Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterisation of the spoilage bacterial microbiota in oyster gills during storage at different temperatures.

BACKGROUND The spoilage bacterial community in oyster gill was investigated during storage at 4, 10 and 20 °C. Aerobic plate counts and pH values were determined. Total bacterial DNA was extracted from oyster gill and bulk cells of plate count media. The major bacterial species during fresh or different temperatures storage were determined by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). RESULTS The initial aerobic plate count in oyster gill reached 6.70 log CFU g(-1). PCR-DGGE fingerprinting analysis of the 16S rRNA gene V3 region revealed that most of the strains in fresh oyster gill belonged to the genera Lactococcus and Enterobacter. The major spoilage bacteria at a storage temperature of 20 °C were Leuconostoc pseudomesenteroides, an uncultured bacterium, Cytophaga fermentans, Lactococcus lactis, Pseudoalteromonas sp. , Enterococcus mundtii, Clostridium difficile and an uncultured Fusobacteria; those at 10 °C were Lactococcus spp. , Lactobacillus curvatus, Weissella confusa and C. difficile; those at 4 °C were Lactococcus, Weissella, Enterobacter and Aeromonas. The other minor species were L. curvatus, Pseudomonas sp. and E. mundtii. Lactococcus spp. was the most common main spoilage bacteria in oyster gill during chilled storage. CONCLUSION PCR-DGGE revealed the complexity of the bacterial microbiota and the major bacteria species in oyster gill for fresh and storage.
Energy infrastructure transition in urban informal households in South Africa

ii Opsomming . iii Acknowledgements . iv List of figures . viii List of acronyms and abbreviations . x List of tables . xi CHAPTER 1: INTRODUCTION . 1 1.1 Background . 1 1.2 Energy challenges in urban informal households . 3 1.3 Research problem . 6 1.4 Research questions . 6 1.5 Significance of the research . 7 1.6 Limitations of the study . 8 1.7 Assumptions of the study . 8 1.8 Research design. 9 1.9 Chapter Outline . 9 CHAPTER 2: LITERATURE REVIEW . 11 2.
90-kDa Ribosomal S6 Kinase Is Phosphorylated and Activated by 3-Phosphoinositide-dependent Protein Kinase-1*

90-kDa ribosomal S6 kinase-2 (RSK2) belongs to a family of growth factor-activated serine/threonine kinases composed of two kinase domains connected by a regulatory linker region. The N-terminal kinase of RSK2 is involved in substrate phosphorylation. Its activation requires phosphorylation of the linker region at Ser369, catalyzed by extracellular signal-regulated kinase (ERK), and at Ser386, catalyzed by the C-terminal kinase, after its activation by ERK. In addition, the N-terminal kinase must be phosphorylated at Ser227 in the activation loop by an as yet unidentified kinase. Here, we show that the isolated N-terminal kinase of RSK2 (amino acids 1–360) is phosphorylated at Ser227 by PDK1, a constitutively active kinase, leading to 100-fold stimulation of kinase activity. In COS7 cells, ectopic PDK1 induced the phosphorylation of full-length RSK2 at Ser227and Ser386, without involvement of ERK, leading to partial activation of RSK2. Similarly, two other members of the RSK family, RSK1 and RSK3, were partially activated by PDK1 in COS7 cells. Finally, our data indicate that full activation of RSK2 by growth factor requires the cooperation of ERK and PDK1 through phosphorylation of Ser227, Ser369, and Ser386. Our study extend recent findings which implicate PDK1 in the activation of protein kinases B and C and p70S6K, suggesting that PDK1 controls several major growth factor-activated signal transduction pathways.
A Statistical Meta-analysis of the Design Components of New Urbanism on Housing Prices

The principles of New Urbanism such as increased density, mixed land uses, and street connectivity are often recommended in response to the typical conditions of suburban developments. Much current empirical research has begun to test whether these principles can increase property values. The findings of these studies have, however, been quite inconsistent. This research attempts to quantitatively synthesize these conflicting findings through a statistical meta-analysis. This study finds that a lower density, decreased street connectivity, and a closer proximity to a transit stop can contribute to increased housing premiums, while mixed land uses are not shown to always do so.
Effect of Maternal Protein Restriction in Rats on Cardiac Fibrosis and Capillarization in Adulthood

This study examines the effect of maternal protein restriction in rats on levels of cardiac fibrosis, myocardial capillarization, and media:lumen ratio of intramyocardial arteries in adult offspring. Female Wistar Kyoto rats were fed either a normal protein diet (NPD; 20% casein) or a low-protein diet (LPD; 8.7% casein) during pregnancy and lactation. Female offspring (seven per group) were weaned at 4 wk of age and grown to adulthood. At 24 wk of age, the offspring were perfusion fixed. Cardiac fibrosis and media:lumen ratio of intramyocardial arterioles was assessed using image analysis and cardiac capillarization was stereologically investigated. Body weights at 2 and 24 wk of age were significantly reduced (31% and 8%, respectively) in the LPD offspring; however, heart size was not different at 24 wk. Importantly by adulthood, there was a significant 15% increase in left ventricular interstitial fibrosis in LPD offspring. There were no differences in levels of perivascular fibrosis, myocardial capillarization, or in the media:lumen ratio of intramyocardial arteries between groups. Because cardiac fibrosis is associated with impaired cardiac contractility and arrhythmia, our results suggest that induction of interstitial fibrosis may contribute to the increased cardiac disease in adult subjects who were exposed to an adverse intrauterine environment.
Effectiveness of therapeutic massage for generalized anxiety disorder: a randomized controlled trial

Background: Although massage is one of the most popular complementary and alternative medical (CAM) treatments for anxiety, its effectiveness has never been rigorously evaluated for a diagnosed anxiety disorder. This study evaluates the effectiveness of therapeutic massage for persons with generalized anxiety disorder (GAD). Methods: Sixty‐eight persons with GAD were randomized to therapeutic massage (n=23), thermotherapy (n=22), or relaxing room therapy (n=23) for a total of 10 sessions over 12 weeks. Mean reduction in anxiety was measured by the Hamilton Anxiety Rating Scale (HARS). Secondary outcomes included 50% reduction in HARS and symptom resolution of GAD, changes in depressive symptoms (Patient Health Questionnaire (PHQ‐8)), worry and GAD‐related disability. We compared changes in these outcomes in the massage and control groups posttreatment and at 6 months using generalized estimating equation (GEE) regression. Results: All groups had improved by the end of treatment (adjusted mean change scores for the HARS ranged from −10.0 to −13.0; P<.001) and maintained their gains at the 26‐week followup. No differences were seen between groups (P=.39). Symptom reduction and resolution of GAD, depressive symptoms, worry and disability showed similar patterns. Conclusions: Massage was not superior to the control treatments, and all showed some clinically important improvements, likely due to some beneficial but generalized relaxation response. Because the relaxing room treatment is substantially less expensive than the other treatments, a similar treatment packaged in a clinically credible manner might be the most cost effective option for persons with GAD who want to try relaxation‐oriented CAM therapies. Depression and Anxiety, 2010. © 2010 Wiley‐Liss, Inc.
Analysing the Lexical Demands of Subject Textbooks Used in Irish Post-Primary Education to Facilitate Immigrant Students’ Curriculum Access

This research uses a corpus-based methodology to analyse the lexical features of textbooks used in six curriculum subjects of Irish post-primary education (namely, English, History, Civic, Social and Political Education, Mathematics, and Science) to inform the English language support that is provided to immigrant students. The empirical analysis illuminates the commonest words, collocations and 4-word clusters in subject-specific registers, demonstrating the lexical variation that is manifested across subjects. From a pedagogical perspective, the discussion describes important features of students’ target linguistic repertoire. Although the results are context-specific, the research methodology becomes relevant to any other context with similar pedagogical needs.
Comparison of color thresholding and global thresholding for Ziehl-Neelsen TB bacilli slide images in sputum samples

Image segmentation is important in analysis of medical images. However, there are many constraints that must be faced such as variety of biological system and also limitation of mechine equipment. Thus, effective and precise method are needed to obtain correct diagnosis of quantitative medical samples. This paper studies the comparison between color thresholding and global thresholding techniques for segmenting Ziehl-Neelsen TB bacilli slide images in sputum samples. Color thresholding use RGB image as input while global thresholding used C-Y image as input. This technique has been tested onto 50 different images. The results obtained indicate that global thresholding method have better potential to ease next stage of image processing.
An Analytical Model to Estimate ${V}_{T}$ Distribution of Partially Correlated Fin Edges in FinFETs Due to Fin-Edge Roughness

Line edge roughness (LER) is a critical variability source in scaled FinFETs. LER produces line width roughness (LWR) that causes threshold voltage (<inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula>) variability. Various lithography techniques demonstrate characteristic LER-LWR relationship. For translating LER/LWR to the <inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula> distribution, an analytical model for uncorrelated fin edges (correlation coefficient, <inline-formula> <tex-math notation="LaTeX">$\rho ={0}$ </tex-math></inline-formula>) has been presented in the literature. However, a range of correlation coefficients (<inline-formula> <tex-math notation="LaTeX">${0}\le \rho \le {0.85}$ </tex-math></inline-formula>) between two fin edges is experimentally observed for various lithography techniques. In this paper, we present an analytical model to predict <inline-formula> <tex-math notation="LaTeX">$\rho $ </tex-math></inline-formula> dependent <inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula> distribution for partially correlated fin edges in FinFETs. First, an analytical model of mean (<inline-formula> <tex-math notation="LaTeX">$\mu $ </tex-math></inline-formula>) and standard deviation (<inline-formula> <tex-math notation="LaTeX">$\sigma $ </tex-math></inline-formula>) for <inline-formula> <tex-math notation="LaTeX">$\rho $ </tex-math></inline-formula> dependent minimum, maximum, and average fin width is presented. This is used to construct an equivalent simplified trapezoidal fin distribution. Second, percolation theory-based model is used to compute <inline-formula> <tex-math notation="LaTeX">${V}_{T}$ </tex-math></inline-formula> distribution from the fin distribution. The model is validated against well-calibrated TCAD simulations for a wide range of geometrical (channel length <inline-formula> <tex-math notation="LaTeX">${L}_{G}$ </tex-math></inline-formula> and nominal fin width <inline-formula> <tex-math notation="LaTeX">${W}_{\text {fin}})$ </tex-math></inline-formula> and LER variability (correlation length <inline-formula> <tex-math notation="LaTeX">$\Lambda $ </tex-math></inline-formula> and correlation coefficient <inline-formula> <tex-math notation="LaTeX">$\rho $ </tex-math></inline-formula>) parameters to show excellent match. The model is 1000 times faster compared with TCAD simulations.
Repeat protein architectures predicted by a continuum representation of fold space

It is an open question whether nature has utilized all possible protein folds. For a simple protein architecture, the helical repeats, we report a method to address this question based on a mapping between the set of repetitive curves and a space of parameters specifying the curve. The exploration of the parameter space for a particular architecture enables a systematic exploration of the fold space for that protein architecture. In a planar subspace of the parameter space of helical repeats we have identified points corresponding to both naturally occurring folds and potential folds not observed so far.
COSTS AND BENEFITS OF VARIABLE BREEDING PLUMAGE IN THE RED‐BACKED FAIRY‐WREN

Abstract The red‐backed fairy‐wren is a socially monogamous passerine bird which exhibits two distinct types of breeding male, bright males that breed in bright red and black plumage and dull males that breed in dull brown plumage. Most males spe006Ed their first potential breeding season in dull plumage and subsequent breeding seasons in bright plumage, but a relatively small proportion of males develop bright plumage in their first breeding season. This study quantifies morphology, behavior, and reproductive success of dull and bright males to assess the adaptive costs and benefits of bright plumage while controlling for age. Older bright males (two years of age or older) attempted to increase their reproductive success via copulations with extra pair females, whereas younger (one‐year old) bright males and dull males did not. Thus, older bright males spent less time on their own territories, intruded on neighboring groups with fertile females more frequently, gave more courtship displays, and had larger sperm storage organs than did younger bright males and dull males. Micro satellite analyses of paternity indicate that the red‐backed fairy‐wren has extremely high levels of sexual promiscuity, and that older bright males had higher within‐brood paternity than dull males or younger bright males. Regardless of age, bright males were more attractive to females in controlled mate choice trials than were dull males, and both age classes of bright males obtained higher quality mates earlier in the breeding season than did dull males, when nesting success was higher. In conclusion, although it appears that bright plumage increases access to higher quality mates, age also plays a central role in determining a male's overall reproductive success because of the high levels of sexual promiscuity exhibited by the red‐backed fairy‐wren.
OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY OF TYPE 3 NEOVASCULARIZATION SECONDARY TO AGE-RELATED MACULAR DEGENERATION

Purpose: To characterize the vascular structure of Type 3 neovascularization secondary to age-related macular degeneration using optical coherence tomography angiography. Methods: Optical coherence tomography angiography cube scans (3 mm × 3 mm) were acquired in 29 eyes of 24 patients with Type 3 lesions secondary to age-related macular degeneration using the RTVue XR Avanti with AngioVue, Split-spectrum amplitude-decorrelation, and motion correction technology. Automated layer segmentation boundaries were adjusted to best visualize the neovascular complex on en face projection images. Results: A distinct neovascular complex could be identified in 10 (34%) eyes, all of which were active on optical coherence tomography imaging. In all 10 eyes, the neovascular complex appeared as a small tuft of bright, high-flow tiny vessels with curvilinear morphology located in the outer retinal layers with a feeder vessel communicating with the inner retinal circulation (i.e., deep retinal capillary plexus). The mean (SD) size of the neovascular complex measured 0.07 (± 0.07) mm2. Conclusion: With optical coherence tomography angiography, it is possible to identify small intraretinal neovascular complexes communicating with the deep retinal capillary plexus in eyes with Type 3 neovascularization secondary to age-related macular degeneration. Qualitative and quantitative analyses of Type 3 neovascular complexes can be performed using optical coherence tomography angiography.
Natural Course of Fever During Influenza Virus Infection in Children

During the 2001-2002 epidemic of influenza virus A/H1N1, A/H3N2, and B, the authors obtained detailed profiles of fever from 118 infected children. The only treatment given was acetaminophen for temperatures greater than 39.0°C. Fever was most prominent in A/H3N2 and young children. Secondary fever was observed frequently at 72 to 132 hours in all types. The duration of fever was associated negatively with the age of the child and positively with the maximal temperature. The information will be no longer available in current era of oseltamivir therapy.
Rapid Simultaneous Detection of Enterovirus and Parechovirus RNAs in Clinical Samples by One-Step Real-Time Reverse Transcription-PCR Assay

ABSTRACT Enteroviruses (EVs) are recognized as the major etiological agent in meningitis in children and young adults. The use of molecular techniques, such as PCR, has substantially improved the sensitivity of enterovirus detection compared to that of virus culture methods. PCR-based methods also can detect a much wider range of EV variants, including those within species A, as well as human parechoviruses (HPeVs) that often grow poorly in vitro and which previously have been underdiagnosed by traditional methods. To exploit these developments, we developed a real-time one-step reverse transcription-PCR (RT-PCR) for the rapid and sensitive detection of EV and HPeV in clinical specimens. Two commercially available RT-PCR kits were used (method I, Platinum one-step kit; method II, Express qPCR one-step kit) with primers and probes targeting the EV and HPeV 5′-untranslated regions (5′UTR). Amplification dynamics (threshold cycle [CT ]values and efficiencies) of absolutely quantified full-length RNA transcripts representative of EV species A to D and HPeV were similar, demonstrating the effectiveness of both assays across the range of currently described human EV and HPeV variants. Probit analysis of multiple endpoint replicates demonstrated comparable sensitivities of the assays for EV and HPeV (method I, approximately 10 copies per reaction for both targets; method II, 20 copies per reaction). CT values were highly reproducible on repeat testing of positive controls within assays and between assay runs. Considering the sample turnaround time of less than 3 h, the multiplexed one-step RT-PCR method provides rapid diagnostic testing for EV and HPeV in cases of suspected central nervous system infections in a clinically relevant time frame.
Detection of lead contamination of water and VOC contamination of air using SOI micro-optical devices

Micro-photonic SOI Mach-Zehnder interferometers were coated with solid-phase micro-extraction materials derived from polydimethylsiloxane to enable sensing of volatile organic compounds of the BTEX class in air. A different coating based on functionalized mesoporous silicates is used to detect lead Pb(II) with a detection limit of < 100 ppb in water.
Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases

Type-II topoisomerases are responsible for untangling DNA during replication by removing supercoiled and interlinked DNA structures. Using a single-molecule micromanipulation setup, we follow the real-time decatenation of two mechanically braided DNA molecules by Drosophila melanogaster topoisomerase (Topo) II and Escherichia coli Topo IV. Although Topo II relaxes left-handed (L) and right-handed (R-) braids similarly at a rate of ≈2.9 s–1, Topo IV has a marked preference for L-braids, which it relaxes completely and processively at a rate of ≈2.4 s–1. However, Topo IV can unlink R-braids at about half that rate when they supercoil to form L-plectonemes. These results imply that the preferred substrate for unlinking by Topo IV has the symmetry of an L-crossing and shed new light on the decatenation of daughter strands during DNA replication, which are usually assumed to be linked in an R-braid.
Association of Genetic Variation in Genes Implicated in the β-Catenin Destruction Complex with Risk of Breast Cancer

Aberrant Wnt/β-catenin signaling leading to nuclear accumulation of the oncogene product β-catenin is observed in a wide spectrum of human malignancies. The destruction complex in the Wnt/β-catenin pathway is critical for regulating the level of β-catenin in the cytoplasm and in the nucleus. Here, we report a comprehensive study of the contribution of genetic variation in six genes encoding the β-catenin destruction complex (APC, AXIN1, AXIN2, CSNK1D, CSNK1E, and GSK3B) to breast cancer using a Mayo Clinic Breast Cancer Case-Control Study. A total of 79 candidate functional and tagging single nucleotide polymorphisms (SNP) were genotyped in 798 invasive cases and 843 unaffected controls. Of these, rs454886 in the APC tumor suppressor gene was associated with increased breast cancer risk (per allele odds ratio, 1.23; 95% confidence intervals, 1.05-1.43; Ptrend = 0.01). In addition, five SNPs in AXIN2 were associated with increased risk of breast cancer (Ptrend < 0.05). Haplotype-based tests identified significant associations between specific haplotypes in APC and AXIN2 (P ≤ 0.03) and breast cancer risk. Further characterization of the APC and AXIN2 variants suggested that AXIN2 rs4791171 was significantly associated with risk in premenopausal (Ptrend = 0.0002) but not in postmenopausal women. The combination of our findings and numerous genetic and functional studies showing that APC and AXIN2 perform crucial tumor suppressor functions suggest that further investigation of the contribution of AXIN2 and APC SNPs to breast cancer risk are needed. (Cancer Epidemiol Biomarkers Prev 2008;17(8):2101–8)
Anthrax toxin receptor 2 mediates Bacillus anthracis killing of macrophages following spore challenge

Initiation of inhalation anthrax is believed to involve phagocytosis of Bacillus anthracis spores by alveolar macrophages, followed by spore germination within the phagolysosome. In order to establish a systemic infection, it is predicted that bacilli then escape from the macrophage and replicate extracellularly. Mechanisms utilized by B. anthracis to escape from the macrophage are not well characterized, but a role for anthrax toxin has been proposed. Here we report the isolation of an anthrax toxin‐resistant cell line (R3D) following chemical mutagenesis of toxin‐sensitive RAW 264.7 murine macrophage cells. Both R3D and RAW 264.7 cells phagocytize spores of a B. anthracis Sterne strain. However, RAW 264.7 cells are killed following spore challenge, whereas R3D cells survive. Resistance to toxin and spore challenge correlates with loss of expression of anthrax toxin receptor 2 (ANTXR2/CMG‐2). When R3D cells are complemented with cDNA encoding either murine ANTXR2 or human anthrax toxin receptor 1 (ANTXR1/TEM‐8), toxin and spore challenge susceptibility are restored, indicating that over‐expression of either ANTXR can confer susceptibility to anthrax spore challenge. Taken together, these results indicate that anthrax toxin expression by the germinated spore enables B. anthracis killing of the macrophage from within.