bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled reactive ion etching and plasma regrowth of titanium oxides of known thickness for production of metal‐oxide‐metal diodes
Authors: Dodd Linzi E. , Gallant Andrew J. , Wood David 
Published: August 2013

The successful production, via two different oxidation processes, of metal‐oxide‐metal (MOM) diodes is presented. An innovative reactive ion etching and plasma assisted regrowth process has been used to provide oxides, which are in the thickness range 4.0–5.1 nm. These are thinner and physically more uniform than oxides grown in a furnace, resulting in diodes which should conduct via electron tunnelling across the MOM junction. Transmission electron microscopy analysis has been used in conjunction with time of flight secondary ion mass spectrometry analysis to verify oxide thickness and uniformity.
Transitions of bandgap and built-in stress for sputtered HfZnO thin films after thermal treatments
Authors: Li Chih-Hung , Chen Jian-Zhang , Cheng I-Chun 
Published: August 2013

HfZnO thin films with various Hf contents are sputter-deposited on glass substrates from HfxZn1−xO (x = 0, 2.5, 5, 7.5, and 10 at. %) targets at room temperature. The incorporation of Hf in the ZnO film leads to the amorphorization of the materials. The amorphous structures of high-Hf-content films remain after annealing at 600 °C for 30 min. The built-in stresses of as-deposited films are compressive. As the annealing temperature increases, the stresses are relaxed and even become tensile. The films exhibit a high transmission of 80% in the visible region. The optical bandgap increases with the Hf content, but it decreases with the annealing temperature. This can be attributed to the alteration of strain (stress) status in the films and atomic substitution. The reduction of bandgap partly results from the grain growth, which is due to the quantum confinement effect of the small grains. Hf doping increases the resistivity of ZnO owing to the disorder of the material structure and the higher bandgap, which result in more carrier traps and less thermally excited carriers in the conduction bands.
ERK signaling couples nutrient status to antiviral defense in the insect gut
Authors: Xu Jie , Hopkins Kaycie , Sabin Leah , Yasunaga Ari , Subramanian Harry , Lamborn Ian , Gordesky-Gold Beth , Cherry Sara 
Published: August 2013

Significance
A unique facet of arthropod-borne virus infection is that the pathogens are orally acquired by insects during the taking of a blood meal. Hence, there is a direct link between nutrient acquisition and pathogen challenge. We found that the classic nutrient-responsive ERK pathway is a molecular determinant of this “midgut barrier”; ERK signaling is essential for antiviral defense in the insect intestinal epithelial cells. Surprisingly, we also found vertebrate insulin, which activates ERK signaling during a blood meal, both restricts viral infection in insect cells and protects against viral invasion of the gut epithelium. ERK signaling in the insect intestines restricts viral infection, suggesting that insects may take advantage of cross-species signals in the meal to preemptively activate antiviral immunity.
Quantitative basis for neuroimaging of cortical laminae with calibrated functional MRI
Authors: Herman Peter , Sanganahalli Basavaraju G. , Blumenfeld Hal , Rothman Douglas L. , Hyder Fahmeed 
Published: August 2013

Significance
This work challenges the notion that conventional functional magnetic resonance imaging (fMRI), that is, blood oxygenation level-dependent signal alone, can accurately reflect laminar neural activity. Instead, we show that calibrated fMRI methods for metabolic and hemodynamic measurements can better reflect laminar neuronal activities.
Emphasis of spatial cues in the temporal fine structure during the rising segments of amplitude-modulated sounds
Authors: Dietz Mathias , Marquardt Torsten , Salminen Nelli H. , McAlpine David 
Published: August 2013

Significance
Sound localization in rooms is challenging, especially for hearing-impaired listeners or technical devices. Reflections from walls and ceilings make it difficult to distinguish sounds arriving direct from a source from the mixture of potentially confounding sounds arriving a few milliseconds later. Nevertheless, normal-hearing listeners show remarkable localization abilities under such challenging listening conditions. The current study investigates the underlying mechanisms responsible for accurate localization performance. Stimuli we named amplitude modulated binaural beats are introduced. These stimuli allow for a more controlled testing than speech stimuli. Results from two experimental procedures (psychoacoustics and the brain-imaging technique magnetoencephalography) reveal that listeners appear to “glimpse” reliable spatial information during the early, rising portions of modulated sounds, ignoring later-arriving, potentially conflicting, spatial cues.
Spin-dependent electron transmission through bacteriorhodopsin embedded in purple membrane
Authors: Mishra Debabrata , Markus Tal Z. , Naaman Ron , Kettner Matthias , Göhler Benjamin , Zacharias Helmut , Friedman Noga , Sheves Mordechai , Fontanesi Claudio 
Published: August 2013

Significance
The role of the electron spin in chemistry and biology has been receiving much attention because of a plausible relation to electromagnetic field effects on living organisms. Part of the difficulty in studying the subject arises from the lack of a physical model that can rationalize these phenomena. Recently the chiral-induced spin selectivity effect was observed in electron transmission through organic molecules. The question is to what extent the effect takes place in proteins. In the present study, we probed bacteriorhodopsin embedded in its native membrane environment. We observed clear evidence for spin-dependent electron transmission through this system. The results point to the possibility that the effect may play a role in electron transfer in biological systems.
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
Authors: He Yi , Mozolewska Magdalena A. , Krupa Paweł , Sieradzan Adam K. , Wirecki Tomasz K. , Liwo Adam , Kachlishvili Khatuna , Rackovsky Shalom , Jagieła Dawid , Ślusarz Rafał , Czaplewski Cezary R. , Ołdziej Stanisław , Scheraga Harold A. 
Published: August 2013

SignificanceWith the example of the coarse-grained United Residue model of polypeptide chains, this paper demonstrates that the physics-based approach for protein-structure prediction can lead to exceptionally good results when correct domain packing is an issue, even for a highly homologous target. The reason for this is probably that emphasis is placed on energetically favorable residue–residue interactions, including those with residues in relatively flexible linker regions; these regions are usually very different in the target compared with those of proteins in the databases used for template-based modeling. The results suggest that a combination of bioinformatics and a physics-based approach could result in a major increase in the prediction capacity of existing approaches.
Superpriming of synaptic vesicles after their recruitment to the readily releasable pool
Authors: Lee Jae Sung , Ho Won-Kyung , Neher Erwin , Lee Suk-Ho 
Published: August 2013

Significance
During sustained nerve activity, synapses must continuously recycle vesicles. We used the unique opportunities for quantitative analysis offered by the calyx of Held synapse to study late stages in the process that renders vesicles release-ready. We dissect two sequential steps with distinct pharmacology and kinetics, the characterization of which is essential for an understanding of molecular mechanisms of transmitter release and short-term plasticity.
Definition of a thirdVLRgene in hagfish
Authors: Li Jianxu , Das Sabyasachi , Herrin Brantley R. , Hirano Masayuki , Cooper Max D. 
Published: August 2013

SignificanceThe jawless vertebrates (hagfish and lampreys) possess an alternative adaptive immune system in which variable lymphocyte receptors (VLRs) constructed of leucine-rich repeats are used to recognize foreign antigens. ThreeVLRgenes have been identified in lampreys (VLRA,VLRB, andVLRC), but only two (VLRAandVLRB) have been found in hagfish. Here, we identified and characterized a third hagfishVLRgene. Our analysis indicates that the third hagfishVLRis the ortholog of lampreyVLRA, while the previously identified hagfish “VLRA” is the counterpart of lampreyVLRC. The demonstration of three orthologousVLRgenes in hagfish and lampreys suggests that this anticipatory receptor system evolved in a common ancestor of the two jawless vertebrate lineages ∼480 Mya.
Coherent delta-band oscillations between cortical areas correlate with decision making
Authors: Nácher Verónica , Ledberg Anders , Deco Gustavo , Romo Ranulfo 
Published: August 2013

Significance
Delta oscillations have been largely associated with slow-wave sleep and anesthesia, when no conscious functions take place during these states. However, our study demonstrates that coherent delta-band oscillations reflect the linkage between distant parietal and frontal cortical circuits during decision making. Thus, these findings open an avenue for investigating whether the activity between distant cortical circuits oscillates in the delta frequency range during other cognitive functions.
Anatomy of the meninges: structural and functional aspects.
Authors: Weller R. O. 
Published: August 2013

Abstract

This chapter deals with the structure and functional aspects of the human meninges. It is shown that, although grouped together under the general heading of meninges, the dura mater and the leptomeninges, consisting of the arachnoid and pia mater, have distinctly different structures and functions. There are 4 major fluid compartments in the central nervous system: blood, cerebrospinal fluid (CSF), interstitial (extracellular) fluid, and intracellular fluid. This chapter focuses mainly on blood, CSF and interstitial fluid, and the interrelations between these 3 fluids.
Pathogenesis of cerebrospinal meningitis caused by Neisseria meningitidis.
Authors: Coureuil M. , Miller F. , Join-Lambert O. , Lécuyer H. , Bourdoulous S. , Marullo S. , Nassif X. 
Published: August 2013

Abstract

This chapter describes the pathogenesis of Neisseria meningitidis-related cerebrospinal meningitis, and examines the 2 main obstacles that N. meningitidis has to overcome before reaching the meninges: the bloodstream and the blood-brain barrier (BBB). The mechanisms and consequences of N. meningitidis-endothelial cell interactions on meningeal invasion are explored.
Haemophilus influenzae meningitis.
Authors: Hill D. J. , Christodoulides M. 
Published: August 2013

Abstract

This chapter reviews the pathogenesis of Haemophilus influenzae type b (Hib) meningitis, a multistep process that begins with: (i) colonization of the nasopharynx; (ii) subsequent invasion into the blood, which leads to haematogenous dissemination; (iii) bacterial penetration of the blood-cerebrospinal fluid barrier/blood-brain barrier and entry into the subarachnoid space; which leads to (iv) a compartmentalized host inflammatory response. A newborn rat model for Hib meningitis is proposed, which is based on current knowledge of bacterial virulence factors and host cell receptor recognition of these ligands.
Chronic meningitis.
Authors: Schmutzhard E. , Helbok R. 
Published: August 2013

Abstract

This chapter deals exclusively with common infectious causes of chronic meningitis in the immunocompetent patient, citing particular examples of bacterial, fungal and helminthic causes. The following types of infectious meningitis are described in terms of symptoms, diagnosis and treatment: tuberculous meningitis, cryptococcal meningitis, Coccidioides immitis meningitis, Treponema pallidum meningitis, and Taenia solium meningitis,.
Streptococcus suis meningitis.
Authors: Gottschalk M. , Fittipaldi N. , Segura M. 
Published: August 2013

Abstract

This chapter first reviews the epidemiology of Streptococcus suis infections in humans and pigs, then describes the pathogenesis and clinical course of S. suis meningitis in humans, the role of bacteraemia in S. suis invasion of the central nervous system, and the inflammatory processes involved in S. suis meningitis.
Inflammation in the subarachnoid space.
Authors: Christodoulides M. 
Published: August 2013

Abstract

Classical pyogenic leptomeningitis is an acute, compartmentalized intracranial inflammatory response induced in the cerebrospinal fluid (CSF)-filled spaces of the subarachnoid space (SAS) and is characterized by the upregulated accumulation of a wide variety of host response factors and the production of 'pus'. This chapter describes the proinflammatory cytokines, chemokines, reactive oxygen species, nitric oxide, matrix metalloproteinases, and the other molecules that are produced in the SAS in response to invading bacteria.
Weekday and weekend physical activity patterns of French and Spanish adolescents
Authors: Aibar Alberto , Bois Julien E. , Zaragoza Casterad Javier , Generelo Eduardo , Paillard Thierry , Fairclough Stuart 
Published: August 2013

AbstractAdolescents' objectively assessed physical activity (PA) patterns during specific segments of the day remain unclear. In order to develop a clearer understanding this study examined country and gender differences in moderate to vigorous physical activity (MVPA) levels during specific segments of weekdays and weekend days, and explored the contribution of each segment to PA guidelines. Morpho‐demographic, socio‐economic and PA data were collected from a sample of 829 French and Spanish adolescents (45.0% Spanish; 55.2% females; 14.33±.73 years). Actigraph GT3X accelerometers were worn for seven days to assess adolescents' MVPA for three segments of weekdays (school‐travel‐time, school‐time, and non‐school‐time), and weekend days (morning‐time, afternoon‐time and night‐time). Data were analysed using multilevel modelling. The most active segments were non‐school‐time (29.2±17.5 min) and school‐time (25.8±14.2 min) during weekdays, and morning‐time (28.2±25.8 min) on weekend days. Except for school‐time, Spanish adolescents were more significantly active than French adolescents during all segments. Significant gender differences were found in all segments. Country differences highlight the need to recognise cultural contexts that influence adolescents' PA. Common European‐wide strategies may be insufficient to increase MVPA levels if cultural variability is not considered. Spanish and French PA intervention programmes should target girls and low‐active boys during non‐school‐time and weekends.
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples
Authors: Behr Jonas , Kahles André , Zhong Yi , Sreedharan Vipin T. , Drewe Philipp , Rätsch Gunnar 
Published: August 2013

Abstract
Motivation: High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction.
Results: We present the novel framework MITIE (Mixed Integer Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data and show how to find the optimal solution using Mixed Integer Programming. MITIE can (i) take advantage of known transcripts, (ii) reconstruct and quantify transcripts simultaneously in multiple samples, and (iii) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. We present an extensive study based on realistic simulated RNA-Seq data. When compared with state-of-the-art approaches, MITIE proves to be significantly more sensitive and overall more accurate. Moreover, MITIE yields substantial performance gains when used with multiple samples. We applied our system to 38 Drosophila melanogaster modENCODE RNA-Seq libraries and estimated the sensitivity of reconstructing omitted transcript annotations and the specificity with respect to annotated transcripts. Our results corroborate that a well-motivated objective paired with appropriate optimization techniques lead to significant improvements over the state-of-the-art in transcriptome reconstruction.
Availability: MITIE is implemented in C++ and is available from http://bioweb.me/mitie under the GPL license.
Contact: Jonas_Behr@web.de and raetsch@cbio.mskcc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of Ferulic and p‐Coumaric Acids in Japanese Rice for Sake Brewing
Authors: Hashizume Katsumi , Ito Toshihiko , Nakayama Airi , Okuda Masaki 
Published: August 2013

ABSTRACTFerulic and p‐coumaric acids were analyzed in 50 rice (Oryza sativa L.) samples from 32 cultivars harvested in Japan. In brown rice, ferulic and p‐coumaric acid levels ranged from 309 to 607 mg/kg and from 49 to 100 mg/kg, respectively. In 70% polished rice, ferulic and p‐coumaric acid levels ranged from 27 to 103 mg/kg and from 0.4 to 3.5 mg/kg, respectively. Ratios of average phenolic acid levels in the 70% polished rice to the brown rice were 13.9% for ferulic acid and 1.9% for p‐coumaric acid. The ferulic acid level was highly correlated between brown and 70% polished rice (R = 0.815; P < 0.01), but there was no clear correlation for p‐coumaric acid. Phenolic acid levels in the 70% polished rice did not show any clear correlations between the analytical index measurements for sake brewing suitability (weight of 1,000 grains, water absorption, digestibility, crude protein, and potassium content). Phenolic acid levels in the 70% polished rice directly affected levels in the rice koji enzyme digest. The results indicated that phenolic acid levels in sake were affected by the levels in ingredient rice grains, which may then influence the sensory quality of sake.
Effects of forest successional status on microenvironmental conditions, diversity, and distribution of filmy fern species in a temperate rainforest
Authors: Saldaña Alfredo , Parra Maria J. , Flores‐Bavestrello Alejandra , Corcuera Luis J. , Bravo León A. 
Published: August 2013

AbstractThe vertical distribution of Hymenophyllaceae species has been related to microenvironmental variations around host trees. We addressed the questions: Do the vertical microenvironmental conditions within forest stands of differing successional statuses vary significantly? Does the diversity of Hymenophyllaceae species differ between forest successional statuses? Are the vertical distribution and diversity of Hymenophyllaceae species related more to humidity or light availability? Are there any interspecific differences in the desiccation tolerance of these species which can be related to their vertical distribution? We characterized the microhabitat conditions (vapor pressure deficit [VPD], air relative humidity [RH], and light availability [PAR]) and the vertical distribution of Hymenophyllaceae species in host trees, in both a secondary forest and an old‐growth temperate rainforest in Chile. Chlorophyll fluorescence was used to monitor the integrity of the photosynthetic apparatus during desiccation experiments. The stand basal area, tree height, and leaf area index were all significantly greater in the old‐growth forest stands, but VPD, RH, and PAR showed no significant differences between the two forests. Both successional statuses showed the same amount of filmy fern species in terms of both abundance and diversity. In both successional statuses VPD and RH decreased while PAR increased with the height of the hosts. Regardless of the forest's age, abundance and diversity of filmy ferns were greater in microsites of greater humidity and less light availability. Desiccation tolerance differed significantly among Hymenophyllaceae species. The distribution pattern could be better explained by the specific microenvironmental requirements and desiccation tolerance rather than the forest's successional status.
Impacts of Recombinant Human Erythropoietin Treatment During Predialysis Periods on the Progression of Chronic Kidney Disease in a Large‐Scale Cohort Study (Co‐JET study)
Authors: Akizawa Tadao , Saito Akira , Gejyo Fumitake , Suzuki Masashi , Nishizawa Yoshiki , Tomino Yasuhiko , Tsubakihara Yoshiharu , Akiba Takashi , Hirakata Hideki , Watanabe Yuzo , Kawanishi Hideki , Bessho Masami , Udagawa Yukio , Aoki Kotonari , Uemura Yukari , Ohashi Yasuo ,   Co‐JET Study Group
Published: August 2013

AbstractThe effect of recombinant human erythropoietin (rHuEPO) treatment on the progression of chronic kidney disease (CKD) has not been fully evaluated in Japan. We therefore retrospectively evaluated this in a sub‐cohort of a prospective multicenter study to investigate optimal hemoglobin (Hb) level of CKD patients on hemodialysis (HD) treated with rHuEPO; Japan Erythropoietin Treatment Study for Target Hb and Survival (JET study). Effect of rHuEPO treatment during predialysis period to delay initiation of HD was retrospectively assessed in 2434 patients from the JET study comparing groups with and without rHuEPO treatment. The assessment was done by Cox proportional hazards regression analysis and inverse probability‐weighted (IPW) analysis to adjust for time‐dependent confounders. The weights used in the IPW analysis were calculated using a logistic model that included baseline confounders and time‐dependent variables. During the predialysis period, 71.7% (1746 patients) were treated with rHuEPO (mean Hb level of 8.7 g/dL at initiation of rHuEPO treatment). Covariates significantly associated with initiation of rHuEPO treatment were Hb level, serum creatinine level, age, diabetes, cardiac insufficiency, and hypertension. The adjusted hazard ratio for time until HD initiation under rHuEPO treatment was 0.272 (95% CI, 0.223–0.331; P < 0.001) in the Cox analysis and 0.63 (95% CI, 0.53–0.76; P < 0.0001) in the IPW analysis. This retrospective study suggests that rHuEPO treatment during the predialysis period has preventive effects on the progression of CKD although further prospective investigation on the efficacy is needed.