two phenotypically (differences concerning antimicrobial susceptibility) and genetically distinct SCV strains in one patient, as well as the growth of two genetically related SCVs that differed in terms of their morphology and the type of auxotrophy in another. Seven out of eight SCVs were resistant to meticillin and gentamicin. In addition, antibiotic sensitivity testing revealed three multidrug-resistant SCV–normal-morphology isolate pairs. One S. epidermidis SCV harboured icaADBC genes and was found to be a proficient biofilm producer. This paper highlights the involvement of CNS SCVs in the aetiology of PJIs, including what is believed to be the first report of a S. warneri SCV. These subpopulations must be actively sought in the routine diagnosis of implant-associated infections. Moreover, in view of the phenotypic and genetic diversity of some SCV pairs, particular attention should be paid to the investigation of all types of observed colony morphologies, and isolates should be subjected to antimicrobial susceptibility testing.
Concurrent effects of age class and food distribution on immigration success and population dynamics in a small mammal
Authors: Rémy Alice , Le Galliard Jean‐François , Odden Morten , Andreassen Harry P.
Published: November 2013

During the settlement stage of dispersal, the outcome of conflicts between residents and immigrants should depend on the social organization of resident populations as well as on individual traits of immigrants, such as their age class, body mass and/or behaviour.

We have previously shown that spatial distribution of food influences the social organization of female bank voles (Myodes glareolus). Here, we aimed to determine the relative impact of food distribution and immigrant age class on the success and demographic consequences of female bank vole immigration. We manipulated the spatial distribution of food within populations having either clumped or dispersed food. After a pre‐experimental period, we released either adult immigrants or juvenile immigrants, for which we scored sociability and aggressiveness prior to introduction.

We found that immigrant females survived less well and moved more between populations than resident females, which suggest settlement costs. However, settled juvenile immigrants had a higher probability to reproduce than field‐born juveniles.

Food distribution had little effects on the settlement success of immigrant females. Survival and settlement probabilities of immigrants were influenced by adult female density in opposite ways for adult and juvenile immigrants, suggesting a strong adult–adult competition. Moreover, females of higher body mass at release had a lower probability to survive, and the breeding probability of settled immigrants increased with their aggressiveness and decreased with their sociability.

Prior to the introduction of immigrants, resident females were more aggregated in the clumped food treatment than in the dispersed food treatment, but immigration reversed this relationship. In addition, differences in growth trajectories were seen during the breeding season, with populations reaching higher densities when adult immigrants were introduced in a plot with dispersed food, or when juvenile immigrants were introduced in a plot with clumped food.

These results indicate the relative importance of intrinsic and extrinsic factors on immigration success and demographic consequences of dispersal and are of relevance to conservation actions, such as reinforcement of small populations.
GC Analysis of Black Gel Pen Ink Stored under Different Conditions
Authors: Li Biao , Xie Peng , Guo Ying‐min , Fei Qing
Published: November 2013

In many criminal and civil cases in China, the most commonly questioned documents are those written with gel pen ink. An important task for forensic document examiners is to identify whether two or more ink entries in one or more documents were written with the same ink type. The identification of the age of gel ink entries made poses an important and difficult problem for forensic document examiners. In this paper, the volatile components of gel ink were determined and the gel ink was classified by gas chromatography with a flame ionization detector. Calibration curves were created to express the relationship between the content of volatile gel ink components and the age of gel ink entries stored under natural and UV‐induced aging conditions. The correspondence between the natural and UV‐induced aging conditions was also established. The experimental results showed that GC was useful in the analysis of black gel ink and applicable for determining the relative age of gel ink entries under certain conditions.
Infrared Spectra of U.S. Automobile Original Finishes (Post – 1989). VIII: In Situ Identification of Bismuth Vanadate Using Extended Range FT‐IR Spectroscopy, Raman Spectroscopy, and X‐Ray Fluorescence Spectrometry
Authors: Suzuki Edward M.
Published: November 2013

Chrome Yellow (PbCrO4·xPbSO4) was a common pigment in U.S. automobile OEM finishes for more than three decades, but in the early 1990s its use was discontinued. One of its main replacements was Bismuth Vanadate (BiVO4·nBi2MoO6, n = 0–2), which was commercially introduced in 1985, as this inorganic pigment also produces a very bright hue and has excellent outdoor durability. This paper describes the in situ identification of Bismuth Vanadate in automotive finishes using FT‐IR and dispersive Raman spectroscopy and XRF spectrometry. Some differentiation of commercial formulations of this pigment is possible based on far‐infrared absorptions, Raman data, and elemental analysis. The spectral differences arise from the presence or absence of molybdenum, the use of two crystal polymorphs of BiVO4, and differences in pigment stabilizers. Bismuth Vanadate is usually not used alone, and it is typically found with Isoindoline Yellow, hydrous ferric oxide, rutile, Isoindolinone Yellow 3R, or various combinations of these.
Effect of Temperature on the Visualization by Digital Color Mapping of Latent Fingerprint Deposits on Metal
Authors: Peel Alicia , Bond John W.
Published: November 2013

Visualization of fingerprint deposits by digital color mapping of light reflected from the surface of heated brass, copper, aluminum, and tin has been investigated using Adobe® Photoshop®. Metals were heated to a range of temperatures (T) between 50°C and 500°C in 50°C intervals with enhancement being optimal when the metals are heated to 250°C, 350°C, 50°C, and 300°C, respectively, and the hue values adjusted to 247°, 245°, 5°, and 34°, respectively. Fingerprint visualization after color mapping was not degraded by subsequent washing of the metals and color mapping did not compromise the visibility of the fingerprint for all values of T. The optimum value of T for fingerprint visibility is significantly dependent of the standard reduction potential of the metal with Kendall's Tau (τ) = 0.953 (p < 0.001). For brass, this correlation is obtained when considering the standard reduction potential of zinc rather than copper.
Overview of: “Valuing Developmental Crime Prevention”
Authors: Manning Matthew , Smith Christine , Homel Ross
Published: November 2013

Research Summary

Developmental crime prevention programs produce positive returns on investment. Previous studies of such returns have not adequately quantified and weighted impacts across multiple domains of quality of life (e.g., social‐emotional development and family well‐being) or have provided a protocol for deciding between programs that recognizes these multiple domains (i.e., propose a method for the ranking of program alternatives). We adapted a multiple‐criteria decision‐making (MCDM) technique to address these deficiencies. Incorporating subjective decisions (a survey of those individuals who directly affect policy decisions) and objective evidence (the effect sizes from a meta‐analysis of longitudinal intervention outcomes) allowed us to construct a common metric for making structured choices between diverse developmental crime prevention program options. Our results show that a structured preschool program that incorporates family intervention and support was the most preferred option to reduce youth crime.

Policy Implications

The adapted MCDM technique employed in this study can be used to evaluate many crime prevention policy options that have effects that are spread across multiple domains and for which objective evidence from past research can usefully be combined with stakeholder judgments to recommend a preferred option.
Multi‐element Fingerprinting as a Tool in Origin Authentication of Four East China Marine Species
Authors: Guo Lipan , Gong Like , Yu Yanlei , Zhang Hong
Published: November 2013

The contents of 25 elements in 4 types of commercial marine species from the East China Sea were determined by inductively coupled plasma mass spectrometry and atomic absorption spectrometry. The elemental composition was used to differentiate marine species according to geographical origin by multivariate statistical analysis. The results showed that principal component analysis could distinguish samples from different areas and reveal the elements which played the most important role in origin diversity. The established models by partial least squares discriminant analysis (PLS‐DA) and by probabilistic neural network (PNN) can both precisely predict the origin of the marine species. Further study indicated that PLS‐DA and PNN were efficacious in regional discrimination. The models from these 2 statistical methods, with an accuracy of 97.92% and 100%, respectively, could both distinguish samples from different areas without the need for species differentiation.
Xanthine Oxidase Inhibitory Activity and Hypouricemic Effect of Aspalathin from Unfermented Rooibos
Authors: Kondo Makoto , Hirano Yoshiaki , Nishio Masahiro , Furuya Yutaka , Nakamura Hiromichi , Watanabe Tsuyoshi
Published: November 2013

Rooibos is rich in flavonoids such as aspalathin, which is a unique C‐glycosyl dihydrochalcone, that is used as a traditional herbal tea. This study was designed to evaluate the in vitro xanthine oxidase (XOD) inhibitory activity of the aspalathin‐rich fraction (ARF) and purified aspalathin from rooibos. The hypouricemic effects of the ARF and aspalathin on hyperuricemic mice were also assessed. The ARF was prepared from aqueous extract of unfermented rooibos leaves and stems, and it was collected by column chromatography; the aspalathin content in this fraction was 21.4%. The ARF and aspalathin inhibited XOD in a dose‐dependent manner. The concentrations of the ARF and aspalathin required to inhibit XOD at 50% (IC50) were 20.4 μg/mL (4.4 μg/mL aspalathin equivalents) and 4.5 μg/mL, respectively. Lineweaver–Burk plot analysis indicated that aspalathin was a competitive inhibitor of XOD, and the inhibition constant (Ki) was 3.1 μM. In hyperuricemic mice induced by inosine‐5’‐monophosphate, treatment with the ARF and aspalathin significantly suppressed the increased plasma uric acid level in a dose‐dependent manner. The suppressed plasma uric acid level in mice could be attributed to the XOD inhibitory activity of the ARF and aspalathin. Further study is required to determine the effect of aspalathin or its metabolites on XOD activity in vivo.
Group music therapy for severe mental illness: a randomized embedded‐experimental mixed methods study
Authors: Grocke D. , Bloch S. , Castle D. , Thompson G. , Newton R. , Stewart S. , Gold C.
Published: November 2013

Objective

Music therapy is an innovative approach to support people with severe mental illness (SMI). The aim of the study was to determine whether group music therapy (GMT) positively impacted on quality of life (QoL), social enrichment, self‐esteem, spirituality and psychiatric symptoms of participants with SMI and how they experienced the intervention.

Method

The primary outcome was QoL; secondary measures assessed social enrichment, self‐esteem, spirituality and psychiatric symptoms. The 13‐week intervention comprised singing familiar songs and composing original songs recorded in a professional studio. Qualitative data were generated from focus group interviews and song lyric analysis.

Results

Ninety‐nine adults (57 female) were recruited, with an initial cohort (n = 75) randomized to either: weekly GMT followed by standard care (SC) or SC followed by GMT. Crossover occurred after 13 weeks. Measures were conducted at baseline, 13, 26 and 39 weeks. A second cohort (n = 24) could not be randomized and were assigned to GMT followed by SC. Intention‐to‐treat analysis showed a significant difference between GMT and SC on QoL and spirituality. This was robust to different assumptions about missing data (listwise deletion, last observation carried forward or multiple imputation). Per‐protocol analysis suggested greater benefit for those receiving more sessions. Focus group interview and song lyric analyses suggested that GMT was enjoyable; self‐esteem was enhanced; participants appreciated therapists and peers; and although challenges were experienced, the programme was recommended to others.

Conclusion

Group music therapy may enhance QoL and spirituality of persons with SMI.
Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units
Authors: Vásquez‐Carrillo C. , Friesen V. , Hall L. , Peery M. Z.
Published: November 2013

Conserving genetic variation is critical for maintaining the evolutionary potential and viability of a species. Genetic studies seeking to delineate conservation units, however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major histocompatibility complex (MHC) class II B genes was characterized in four populations of marbled murrelets Brachyramphus marmoratus, a threatened species in which little neutral genetic population structure has been detected. High diversity, as well as evidence of balancing selection, was detected in exon 2 of these genes. Genetic population structure based on MHC markers was uncorrelated to genetic structure estimated with neutral markers, suggesting that selection played a more important role in shaping population structure at these markers than genetic drift. A high proportion of alleles and inferred peptides were unique to a single population, with the Aleutian Islands and southeast Alaska having the highest richness of both. Murrelets sampled in Oregon had low MHC exon 2 allele and inferred peptide richness, and were significantly differentiated from individuals sampled in the Aleutian Islands based on the frequency of exon 2 alleles. In addition, murrelets sampled in Oregon were differentiated from murrelets in both the Aleutian Islands and southeast Alaska based on inferred peptide frequencies, suggesting that the Oregon population could be prioritized for conservation measures. More broadly, combining information from neutral and adaptive genetic markers can improve the delineation of conservation units in threatened species.
Construction of confidence regions in the ROC space after the estimation of the optimal Youden index‐based cut‐off point
Authors: Bantis Leonidas E. , Nakas Christos T. , Reiser Benjamin
Published: November 2013

After establishing the utility of a continuous diagnostic marker investigators will typically address the question of determining a cut‐off point which will be used for diagnostic purposes in clinical decision making. The most commonly used optimality criterion for cut‐off point selection in the context of ROC curve analysis is the maximum of the Youden index. The pair of sensitivity and specificity proportions that correspond to the Youden index‐based cut‐off point characterize the performance of the diagnostic marker. Confidence intervals for sensitivity and specificity are routinely estimated based on the assumption that sensitivity and specificity are independent binomial proportions as they arise from the independent populations of diseased and healthy subjects, respectively. The Youden index‐based cut‐off point is estimated from the data and as such the resulting sensitivity and specificity proportions are in fact correlated. This correlation needs to be taken into account in order to calculate confidence intervals that result in the anticipated coverage. In this article we study parametric and non‐parametric approaches for the construction of confidence intervals for the pair of sensitivity and specificity proportions that correspond to the Youden index‐based optimal cut‐off point. These approaches result in the anticipated coverage under different scenarios for the distributions of the healthy and diseased subjects. We find that a parametric approach based on a Box–Cox transformation to normality often works well. For biomarkers following more complex distributions a non‐parametric procedure using logspline density estimation can be used.
If there is an evolutionary selection pressure for the high frequency ofMBL2polymorphisms, what is it?
Authors: Eisen D P , Osthoff M
Published: November 2013

Either immune selection or stochastic processes may have influenced the frequency of highly polymorphic genes such as mannose-binding lectin 2 (MBL2). This pattern recognition receptor of the innate immune system recognizes and binds to pathogenic microorganisms and apoptotic cells leading to lectin pathway complement killing or clearance. In almost all of a large number of studies in different ethnic groups worldwide there is 20–25% carriage of low MBL2 haplotypes, with 8–10% of each population having no MBL detectable in the blood. The source of this high variability of MBL2 remains cryptic. It arises from six main snps in the prompter and exon regions of the gene that assort into seven common haplotypes under linkage disequilibrium. While global studies of MBL2 show that it is not under immune selection pressure, these results are not the same when the same population genetic tools are used on large national studies. Other analyses point to the silenced MBL1 pseudogene and development of promoter polymorphisms in humans as evidence of selection pressure favouring low-producing haplotypes. While these analyses cannot be reconciled readily, there are two processes by which MBL heterozygosity could have been advantageous in an evolutionary sense; protection against adverse effects of various infectious diseases and lethal manifestations of atherosclerosis – a disease that now seems to have a more ancient history than assumed previously. Ultimately, consideration of the context for possible future therapeutic manipulation of MBL means that this can proceed independently of resolution of the evolutionary forces that have shaped MBL2 polymorphism.