Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical and Cellular Characterization of Helicobacter pylori RecA, a Protein with High-Level Constitutive Expression

ABSTRACT Helicobacter pylori is a bacterial pathogen colonizing half of the world's human population. It has been implicated in a number of gastric diseases, from asymptomatic gastritis to cancer. It is characterized by an amazing genetic variability that results from high mutation rates and efficient DNA homologous recombination and transformation systems. Here, we report the characterization of H. pylori RecA (HpRecA), a protein shown to be involved in DNA repair, transformation, and mouse colonization. The biochemical characterization of the purified recombinase reveals activities similar to those of Escherichia coli RecA (EcRecA). We show that in H. pylori, HpRecA is present in about 80,000 copies per cell during exponential growth and decreases to about 50,000 copies in stationary phase. The amount of HpRecA remains unchanged after induction of DNA lesions, suggesting that HpRecA is always expressed at a high level in order to repair DNA damage or facilitate recombination. We performed HpRecA localization analysis by adding a Flag tag to the protein, revealing two different patterns of localization. During exponential growth, RecA-Flag presents a diffuse pattern, overlapping with the DAPI (4′,6-diamidino-2-phenylindole) staining of DNA, whereas during stationary phase, the protein is present in more defined areas devoid of DAPI staining. These localizations are not affected by inactivation of competence or DNA recombination genes. Neither UV irradiation nor gamma irradiation modified HpRecA localization, suggesting the existence of a constitutive DNA damage adaptation system.
A dynamic-trace-driven simulator for evaluating parallelism

An efficient simulation method is presented that can model the performance of a given algorithm on an idealized multiprocessor while modeling state changes by executing equivalent code on a host processor. Characteristics of the target multiprocessor can be defined independently of the algorithm specification permitting the evaluation of an algorithm over several different machines, or conversely, the performance of a given machine for differing workloads. Performance metrics relating to both hardware and software overheads can be recorded during any given simulation run. The simulator is efficient enough to be run interactively on a current-model superminicomputer. <<ETX>>
Consumer behaviour, feedback information and the supermarket industry.

The purpose of this thesis is threefold: First, to explain how learning shapes consumer behaviour over a comestible (experience) good. Second, to examine the role of feedback information and information aggregation for consumer choices and market performance in markets for experience goods. Third, to understand how firms react to heterogeneous consumer choices in the supermarket industry when faced with institutional constraints. To shed light on how learning influences consumer choices over time in particular when new products or new characteristics are introduced, we employ in Chapter 2 a model of reinforcement learning over products as well as characteristics and apply it to yoghurt drink purchases from a large British consumer panel. We find that learning over both, products and characteristics, is important in explaining consumer choices over time. How consumer choices are influenced by the choice of others is analysed in Chapter 3 which introduces and studies a new model of aggregate information cascades. We find that if only one of two possible actions is observable say, how many others bought a particular product but not how many chose not to buy it only one type of cascade arises in equilibrium. Herding only takes place on the observable action. A different angle on how the provision of information bears on choices is taken in Chapter 4 on learning trust. Here we examine the effect of different forms of feedback information to consumers and sellers in a market with sequential exchange. Experimental evidence shows that both feedback information on sellers' history to consumers but also feedback information about sellers trading history to other sellers improves market efficiency. How firms optimally react to institutional constraints when consumer choice heterogeneity is important is developed in Chapter 5 in a model of supermarket entry into different store formats and applied to data from the UK. We are interested in estimating the cost of the institutional constraint of restrictive planning regulation. We find that the institutional set up matters but the impact of restrictive planning regulation on firm profits is small and increases barriers to entry for large supermarkets only.
Alcohol consumption and colon and rectal cancer in postmenopausal women.

The associations between alcohol and colon and rectal cancers were examined in the Iowa Women's Health Study. In January 1986, 41 837 postmenopausal women, aged 55-69, completed a questionnaire including usual alcohol intake and other information. Through December 1990, 237 incident colon and 75 rectal cancer cases occurred. Mantel-Haenszel age-adjusted relative risks (RR) and 95% confidence intervals (CI) for consumers of < 4.0 and > or = 4.0 g of alcohol per day compared to abstainers were 1.07 (0.61-1.89) and 1.27 (0.72-2.24) (P for trend = 0.46) for rectal cancer. Alcohol intake was inversely associated with distal colon cancer (RR for < 4.0 and > or = 4.0 g of alcohol per day were 0.64 and 0.69 respectively, P for trend = 0.04), which was specific to wine; however, no association was observed with proximal colon cancer (P for trend = 0.94). This is the only report of an inverse association between alcohol and colon cancer in women. Because gut physiology and alcohol metabolism differ between men and women, more research on the association between alcohol and colon cancer in women only, is warranted.
Inspection of Yarn Nep Based on Wavelet Analysis

The yarn nep often shows severe local-extent change of the signal. Because the wavelet transform can inspect the singularity of the signal, we use the wavelet transform to deal with the yarn signal and identify the nep. A new method of identifying the yarn nep based on the wavelet analysis is given in this paper, the result of the experiment shows that identifying rate of the cotton neps can attain 97%.
Analysis of B- and T-cell clonality and HLA class II alleles in patients with idiopathic thrombocytopenic purpura: Correlation with Helicobacter pylori infection and response to eradication treatment

Many authors have recently found a positive correlation between Helicobacter pylori infection and idiopathic thrombocytopenic purpura (ITP), the most common autoimmune hematological disorder. In order to clarify the pathogenic mechanism of H. pylori-associated ITP, we have investigated 52 consecutive ITP adult patients for Helicobacter pylori infection, B- and T-cell clonality and HLA class II alleles. Thirty-four ITP patients (65.4%) were infected by H. pylori and bacterium eradication was accompanied by a long-term platelet response in 17 (53.1%) of them. A B-cell clonality was found in three patients (5.8%, two patients H. pylori-negative and one patient H. pylori-positive). The ITP patients with H. pylori infection showed a HLA–DRB1*11, *14 and –DQB1*03 frequencies significantly higher and a –DRB1*03 frequency significantly lower than in H. pylori-negative patients. Moreover, an HLA–DQB1*03 pattern was associated with a higher probability of platelet response to eradication treatment. If our study documents the efficacy of eradication treatment in H. pylori-infected ITP patients, it may also help to identify different subgroups of ITP patients with probably different pathogeneses of thrombocytopenia and, finally, different responses to eradication treatment.
Nonlinear Predictive Control with Disturbance Observer for Induction Motor Drive

A nonlinear predictive control (NPC) law with a disturbance observer is presented. It is applied to induction motor in order to track speed and flux profiles. The prediction defined on finite horizon is carried out via Taylor series expansion. The load torque is considered as an unknown disturbance and it is estimated by a nonlinear observer. Using the nonlinear predictive control has simplified the structure of the dynamic observer. The combination of the predictive controller and the observer works as a nonlinear controller with an integral action. The stability of the whole system can be achieved by simple design parameters. The simulations show very satisfactory performance of the proposed controller for trajectories tracking, the robustness to parameters variations and the disturbance rejection are successfully achieved
TCRμ Recombination and Transcription Relative to the Conventional TCR during Postnatal Development in Opossums1

Marsupials are a distinct lineage of mammals notable for giving birth to highly altricial (relatively less developed) young. The recent discovery of a unique TCR chain in marsupials, TCRμ, raises questions about its possible role in early development. Here we compare the timing of V(D)J recombination and appearance of TCRμ transcripts relative to the conventional TCRα, β, γ, and δ mRNA during postnatal development in the opossum. There are two TCRμ transcript isoforms, TCRμ1. 0 and TCRμ2. 0. TCRμ1. 0, which uses prejoined V(D)J segments, is detectable as early as day 1, when the thymus is primarily undifferentiated epithelium. The other isoform, TCRμ2. 0, which requires V(D)J recombination and contains an unusual double V configuration, is not detectable until day 13 when the thymus is histologically mature. Surprisingly, we were able to detect TCRα, β, and δ mRNA transcribed from loci that had completed V(D)J recombination as early as day 1 as well. At this early age there is apparent evidence for preference in the V segments used in the TCRα and β genes. In the case of Vα this preference appears to be associated with position in the TCRα/δ locus. In Vβ, however, preference may be due to the use of microhomology in the V, D, and J segments. Mature TCRγ transcripts were not detected until day 8, suggesting that, in contrast to eutherian mammals, in the opossum αβ T cell development precedes γδ T cell development. The results support that there may be differences in T cell subset development between marsupials and placental mammals.
Therapeutic efficacy of Cernilton in benign prostatic hyperplasia patients with histological prostatitis after transurethral resection of the prostate.

OBJECTIVE This study was to prospectively evaluate the therapeutic efficacy of Cernilton in benign prostatic hyperplasia (BPH) patients with histological prostatitis after transurethral resection of the prostate (TURP). MATERIALS AND METHODS One hundred patients with histological prostatitis were recruited from January 2007 to January 2013. All patients were divided into groups A (mild), B (moderate), and C (severe) based on symptom severity, and then randomly subgrouped into Cernilton group and control group. Patients in Cernilton group were treated with Cernilton for 3 months after TURP, while patients in control group received placebo. A series of patient indicators were evaluated before, perioperatively (peri), and after TURP. RESULTS The assessed indicators remained unchanged peri-TURP as compared to those before surgery. 6 months after TURP, indicators remained stable in group A, and significant differences were observed in the International Index of Erectile Function-5 (IIEF-5) in group B and in the storage symptom score (Ss), quality of life (QoL) and IEFF-5 in group C. In addition, there were significant differences in Ss, QoL and IEFF-5 between Cernilton group and control group. CONCLUSION In BPH patients with histological prostatitis after TURP, Cernilton can improve the lower urinary tract symptoms and sexual dysfunction depending on the grade of prostatitis.
CD38 Signaling in T Cells Is Initiated within a Subset of Membrane Rafts Containing Lck and the CD3-ζ Subunit of the T Cell Antigen Receptor*

In this study we present data supporting that most CD38 is pre-assembled in a subset of Brij 98-resistant raft vesicles, which were stable at 37 °C, and have relatively high levels of Lck and the CD3-ζ subunit of T cell antigen receptor-CD3 complex in contrast with a Brij 98-soluble pool, where CD38 is associated with CD3-ζ, and Lck is not detected. Our data further indicate that following CD38 engagement, LAT and Lck are tyrosinephosphorylated exclusively in Brij 98-resistant rafts, and some key signaling components translocate into rafts (i.e. Sos and p85-phosphatidylinositol 3-kinase). Moreover, N-Ras results activated within rafts immediately upon CD38 ligation, whereas activated Erk was mainly found in soluble fractions with delayed kinetics respective to Ras activation. Furthermore, full phosphorylation of CD3-ζ and CD3-ϵ only occurs in rafts, whereas partial CD3-ζ tyrosine phosphorylation occurs exclusively in the soluble pool, which correlated with increased levels of c-Cbl tyrosine phosphorylation in the non-raft fractions. Taken together, these results suggest that, unlike the non-raft pool, CD38 in rafts is able to initiate and propagate several activating signaling pathways, possibly by facilitating critical associations within other raft subsets, for example, LAT rafts via its capacity to interact with Lck and CD3-ζ. Overall, these findings provide the first evidence that CD38 operates in two functionally distinct microdomains of the plasma membrane.
New strategy for expression of recombinant hydroxylated human collagen α1(III) chains in Pichia pastoris GS115

Type III collagen is one of the most abundant proteins in the human body, which forms collagen fibrils and provides the stiff, resilient characteristics of many tissues. In this paper, a new method for secretory expression of recombinant hydroxylated human collagen α1(III) chain in Pichia pastoris GS115 was applied. The gene encoding for full‐length human collagen α1(III) chain (COL3A1) without N‐terminal propeptide and C‐terminal propeptide was cloned in the pPIC9K expression vector. The prolyl 4‐hydroxylase (P4H, EC 1.14.11.2) α‐subunit (P4Hα) and β‐subunit (P4Hβ) genes were cloned in the same expression vector, pPICZB. Fluorogenic quantitative PCR indicates that COL3A1 and P4H genes have been expressed in mRNA level. SDS‐PAGE shows that secretory expression of recombinant human collagen α1(III) chain was successfully achieved in P. pastoris GS115. In addition, the result of amino acids composition analysis shows that the recombinant human collagen α1(III) chain contains hydroxyproline by coexpression with the P4H. Furthermore, liquid chromatography coupled with tandem mass spectrometry analysis demonstrates that proline residues of the recombinant human collagen α1(III) chain were hydroxylated in the X or Y positions of Gly–X–Y triplets.
Are LNG regasification facilities a financially viable investment to diversify natural gas markets

This thesis looks at the value of having the option to buy gas on the world Liquiﬁed Natural Gas-market rather than just relying on one distributor via pipeline. The world market for natural gas is characterized by rigid distribution methods and there is no short term ﬂexibility of destination for the seller and almost no possibility for buyers to buy gas on a competitive market. The investment is evaluated using real option analysis. The computational method for the valuation is Monte Carlo simulations and pipeline gas prices and Liquid Natural Gas prices will be modelled through stochastic modelling and the prices are assumed to be characterized by mean reversion and price convergence. The model will be developed following Yepes Rodriguez (2008) model of natural gas price progression. The main conclusion is that he value of investing in a regasiﬁcation facility is found to be positive and that LNG regasiﬁcation facilities a ﬁnancially viable investments to diversify natural gas markets.
Programmable NoC scheduling based on multi-core processor

Traditional multi-processor interconnection structure can not be suitable for highly integrated SoC multi-core processor because of high resource overhead, and NoC can solve the problem of multi-core processor interconnection on SoC with high-bandwidth, low power, scalability and parallel communication. Based on multi-core NoC simulation platform, task-oriented NoC scheduling policy is proposed, and median filter algorithm is optimized as typical application for parallel scheduling. SoClib simulation platform with SystemC language is used for validation and analysis variation of multi-core NoC speedup when cores number is changed.
Mitochondrial Aconitase Is a Source of Hydroxyl Radical

Mitochondrial aconitase (m-aconitase) contains a [4Fe-4S]2+ cluster in its active site that catalyzes the stereospecific dehydration-rehydration of citrate to isocitrate in the Krebs cycle. It has been proposed that the [4Fe-4S]2+ aconitase is oxidized by superoxide, generating the inactive [3Fe-4S]1+ aconitase. In this reaction, the likely products are iron(II) and hydrogen peroxide. Consequently, the inactivation of m-aconitase by superoxide may increase the formation of hydroxyl radical (⋅OH) through the Fenton reaction in mitochondria. In this work, evidence for the generation of ⋅OH from the reaction of m-aconitase with superoxide is provided using ESR spin trapping experiments with 5-diethoxyphosphoryl-5-methyl-1-pyrroline N-oxide and α-phenyl-N-tert-butylnitrone. Formation of free ⋅OH was verified with the ⋅OH scavenger Me2SO, which forms methyl radical upon reacting with⋅OH. The addition of Me2SO to incubation mixtures containing m-aconitase and xanthine/xanthine oxidase yielded methyl radical, which was detected by ESR spin trapping. Methyl radical formation was further confirmed using [13C]Me2SO. Parallel low temperature ESR experiments demonstrated that the generation of the [3Fe-4S]1+ cluster increased with increasing additions of superoxide to m-aconitase. This reaction was reversible, as >90% of the initial aconitase activity was recovered upon treatment with glutathione and iron(II). This mechanism presents a scenario in which⋅OH may be continuously generated in the mitochondria.
Transverse relaxation and magnetization transfer in skeletal muscle: Effect of pH

Exercise increases the intracellular T2 (T2,i) of contracting muscles. The mechanism(s) for the T2,i increase have not been fully described, and may include increased intracellular free water and acidification. These changes may alter chemical exchange processes between intracellular free water and proteins. In this study, the hypotheses were tested that (a) pH changes T2,i by affecting the rate of magnetization transfer (MT) between free intracellular water and intracellular proteins, and (b) the magnitude of the T2,i effect depends on acquisition mode (localized or nonlocalized) and echo spacing. Frog gastrocnemius muscles were excised and their intracellular pH was either kept at physiological pH (7.0) or modified to model exercising muscle (pH 6.5). The intracellular transverse relaxation rate (R2,i = 1/T2,i) always decreased in the acidic muscles, but the changes were greater when measured using more rapid refocusing rates. The MT rate from the macromolecular proton pool to the free water proton pool, its reverse rate, and the spin‐lattice relaxation rate of water decreased in acidic muscles. It is concluded that intracellular acidification alters the R2,i of muscle water in a refocusing rate‐dependent manner, and that the R2,i changes are correlated with changes in the MT rate between macromolecules and free intracellular water. Magn Reson Med, 2009. © 2008 Wiley‐Liss, Inc.
Trajectories of language delay from age 3 to 5: persistence, recovery and late onset.

BACKGROUND Knowledge is scarce on what contributes to whether children with early language delay (LD) show persistent, recovering or sometimes late-onset LD without a prior history of early LD in subsequent preschool years. AIMS To explore whether an integrative model of vital risk factors, including poor early communication skills, family history of language-related difficulties and male gender, predicts the development of persistent, recovering or late-onset LD trajectories from 3 to 5 years quantitatively and qualitatively differently. METHODS & PROCEDURES LD was assessed by maternal reports on the Ages and Stages Questionnaire at 3 and 5 years for 10 587 children in The Norwegian Mother and Child Cohort Study. Children were classified across time as having no, late onset, transient or persistent LD. Multinomial logistic regression analyses included the integrative model of vital risk factors and covariates. OUTCOME & RESULTS Across time, 3%, 5% and 6.5% of the children displayed persistent, transient and late-onset LD, respectively. The odds for persistent LD were doubled for boys and children with low language comprehension at 1.5 years; and tripled by late-talking familial risk. These same odds decreased for transient LD, and even further for late-onset LD. Familial risk for writing and reading difficulties especially increased the odds for late-onset and persistent LD, while familial risk of unintelligible speech increased the odds for transient LD. Although girls had on average far better language comprehension than boys, low language comprehension was a stronger risk factor for persistent LD in girls. CONCLUSIONS & IMPLICATIONS Preschool LD trajectories were uniquely predicted from the integrative risk model of poor early communicative skills, family history and male gender. This might benefit identification of different LD trajectories by supporting broader severe vulnerability for persistent LD, milder vulnerability for transient LD, and possibly a specific risk for reading and learning difficulties for children with late-onset LD.
Factors Influencing Germination of Bacillus subtilis Spores via Activation of Nutrient Receptors by High Pressure

ABSTRACT Different nutrient receptors varied in triggering germination of Bacillus subtilis spores with a pressure of 150 MPa, the GerA receptor being more responsive than the GerB receptor and even more responsive than the GerK receptor. This hierarchy in receptor responsiveness to pressure was the same as receptor responsiveness to a mixture of nutrients. The levels of nutrient receptors influenced rates of pressure germination, since the GerA receptor is more abundant than the GerB receptor and elevated levels of individual receptors increased spore germination by 150 MPa of pressure. However, GerB receptor variants with relaxed specificity for nutrient germinants responded as well as the GerA receptor to this pressure. Spores lacking dipicolinic acid did not germinate with this pressure, and pressure activation of the GerA receptor required covalent addition of diacylglycerol. However, pressure activation of the GerB and GerK receptors displayed only a partial (GerB) or no (GerK) diacylglycerylation requirement. These effects of receptor diacylglycerylation on pressure germination are similar to those on nutrient germination. Wild-type spores prepared at higher temperatures germinated more rapidly with a pressure of 150 MPa than spores prepared at lower temperatures; this was also true for spores with only one receptor, but receptor levels did not increase in spores made at higher temperatures. Changes in inner membrane unsaturated fatty acid levels, lethal treatment with oxidizing agents, or exposure to chemicals that inhibit nutrient germination had no major effect on spore germination by 150 MPa of pressure, except for strong inhibition by HgCl2.
Hotel Productivity: The McKinsey Global Institute Study

Pagtl 1/8 Peter Jones is the Charles Forte Chair of Hotel Management and responsible for the work of the Centre for Hospitality Industry Productivity Research at the University of Surrey. He is the author, editor, co-author or co-editor of nine textbooks and over 30 journal articles in journals ranging from the International Journal of Service Industry Management to the Cornell HRA Quarterly. He has been a consultant to industry firms, professional associations and educational institutions in the field of hospitality management.