bluuebunny/crossref_metadata_2025 huggingface dataset:
Size-controlled synthesis and transport properties of Sb2Te3 nanoplates
Authors: Zhou Nan , Chen Gang , Zhang Xiao-Song , Xu Ying-Cao , Xu Bao-Rong , Li Ming-Qiang
Published: November 2013

Antimony telluride (Sb2Te3) based compounds are very promising materials for thermoelectric applications at room-temperature.
Enantioselective oxidation of secondary alcohols by Candida parapsilosis ATCC 7330
Authors: Sivakumari Thakkellapati , Preetha Radhakrishnan , Chadha Anju
Published: November 2013

Optically pure (R) allylic alcohols and (R) 4-phenylbutan-2-ols were prepared via oxidative kinetic resolution using whole cells of Candida papapsilosis ATCC 7330.
Design of new electrode materials for Li-ion and Na-ion batteries from the bloedite mineral Na2Mg(SO4)2·4H2O
Authors: Reynaud Marine , Rousse Gwenaëlle , Abakumov Artem M. , Sougrati Moulay T. , Van Tendeloo Gustaaf , Chotard Jean-Noël , Tarascon Jean-Marie
Published: November 2013

Starting from the bloedite mineral, we prepared two new electrode materials, Na2Fe(SO4)2·4H2O and Na2Fe(SO4)2, which present high redox potentials of 3.6 V vs. lithium and 3.3–3.4 V vs. sodium.
Modulating the atomic and electronic structures through alloying and heterostructure of single-layer MoS2
Authors: Wei Xiao-Lin , Zhang Hui , Guo Gen-Cai , Li Xi-Bo , Lau Woon-Ming , Liu Li-Min
Published: November 2013

Charge density of the VBM (green) and CBM (blue) for armchair MoS2–WS2 heterostructures, indicating the spontaneous separation of photo-generated electrons and holes, which could strongly enhance the photocatalytic activity due to suppression of the electron–hole recombination.
Rapid detection of oral cancer using Ag–TiO2 nanostructured surface-enhanced Raman spectroscopic substrates
Authors: Girish Chundayil Madathil , Iyer Subramania , Thankappan Krishnakumar , Rani V. V. Divya , Gowd G. Siddaramana , Menon Deepthy , Nair Shantikumar , Koyakutty Manzoor
Published: November 2013

Developed Ag–TiO2 based large area SERS substrate that enables spectroscopic detection and classification of oral squamous cell carcinoma with a specificity and sensitivity of 95.83% and 100%, respectively.
Tuning optical properties of phenanthroline derivatives through varying excitation wavelength and pH values
Authors: Gu Pei-Yang , Gao Junkuo , Zhang Qichun , Liu Gaoyan , Zhou Feng , Xu Qing-Feng , Lu Jian-Mei
Published: November 2013

Two phenanthroline derivatives have been prepared to possess two cores and their tuneable emission behaviors have been investigated.
Autophagy: a two-edged sword in diabetes mellitus
Authors: Yamamoto Suguru , Kazama Junichiro J. , Fukagawa Masafumi
Published: November 2013

A fragility fracture is a serious complication in patients with diabetes mellitus as a result of hyperglycaemia, insulin resistance and the production of AGEs (advanced glycation end-products). In their paper published in the Biochemical Journal, Bartolomé et al. identified a role for autophagy in the differentiation, function and survival of osteoblastic cells in a high-glucose environment, and they also demonstrated that osteoblastic cell survival was limited by chemical and genetic inhibition of autophagy. These novel findings show the possibility of investigating a therapeutic strategy of maintaining autophagy in osteoblasts to lead to the prevention of diabetes-related osteopaenia. Autophagy is one of the common functions for maintaining cellular health, and the regulation of autophagy that is perturbed by diabetes mellitus may induce improvement of cellular functions not only for diabetes-related osteopaenia, but also for other systemic complications. However, systemic activation of autophagy may not always induce beneficial effects for non-targeted healthy cells, and autophagy should be controlled at a proper level at each disease stage in each target organ.
Ductal carcinomain situof the breast: morphological and molecular features implicated in progression
Authors: Carraro Dirce M. , Elias Eliana V. , Andrade Victor P.
Published: November 2013

The spread of mammographic screening programmes around the world, including in developing countries, has substantially contributed to the diagnosis of small non-palpable lesions, which has increased the detection rate of DCIS (ductal carcinoma in situ). DCIS is heterogeneous in several ways, such as its clinical presentation, morphology and genomic profile. Excellent outcomes have been reported; however, many questions remain unanswered. For example, which patients groups are overtreated and could instead benefit from minimal intervention and which patient groups require a more traditional multidisciplinary approach. The development of a comprehensive integrated analysis that includes the radiological, morphological and genetic aspects of DCIS is necessary to answer these questions. This review focuses on discussing the significant findings about the morphological and molecular features of DCIS and its progression that have helped to uncover the biological and genetic heterogeneity of this disease. The knowledge gained in recent years might allow the development of tailored clinical management for women with DCIS in the future.
Beginning to Talk Like an Adult: Increases in Speech-Like Utterances in Young Cochlear Implant Recipients and Typically Developing Children
Authors: Ertmer David J. , Jung Jongmin , Kloiber Diana True
Published: November 2013

Purpose

Speech-like utterances containing rapidly combined consonants and vowels eventually dominate the prelinguistic and early word productions of typically developing (TD) toddlers. It seems reasonable to expect a similar phenomenon in young recipients of cochlear implants (CIs). The authors of this study sought to determine the number of months of robust hearing experience needed to achieve a majority of speech-like utterances in both of these groups.

Method

Speech samples were recorded from CI recipients at 3-month intervals during the first 2 years of CI experience, and from TD children at time points between 6 and 24 months of age. Speech-like utterances were operationally defined as those belonging to the basic canonical syllables (BCS) or advanced forms (AF) levels of the Consolidated Stark Assessment of Early Vocal Development—Revised (Ertmer, Young, & Nathani, 2007).

Results

On average, the CI group achieved a majority of speech-like utterances after 12 months of robust hearing experience and the TD group after 18 months. The CI group produced greater percentages of speech-like utterances at each interval until 24 months, when both groups approximated 80%.

Conclusion

Auditory deprivation did not limit progress in vocal development as young CI recipients showed more-rapid-than-typical speech development during the first 2 years of device use. Implications for the infraphonological model of speech development are considered.
Multiple Myeloma-Associated Amyloidoma of the Sacrum: Case Report and Review of the Literature
Authors: Klenke F. M. , Wirtz C. , Banz Y. , Keel M. J. B. , Klass N. D. , Novak U. , Benneker L. M.
Published: November 2013

Study Design

Case report.

Objectives

With only two previously reported cases, localized amyloidosis of the sacrum is extremely rare. Here we report a 64-year-old woman with a large osteolytic lesion accompanied by weakness and paresthesia of the right leg and difficulties in bladder control.

Methods

Fine needle biopsy and standard staging procedures revealed a primary solitary amyloidoma that was treated with intralesional resection, lumbopelvic stabilization, and consolidation radiotherapy.

Results

Clinical follow-up revealed the diagnosis of multiple myeloma 9 months after initial treatment. At 12 months, no local recurrence has occurred, the neurologic symptoms have resolved, and the systemic disease is in remission.

Conclusions

Intralesional resection with adjuvant radiotherapy of the amyloidoma achieved good local tumor control with limited morbidity.
Nonlinear realizations and the orbit method
Authors: Gonera Joanna
Published: November 2013

Given a symmetry group one can construct the invariant dynamics using the technique of nonlinear realizations or the orbit method. The relationship between these methods is discussed. Few examples are presented.
High spin polarization at room temperature in Ge-substituted Fe3O4 epitaxial thin film grown under high oxygen pressure
Authors: Seki Munetoshi , Takahashi Masanao , Ohshima Toshiyuki , Yamahara Hiroyasu , Tabata Hitoshi
Published: November 2013

Epitaxial thin films of room-temperature ferrimagnetic (Fe,Ge)3O4 were fabricated using pulsed laser deposition. Films with a single-phase spinel structure were grown under high oxygen pressures (0.01–0.6 Pa). The carrier transport across (Fe,Ge)3O4/Nb:SrTiO3 interface was studied to estimate the spin polarization of (Fe, Ge)3O4. Current–voltage curves of Fe2.8Ge0.2O4/Nb:SrTiO3 junction showed rectifying behavior even at 300 K whereas Fe3O4/Nb:SrTiO3 junction showed ohmic behavior. Calculations based on a model for a Schottky contact with a ferromagnetic component yielded a spin polarization of 0.50 at 300 K for Fe2.8Ge0.2O4, indicating its potential as a promising spin injector.
Magnetic field induced dynamical chaos
Authors: Ray Somrita , Baura Alendu , Bag Bidhan Chandra
Published: November 2013

In this article, we have studied the dynamics of a particle having charge in the presence of a magnetic field. The motion of the particle is confined in the x–y plane under a two dimensional nonlinear potential. We have shown that constant magnetic field induced dynamical chaos is possible even for a force which is derived from a simple potential. For a given strength of the magnetic field, initial position, and velocity of the particle, the dynamics may be regular, but it may become chaotic when the field is time dependent. Chaotic dynamics is very often if the field is time dependent. Origin of chaos has been explored using the Hamiltonian function of the dynamics in terms of action and angle variables. Applicability of the present study has been discussed with a few examples.
Visual investigation on the heat dissipation process of a heat sink by using digital holographic interferometry
Authors: Wu Bingjing , Zhao Jianlin , Wang Jun , Di Jianglei , Chen Xin , Liu Junjiang
Published: November 2013

We present a method for visually and quantitatively investigating the heat dissipation process of plate-fin heat sinks by using digital holographic interferometry. A series of phase change maps reflecting the temperature distribution and variation trend of the air field surrounding heat sink during the heat dissipation process are numerically reconstructed based on double-exposure holographic interferometry. According to the phase unwrapping algorithm and the derived relationship between temperature and phase change of the detection beam, the full-field temperature distributions are quantitatively obtained with a reasonably high measurement accuracy. And then the impact of heat sink's channel width on the heat dissipation performance in the case of natural convection is analyzed. In addition, a comparison between simulation and experiment results is given to verify the reliability of this method. The experiment results certify the feasibility and validity of the presented method in full-field, dynamical, and quantitative measurement of the air field temperature distribution, which provides a basis for analyzing the heat dissipation performance of plate-fin heat sinks.
Defect formation in Cu(In,Ga)Se2 thin films due to the presence of potassium during growth by low temperature co-evaporation process
Authors: Pianezzi F. , Reinhard P. , Chirilă A. , Nishiwaki S. , Bissig B. , Buecheler S. , Tiwari A. N.
Published: November 2013

Doping the Cu(In,Ga)Se2 (CIGS) absorber layer with alkaline metals is necessary to process high efficiency solar cells. When growth of CIGS solar cells is performed on soda-lime glass (SLG), the alkaline elements naturally diffuse from the substrate into the absorber layer. On the other hand, when CIGS is grown on alkaline free substrates, the alkaline metals have to be added from another source. In the past, Na was believed to be the most important dopant of the alkaline elements, even though K was also observed to diffuse into CIGS from the SLG. Recently, the beneficial effect of a post deposition treatment with KF was pointed out and enabled the production of a 20.4% CIGS solar cell grown at low substrate temperature (<500 °C). However, possible negative effects of the presence or addition of the alkaline impurities during the low temperature growth process were observed for Na, but were not investigated for K so far. In this study, we investigate in detail the role of K on the defect formation in CIGS layers deposited at low temperature on alkaline free polyimide with intentional addition of K during selected time intervals of the CIGS layer growth. By means of admittance spectroscopy and deep level transient spectroscopy, we identify a deep minority carrier trap at around 280 meV below the conduction band EC in CIGS layers grown with K. Its influence on recombination and minority carrier lifetime in the absorber layer is investigated with external quantum efficiency measurements and time-resolved photoluminescence. Furthermore, to support the experimental findings device simulations were performed using the software SCAPS.
Influence of hydrogen effusion from hydrogenated silicon nitride layers on the regeneration of boron-oxygen related defects in crystalline silicon
Authors: Wilking S. , Ebert S. , Herguth A. , Hahn G.
Published: November 2013

The degradation effect boron doped and oxygen-rich crystalline silicon materials suffer from under illumination can be neutralized in hydrogenated silicon by the application of a regeneration process consisting of a combination of slightly elevated temperature and carrier injection. In this paper, the influence of variations in short high temperature steps on the kinetics of the regeneration process is investigated. It is found that hotter and longer firing steps allowing an effective hydrogenation from a hydrogen-rich silicon nitride passivation layer result in an acceleration of the regeneration process. Additionally, a fast cool down from high temperature to around 550 °C seems to be crucial for a fast regeneration process. It is suggested that high cooling rates suppress hydrogen effusion from the silicon bulk in a temperature range where the hydrogenated passivation layer cannot release hydrogen in considerable amounts. Thus, the hydrogen content of the silicon bulk after the complete high temperature step can be increased resulting in a faster regeneration process. Hence, the data presented here back up the theory that the regeneration process might be a hydrogen passivation of boron-oxygen related defects.
Confinement improvement by fluctuating input power
Authors: Douglas Sarah , Mohamed Mabruka , Kim Eun-jin
Published: November 2013

An interesting effect of the fluctuating input power on plasma confinement is reported. Specifically, the addition of the sinusoidal perturbation, Asin(wt), to constant power q0 is shown to promote the confinement, leading to the L-H transition at a lower value of q0, as compared to the case of constant q0 without the sinusoidal perturbation. In general, higher amplitude (A) and lower frequency (w) are found to be more favorable for the L-H transition while an interesting linear relation between A and w leading to the L-H transition is established for different values of q0.
Relationship between frailty and discharge outcomes in subacute care
Authors: Haley Melanie N. , Wells Yvonne D. , Holland Anne E.
Published: November 2013

Aims
To determine whether level of frailty can predict length of stay, discharge destination, level of participation in physiotherapy, and degree of physical improvement with physiotherapy in older, subacute hospital patients.

Method
The Edmonton Frail Scale (EFS) was administered to 75 older people in a subacute hospital setting. Relationships between EFS score and a range of other measures, including participation in physiotherapy, Elderly Mobility Scale, discharge destination and length of stay, were examined.

Results
Level of frailty did not predict length of stay (rho = –0.13, P = 0.24), discharge destination (t = –1.32, P = 0.19), raw change on the Elderly Mobility Scale (rho = 0.06, P = 0.61) or rate of change on the Elderly Mobility Scale (r = –0.001, P = 0.98). In addition, participants with a high level of frailty were more likely to achieve a satisfactory level of participation in physiotherapy sessions than those with low frailty (OR 1.43, P = 0.02).

Conclusion
Level of frailty measured with the EFS was not a useful predictor of rehabilitation and discharge outcomes for older people in subacute care. These results do not support the routine use of the EFS to measure frailty in subacute care.

What is known about this topic?
In a community-dwelling population, level of frailty has been found to predict poor outcomes from surgery, falls, fractures, disability, need for residential care and mortality. However, little is known about the impacts of frailty in a subacute setting, nor how frailty could best be measured in this setting.

What does this paper add?
The use of the EFS as a predictive tool was not supported by the results of this exploratory study.

What are the implications for practitioners?
Alternative frailty measures may be more suitable than the EFS for patients in a subacute setting.
Structure, Stability, and Cycloaddition Reactions of Nitrile Selenides
Authors: Pasinszki Tibor , Krebsz Melinda , Hajgató Balázs
Published: November 2013

The equilibrium structure, unimolecular reactions, and bimolecular reactions of nitrile selenides (XCNSe, where X = H, F, Cl, Br, CN, CH3) have been investigated using CCSD(T), CCSD(T)//B3LYP, and MR-AQCC//UB3LYP quantum-chemical methods. Nitrile selenides are demonstrated to be stable under isolated conditions at ambient temperature, i.e. in the dilute gas phase or in an inert solid matrix, but unstable in the condensed phase or solutions owing to bimolecular reactions. FCNSe and CH3CNSe cycloaddition with ethynes, ethenes, and nitriles was studied using the MR-AQCC//UB3LYP method. Cycloaddition was predicted to be facile at room temperature with small dipolarophiles.
United Kingdom newsprint media reporting on sexual health and blood-borne viruses in 2010
Authors: Martin Susan , Hilton Shona , McDaid Lisa M.
Published: November 2013

Background Improving sexual health and blood-borne virus (BBV) outcomes continue to be of high priority within the United Kingdom (UK) and it is evident that the media can and do impact the public health agenda. This paper presents the first large-scale exploration of UK national newsprint media representations of sexual health and BBVs. Methods: Using keyword searches in electronic databases, 677 articles published during 2010 were identified from 12 national (UK-wide and Scottish) newspapers. Content analysis was used to identify manifest content and to examine the tone of articles. Results: Although there was a mixed picture overall in terms of tone, negatively toned articles, which focussed on failures or blame, were common, particularly within HIV/AIDS, hepatitis B and C, and other sexually transmissible infection coverage (41% were assessed as containing negative content; 46% had negative headlines). Differences were found by newspaper genre, with ‘serious’ newspaper articles appearing more positive and informative than ‘midmarket’ newspapers or ‘tabloids’. Across the sample, particular individuals, behaviours and risk groups were focussed on, not always accurately, and there was little mention of deprivation and inequalities (9%). A gender imbalance was evident, particularly within reproductive health articles (71% focussed on women; 23% on men), raising questions concerning gender stereotyping. Conclusions: There is a need to challenge the role that media messages have in the reinforcement of a negative culture around sexual health in the UK and for a strong collective advocacy voice to ensure that future media coverage is positively portrayed.
29. Anal cancer trends in Puerto Rico (PR) from 1985 to 2005: impact of HIV status
Authors: Ortiz Ana P. , Ortiz-Ortiz Karen J. , Traverso Maricarmen , Ríos Moraima , Colón-Lopez Vivian , Palefsky Joel
Published: November 2013

Background
PR is one of the US jurisdictions with the highest burden of HIV/AIDS. We describe the proportion of HIV+ anal cancer cases in PR and the impact of HIV status on anal cancer incidence trends, by sex and age. Methods: The PR Central Cancer Registry (PRCCR) and the PR AIDS Surveillance Program databases were linked using a probabilistic linkage algorithm with Link Plus v.2.0 software. The proportion of anal cancer cases with and without HIV in PR were calculated. Temporal trends (1985–2005) in the incidence rates (standardised US 2000 population) of anal cancer (overall and after exclusion of HIV+ cancer cases) were calculated through annual per cent changes (APC) and 95% confidence intervals (CIs), using a Joinpoint log-linear model. Results: From 1985 to 2005, 736 cases of anal cancer were diagnosed in PR; 26 cases were HIV+. While most anal cancer patients were female (70.8%), the proportion of HIV+ patients was higher in males (11.4%) than females (0.77%). In men, incidence increased significantly (APC = 3.23, P < 0.05) when HIV+ cases were considered; the increase was reduced (APC = 0.97) when these were excluded (P > 0.05). In females, incidence increased (APC = 2.01) when HIV+ cases were considered, whereas the increase was reduced (APC = 0.85) when these were excluded; these increases were non-significant (P > 0.05). Conclusions: Consistent with data from the US, the increasing anal cancer incidence rates in PR were strongly influenced by the HIV epidemic in males but were independent of HIV infection in females.
3. Outcome of excision of early invasive squamous carcinomas of the anal canal and perianus
Authors: Berry J. Michael , Jay Naomi , Hernandez Alexandra , Darragh Teresa M. , Palefsky Joel M.
Published: November 2013

Background
Combined modality therapy (CMT) is the standard of care for anal canal (AC) squamous cell carcinoma (SCCA); excision is reserved for small perianal (PA) cancers. Increasingly, asymptomatic, superficially invasive SCCAs (SISCCA) are identified during high-resolution anoscopy (HRA). For AC- and PA-SISCCA, the Lower Anogenital Squamous Terminology Project’s proposed definition is an excised tumour with clear margins, depth of invasion <3 mm, and horizontal extent <7 mm. We report our experience with surgical excision alone of early invasive SCCA (EISCCA), defined as AC- or PA-SISCCA and >SISCCA, but with clear margins. Methods: EISCCA were excised sparing the anal sphincter and anal high-grade squamous intraepithelial lesions (HSIL) were ablated. Those with margins positive for SCCA were referred for CMT. HRA was performed every 4 months; recurrent HSIL/EISCCA was ablated or excised. Patients were referred for CMT if cancer could not be excised without compromising the sphincter. Results: EISCCA was excised in 81 patients: 68 men and 13 women, 57 HIV-infected and 24 HIV-uninfected. Median age was 52 years (range: 33–79). Patients were followed for a median of 43 months (range: 2–230) following excision. Excision of EISCCA was successful in 73 (90%) patients. Eight (10%) required CMT (4 developed inguinal node recurrences, including 2 with systemic metastases). There was no statistically significant difference in outcome by location (AC v. PA EISCCA), HIV status or sex (P > 0.05). Conclusions: Excision of EISCCA, including AC tumours, produces an excellent outcome, sparing most patients CMT, including those with HIV infection.
4. High prevalence of anal HPV infection among HIV-positive male subjects in the absence of anal intercourse
Authors: Nelson Cavallari Eugenio , d'Ettorre Gabriella , Ceccarelli Giancarlo , Serafini Sara , Pierangeli Alessandra , Impagnatiello Alessio , Ascoli Bertoli Tommaso , Bianchi Luigi , Antonelli Guido , Vullo Vincenzo , Indinnimeo Marileda
Published: November 2013

Background
The risk of progression to cancer from HPV infection is increased in HIV-positive subjects. Anal HPV infection is a concern among men who have sex with men (MSM), especially in the setting of HIV infection. Methods: Cross-sectional study including 62 HIV-positive injection drug users (IDUs) without history of receptive anal intercourse and 110 HIV-positive MSM. All patients were receiving HAART with HIV-RNA <37 copies/mL. Patients answered a self-administered questionnaire investigating their sexual habits. Participants underwent anal brushing collecting samples for cytology examination (Bethesda 2001 criteria for cervical cytology) and high resolution anoscopy collecting samples for histological classification. HPV-DNA polymerase chain reaction (PCR) identification was performed. Results: Of the IDUs, 62.5% showed CD4 nadir <200 cell/mmc compared with 12% of MSM (P < 0.05), the actual CD4+ T-cells count did not show a statistical difference. HPV-DNA PCR tested positive in 52% of IDUs and 69% of MSM (P < 0.05). Presence of high-risk genotypes did not show significant difference between the groups (38% of IDUs and 31% of MSM). LSIL prevalence was higher among MSM than IDUs (38% v. 23%), HSIL was higher among IDUs than MSM (26% v. 21%). The prevalence of anal cancer was similar in the two populations (3% in each group). All patients, except for men presenting with anal cancer, were completely asymptomatic. Conclusions: Anal HPV infection and anal SIL may be acquired in the absence of anal intercourse in HIV-infected men. The prevalence of HSIL is high among HIV-positive IDUs. All HIV-infected men, regardless of history of anal intercourse, should be considered for anal cytology screening.
Astrocytes potentiate GABAergic transmission in the thalamic reticular nucleus via endozepine signaling
Authors: Christian Catherine A. , Huguenard John R.
Published: November 2013

Significance

Benzodiazepines are commonly prescribed to treat neuropsychiatric disorders, and produce clinical effects on sleep, anxiety, and seizures by augmenting synaptic inhibitory currents through GABA
A
receptors. Our previous work has indicated that peptides of the diazepam-binding inhibitor family act as endogenous benzodiazepines (endozepines) in the thalamic reticular nucleus (nRT), where they mediate antiepileptic and other effects. Here we report that astrocytes are required for the actions of endozepines on GABAergic transmission in the nRT. Thus, astrocytes in nRT are specialized to contribute to a localized increase in efficacy of synaptic inhibition relevant to endogenous seizure control.
Fractional Hardy-type inequalities in domains with uniformly fat complement
Authors: Edmunds David , Hurri-Syrjänen Ritva , Vähäkangas Antti
Published: November 2013

We establish fractional Hardy-type inequalities in a bounded domain with uniformly fat complement. In particular, our results apply in bounded

C

∞

C^{\infty }

domains and Lipschitz domains.
On the simultaneous association analysis of large genomic regions: a massive multi-locus association test
Authors: Qiao Dandi , Cho Michael H. , Fier Heide , Bakke Per S. , Gulsvik Amund , Silverman Edwin K. , Lange Christoph
Published: November 2013

Motivation: For samples of unrelated individuals, we propose a general analysis framework in which hundred thousands of genetic loci can be tested simultaneously for association with complex phenotypes. The approach is built on spatial-clustering methodology, assuming that genetic loci that are associated with the target phenotype cluster in certain genomic regions. In contrast to standard methodology for multilocus analysis, which has focused on the dimension reduction of the data, our multilocus association-clustering test profits from the availability of large numbers of genetic loci by detecting clusters of loci that are associated with the phenotype.

Results: The approach is computationally fast and powerful, enabling the simultaneous association testing of large genomic regions. Even the entire genome or certain chromosomes can be tested simultaneously. Using simulation studies, the properties of the approach are evaluated. In an application to a genome-wide association study for chronic obstructive pulmonary disease, we illustrate the practical relevance of the proposed method by simultaneously testing all genotyped loci of the genome-wide association study and by testing each chromosome individually. Our findings suggest that statistical methodology that incorporates spatial-clustering information will be especially useful in whole-genome sequencing studies in which millions or billions of base pairs are recorded and grouped by genomic regions or genes, and are tested jointly for association.

Availability and implementation: Implementation of the approach is available upon request.

Contact: daq412@mail.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
myChEMBL: a virtual machine implementation of open data and cheminformatics tools
Authors: Ochoa Rodrigo , Davies Mark , Papadatos George , Atkinson Francis , Overington John P.
Published: November 2013

Summary: myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications.

Availability and implementation: The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

Contact:  jpo@ebi.ac.uk
A novel splicing outcome reveals more than 2000 new mammalian protein isoforms
Authors: Wilson Laurence O. W. , Spriggs Andrew , Taylor Jennifer M. , Fahrer Aude M.
Published: November 2013

Motivation: We have recently characterized an instance of alternative splicing that differs from the canonical gene transcript by deletion of a length of sequence not divisible by three, but where translation can be rescued by an alternative start codon. This results in a predicted protein in which the amino terminus differs markedly in sequence from the known protein product(s), as it is translated from an alternative reading frame. Automated pipelines have annotated thousands of splice variants but have overlooked these protein isoforms, leading to them being underrepresented in current databases.

Results: Here we describe 1849 human and 733 mouse transcripts that can be transcribed from an alternate ATG. Of these, >80% have not been annotated previously. Those conserved between human and mouse genomes (and hence under likely evolutionary selection) are identified. We provide mass spectroscopy evidence for translation of selected transcripts. Of the described splice variants, only one has previously been studied in detail and converted the encoded protein from an activator of cell-function to a suppressor, demonstrating that these splice variants can result in profound functional change. We investigate the potential functional effects of this splicing using a variety of bioinformatic tools. The 2582 variants we describe are involved in a wide variety of biological processes, and therefore open many new avenues of research.

Contact:  aude.fahrer@anu.edu.au

Supplementary Inforation:  Supplementary data are available at Bioinformatics online.
Identification of transcription factors for drug-associated gene modules and biomedical implications
Authors: Xiong Min , Li Bin , Zhu Qiang , Wang Yun-Xing , Zhang Hong-Yu
Published: November 2013

Motivation: One of the major findings in systems biomedicine is that both pathogenesis of diseases and drug mode of action have a module basis. However, the transcription factors (TFs) regulating the modules remain largely unknown.

Results: In this study, by using biclustering approach FABIA (factor analysis for bicluster acquisition), we generate 49 modules for gene expression profiles on 1309 agent treatments. These modules are of biological relevance in terms of functional enrichment, drug–drug interactions and 3D proximity in chromatins. By using the information of drug targets (some of which are TFs) and biological regulation, the links between 28 modules and 12 specific TFs, such as estrogen receptors (ERs), nuclear factor-like 2 and peroxisome proliferator-activated receptor gamma, can be established. Some of the links are supported by 3D transcriptional regulation data [derived from ChIA-PET (chromatin interaction analysis using paired-end tags) experiments] and drug mode of action as well. The relationships between modules and TFs provide new clues to interpreting biological regulation mechanisms, in particular, the lipid metabolism regulation by ERα. In addition, the links between natural products (e.g. polyphenols) and their associated modules and TFs are helpful to elucidate their polypharmacological effects in terms of activating specific TFs, such as ERs, nuclear factor-like 2 and peroxisome proliferator-activated receptor gamma.

Contact:  zhy630@mail.hzau.edu.cn

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The production of strong, broad He ii emission after the tidal disruption of a main-sequence star by a supermassive black hole
Authors: Gaskell C. Martin , Rojas Lobos P. Andrea
Published: November 2013

The tidal disruption event (TDE) PS1-10jh lacked strong Balmer lines but showed strong, broad He ii emission both before maximum light and for at least eight months thereafter. Gezari et al. interpreted this as evidence for the disruption of a rare hydrogen-deficient star. However, Guillochon et al. have argued instead that the disrupted star was a normal main-sequence star and that the strength of the He ii emission compared with the Balmer lines is a result the emission being similar to the broad-line region (BLR) of an active galactic nucleus (AGN), but lacking the outer, lower ionization BLR gas. We show that the profile of He ii λ4686 in PS1-10jh is similar to the blueshifted profiles of high-ionization lines in AGNs. We find an He ii λ4686/Hα ratio for PS1-10jh of ∼3.7. We show that both the high-velocity gas of the inner BLR of normal AGNs and the spectra of Type II-P supernovae right after shock break out also produce very high He ii λ4686/Hα ratios. A high He ii λ4686/Hα ratio can thus be produced with a solar H/He abundance ratio. We demonstrate from photoionization modelling that the estimated He ii λ4686/Hα ratio can be produced with a BLR truncated before the He++ Strömgren length if the density is ∼1011 cm−3. The similarity of the He ii λ4686 emission in PS1-10jh to the emission from the inner BLRs of AGNs supports the idea that the emission after a TDE event is similar to that of normal AGNs.
Adaptation of theHaloarcula hispanicaCRISPR-Cas system to a purified virus strictly requires a priming process
Authors: Li Ming , Wang Rui , Zhao Dahe , Xiang Hua
Published: November 2013

The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system mediates adaptive immunity against foreign nucleic acids in prokaryotes. However, efficient adaptation of a native CRISPR to purified viruses has only been observed for the type II-A system from a Streptococcus thermophilus industry strain, and rarely reported for laboratory strains. Here, we provide a second native system showing efficient adaptation. Infected by a newly isolated virus HHPV-2, Haloarcula hispanica type I-B CRISPR system acquired spacers discriminatively from viral sequences. Unexpectedly, in addition to Cas1, Cas2 and Cas4, this process also requires Cas3 and at least partial Cascade proteins, which are involved in interference and/or CRISPR RNA maturation. Intriguingly, a preexisting spacer partially matching a viral sequence is also required, and spacer acquisition from upstream and downstream sequences of its target sequence (i.e. priming protospacer) shows different strand bias. These evidences strongly indicate that adaptation in this system strictly requires a priming process. This requirement, if validated also true for other CRISPR systems as implied by our bioinformatic analysis, may help to explain failures to observe efficient adaptation to purified viruses in many laboratory strains, and the discrimination mechanism at the adaptation level that has confused scientists for years.
Comparative Analysis of Two Emerging Rice Seed Bacterial Pathogens
Authors: Fory P. A. , Triplett L. , Ballen C. , Abello J. F. , Duitama J. , Aricapa M. G. , Prado G. A. , Correa F. , Hamilton J. , Leach J. E. , Tohme J. , Mosquera G. M.
Published: November 2013

Seed sterility and grain discoloration limit rice production in Colombia and several Central American countries. In samples of discolored rice seed grown in Colombian fields, the species Burkholderia glumae and B. gladioli were isolated, and field isolates were compared phenotypically. An artificial inoculation assay was used to determine that, although both bacterial species cause symptoms on rice grains, B. glumae is a more aggressive pathogen, causing yield reduction and higher levels of grain sterility. To identify putative virulence genes differing between B. glumae and B. gladioli, four previously sequenced genomes of Asian and U.S. strains of the two pathogens were compared with each other and with two draft genomes of Colombian B. glumae and B. gladioli isolates generated for this study. Whereas previously characterized Burkholderia virulence factors are highly conserved between the two species, B. glumae and B. gladioli strains are predicted to encode distinct groups of genes encoding type VI secretion systems, transcriptional regulators, and membrane-sensing proteins. This study shows that both B. glumae and B. gladioli can threaten grain quality, although only one species affects yield. Furthermore, genotypic differences between the two strains are identified that could contribute to disease phenotypic differences.
History of Oilseed Rape Cropping and Geographic Origin Affect the Genetic Structure ofPlasmodiophora brassicaePopulations
Authors: Strehlow Becke , de Mol Friederike , Struck Christine
Published: November 2013

The soilborne pathogen Plasmodiophora brassicae causes clubroot on Brassica crops, a common disease in many oilseed rape growing regions. Here, we investigate genetic diversity and geographic differentiation of P. brassicae populations from different regions in Germany. We compared three regions that differ in oilseed rape cropping history, oilseed rape acreage, and incidence of clubroot. These regions were either spatially separated or separated by the former inner German border. Plasmodiophora isolates were collected from 59 fields (29, 17, and 13 fields per region, respectively) and 174 amplified fragment length polymorphism (AFLP) markers were analyzed. Every field isolate showed a unique genotype pattern; that is, no genotype was shared among the regions and different fields. The mean gene diversity was 0.27, suggesting that P. brassicae is a genetically diverse species. The comparison of indexes (gene diversity, genotypic diversity, and linkage disequilibrium) between the regions does not support our hypotheses that cropping history, oilseed rape acreage, and incidence of clubroot affect these estimates. Principal component analysis (PCA), fixation index (FST), and generalized linear model (GLM) were suitable to specify regional differences. PCA revealed two clusters of isolates based on the geographic origin of the isolates and FSTshowed that these clusters were highly differentiated. Hypotheses about association of genotypes with different spatial scales were tested with GLM: the region, reflecting the cropping history, and the individual field had a significant effect on the AFLP pattern. We propose that individual field isolates represent a discrete population and that geographic differentiation results from low levels of gene flow due to the limited dispersal of this soilborne pathogen and from localized selection pressure as unifying force on the genotypes.
Effects of Various Modes of Mechanical Ventilation in Normal Rats
Authors: Pecchiari Matteo , Monaco Ario , Koutsoukou Antonia , Valle Patrizia Della , Gentile Guendalina , D’Angelo Edgardo
Published: November 2013

Background:

Recent studies in healthy mice and rats have reported that positive pressure ventilation delivered with physiological tidal volumes at normal end-expiratory volume worsens lung mechanics and induces cytokine release, thus suggesting that detrimental effects are due to positive pressure ventilation per se. The aim of this study in healthy animals is to assess whether these adverse outcomes depend on the mode of mechanical ventilation.

Methods:

Rats were subjected to 4 h of spontaneous, positive pressure, and whole-body or thorax-only negative pressure ventilation (N = 8 per group). In all instances the ventilatory pattern was that of spontaneous breathing. Lung mechanics, cytokines concentration in serum and broncho–alveolar lavage fluid, lung wet-to-dry ratio, and histology were assessed. Values from eight animals euthanized shortly after anesthesia served as control.

Results:

No evidence of mechanical ventilation–dependent lung injury was found in terms of lung mechanics, histology, or wet-to-dry ratio. Relative to control, cytokine levels and recruitment of polymorphonuclear leucocytes increased slightly, and to the same extent with spontaneous, positive pressure, and whole-body negative pressure ventilation. Thorax-only negative pressure ventilation caused marked chest and lung distortion, reversible increase of lung elastance, and higher polymorphonuclear leucocyte count and cytokine levels.

Conclusion:

Both positive and negative pressure ventilation performed with tidal volumes and timing of spontaneous, quiet breathing neither elicit an inflammatory response nor cause morpho-functional alterations in normal animals, thus supporting the notion of the presence of a critical volume threshold above which acute lung injury ensues. Distortion of lung parenchyma can induce an inflammatory response, even in the absence of volotrauma.
G8P[6] rotaviruses isolated from Amerindian children in Mato Grosso do Sul, Brazil, during 2009: close relationship of the G and P genes with those of bovine and bat strains
Authors: Luchs Adriana , Timenetsky Maria do Carmo Sampaio Tavares
Published: November 2013

During the 2009 national group A rotavirus (RVA) surveillance, five unusual strains of the human G8P[6] genotype were detected in Brazilian indian children with acute gastroenteritis. The aim of this study was to carry out sequence analysis of the two outer capsid proteins (VP4 and VP7) and the inner capsid protein (VP6) of the G8P[6] strains detected in order to provide further information on the genetic relationship between human and animal RVA. A total of 68 stool samples, collected in Mato Grosso do Sul during 2009, were tested for RVA using ELISA, following by reverse transcriptase-PCR and sequencing. RVA infection was detected in 7.3 % of samples (5/68). The IAL-RN376 G8 sequence shares a clade with bovine and human strains, displaying highest nucleotide identity to African human strains DRC86 and DRC88, followed by African bovine strain NGRBg8. IAL-RN376 and IAL-RN377 P[6] sequences showed highest identity to human strain R330 from Ireland, and a close genetic relationship to African fruit bat RVA strain KE4852/07. Strains IAL-RN376 and IAL-RN377 display genogroup I VP6 specificity and the I2 genotype, and share high nucleotide identities with human strains B1711, 272-BF and 06-242, and moderate identities with bovine (RUBV81, 86 and KJ9-1) and porcine (HP140) strains. This study suggested that a reassortment between bovine and bat RVA strains could have occurred in animal host(s) preceding the transmission to humans. In the indigenous population, zoonotic transmission is probably fairly frequent as the inhabitants live in close contact with animals under conditions of poor hygiene.
(−)-Benzyl 2,3-dideoxy-β-D-erythro-hex-2-enopyranoside
Authors: Ohba Shigeru , Okazaki Hayato , Ueda Yuji , Hanaya Kengo , Shoji Mitsuru , Sugai Takeshi
Published: November 2013

In the title compound, C13H16O4, the six-membered ring of the sugar moiety shows a half-chair conformation. In the crystal, molecules are connectedviaO—H...O hydrogen bonds, forming columns around twofold screw axes along theb-axis direction. There is a disorder of the benzyloxy group, which has two possible orientations with the phenyl group lying on a common plane [site-occupancy factors = 0.589 (9) and 0.411 (9)].
N-(Adamantan-1-yl)-1,2,3,4-tetrahydroisoquinoline-2-carbothioamide
Authors: El-Emam Ali A. , Al-Abdullah Ebtehal S. , Al-Tuwaijri Hanaa M. , Chidan Kumar C. S. , Fun Hoong-Kun
Published: November 2013

In the title compound, C20H26N2S, the N-containing six-membered ring adopts a boat conformation and the dihedral angle between the thiocarbamide group and the benzene ring is 49.67 (9)°. An intramolecular C—H...S hydrogen bond generates anS(6) ring motif. The N—H group is sterically hindered and there are no significant intermolecular interactions beyond van der Waals contacts.
TheP43enantiomorph of Sr2As2O7
Authors: Mbarek Aicha , Edhokkar Fadhila
Published: November 2013

The crystal structure of strontium diarsenate has been reinvestigated from single-crystal X-ray diffraction data. In contrast to the previous determinations of this structure [Weilet al.(2009).Solid State Sci.11, 2111–2117; Edhokkaret al.(2012).Mater. Sci. Eng.,28, 012017] and to all isotypicA2B2O7compounds that crystallize in the space groupP41, the current redetermination revealed theP43enantiomorph of Sr2As2O7with a purity of 96.3 (8)%. The crystal structure is made up from two eclipsed As2O7diarsenate groups (symmetry 1) with characteristically longer As—O bridging bonds [1.756 (4)–1.781 (4) Å] than the terminal As—O bonds [1.636 (4)–1.679 (4) Å] and four Sr2+sites with coordination numbers ranging from seven to nine. The building units are arranged in sheets parallel to (001).
(11aS)-1,5,11,11a-Tetrahydro-1-benzothieno[3,2-f]indolizin-3(2H)-one
Authors: Vrábel Viktor , Sivý Július , Šafář Peter , Kožíšek Jozef
Published: November 2013

The absolute configuration of the title compound, C14H13NOS, was assigned from the synthesis and confirmed by the structure determination. There are two independent molecules in the asymmetric unit. The central six-membered ring of the indolizine moiety adopts an envelope conformation, with the greatest deviations from the mean planes being 0.569 (3) and 0.561 (3) Å for the indolizine bridgehead C atoms of the two molecules. The benzothieno ring attached to the indolizine ring system is planar to within 0.015 (3) Å in both molecules. In the crystal, weak C—H...O and C—H...π interactions lead to the formation of a three-dimensional framework structure.
Long Allele Designations at D2S1338 and D19S433 Loci as Influenced by Various Multiplex STR Kits
Authors: Dell'Ariccia‐Carmon Aviva , Raziel Aliza , Oz Carla , Berdugo Reouven , Zamir Ashira
Published: November 2013

European forensic laboratories are replacing the STR multiplex kits with the new generation 16/17 STR kits. This study examines the influence of the new generation kits and the new Applied Biosystems 3500xL Genetic Analyzer on the designation of long D2S1338 and D19S433 off‐ladder alleles. Different allele calls were obtained using the new NGM™ (Applied Biosystems) and PowerPlex® ESI™ (Promega) kits compared with AmpFℓSTR® SGM Plus™ kit (Applied Biosystems). Sequence analysis was used to determine accurate allele designation. The new multiplex kits and the 3500xL Genetic Analyzer improved accuracy of long allele designations. DNA databases worldwide include countless profiles obtained by previous kits. Discrepancies between the new and former technologies may cause failure to detect hits. Discordance is expected due to primer sequence differences between various kits. An additional discordance, occurring in long alleles, independent of primer sequence is reported in this study.