Miracle-dz/UniFAR-FTUs huggingface dataset:
BdlA, a Chemotaxis Regulator Essential for Biofilm Dispersion in Pseudomonas aeruginosa

ABSTRACT Multiple environmental cues have been shown to trigger biofilm detachment, the transition from surface-attached, highly organized communities known as biofilms to the motile lifestyle. The goal of this study was to identify a gene product involved in sensing environmental cues that trigger biofilm dispersion in Pseudomonas aeruginosa. To do so, we focused on novel putative chemotaxis transducer proteins that could potentially be involved in environmental sensing. We identified a locus encoding such a protein that played a role in detachment, as indicated by the observation that an isogenic mutant biofilm could not disperse in response to a variety of environmental cues. The locus was termed bdlA for biofilm dispersion locus. The BdlA protein harbors an MCP (methyl-accepting chemotaxis protein) domain and two PAS (Per-Arnt-Sint) domains that have been shown to be essential for responding to environmental signals in other proteins. The dispersion-deficient phenotype of the bdlA mutant was confirmed by treatment with the biocide H2O2 and by microscopic observations. The dispersion response was independent of motility. bdlA mutant biofilms were found to have increased adherent properties and increased intracellular levels of cyclic di-GMP (c-di-GMP). Our findings suggest that BdlA may be a link between sensing environmental cues, c-di-GMP levels, and detachment. Based on our findings, a possible involvement of BdlA in a signaling cascade resulting in biofilm dispersion is discussed.
Can neuroimaging help identify effective strategies for constraint therapy in congenital hemiparesis?

a higher risk of cognitive involvement. The involvement of the basal ganglia and thalami (reported in previous studies to be one of the cofactors determining hemiplegia in perinatal arterial infarcts) appears to also play a role in cognitive function, as suggested by the linear regression used in the study. These findings provide further evidence of the possible role of the basal ganglia in modulating brain plasticity at the time of perinatal lesions. The longitudinal study uses both early neurodevelopmental assessments and school-age cognitive tests in children with perinatal arterial infarcts to provide evidence of a decline in cognitive function over time, probably related to difficulties with higher-level cognitive skills that only become obvious at school age. These findings help to clarify the apparent discrepancy between previous studies reporting little evidence of cognitive difficulties in young and preschool children and others showing evidence of cognitive impairment in children assessed at different ages. The study also suggests that postnatal factors, such as epilepsy and/or antiepilepetic drugs, may also influence the risk of developing cognitive difficulties. In summary, the study improves our knowledge on the mechanisms underlying cognitive difficulties in neonatal brain focal lesions, suggesting that the type and the site of lesions, the age at assessment, and postnatal factors (such as epilepsy or antiepileptic drugs) may all contribute to cognitive difficulties. Further studies in larger cohorts allowing multivariate analysis will help to establish the effect of each of these variables and the possible co-dependence of some of these factors (e.g. thalamic lesions and epilepsy).
Fast self-resonant startup procedure for digital MEMS gyroscope system

This paper describes a control procedure for the startup of a digital MEMS gyroscope system. Unlike the normal operating mode in which the gyroscope is actuated by synthesized sinusoidal drive signal, self-resonance of the gyroscope is stimulated by feeding back the drive-sense signal and converting it to a square-wave drive signal. During this procedure the resonant frequency that is near the natural frequency of the gyroscope can be calculated, and then provides a key parameter for the sinusoidal wave synthesizer, which will generate high-quality reference signals for driving and demodulation. Experiment shows a rapid rising of the magnitude of vibration, resulting a faster startup procedure for the system.
A comparison of chronic pain prevalence in Japan, Thailand, and myanmar.

BACKGROUND Pain has been regarded as important in the improvement of quality of life (QOL). In the advanced countries of Europe and the North America, a number of large-scale epidemiological surveys on pain, particularly chronic pain, have thus been performed in general populations. However, few epidemiological surveys of chronic pain have been reported from developing countries, and no surveys appear to have examined chronic pain in the least developed countries. OBJECTIVES To compare the incidence of chronic pain in Asian countries, using Japan as an advanced country, Thailand as a developing country, and Myanmar as one of the least developed countries. STUDY DESIGN Cross-sectional study in 4 hospitals. SETTING A university hospital and a general hospital in Japan, a university hospital in Thailand, and a general hospital in Myanmar. METHODS Patients were 1,000 nursing staff working in Japan, 448 nursing staff working in Thailand, and 405 nursing staff working in Myanmar. The survey was performed by requesting all nursing staff to anonymously answer the questionnaire. Data were used to calculate chronic pain prevalence, pain site, presence or absence of consultation with doctors, methods of handling pain other than consultation with doctors, and whether pain was controlled for each country. The results were then compared between countries. RESULTS The prevalence of chronic pain in Myanmar was 5.9%, which was significantly lower (P < 0.01) than in Japan (17.5%) or Thailand (19.9%). The most frequent pain sites were the lower back, head, and shoulders in Japan, and the shoulders, ankle, upper back, and head in Thailand, whereas in Myanmar, no clear certain tendencies were observed. The most frequent method for handling pain other than consultation with doctors was over-the-counter drugs in Japan, massage in Thailand, and relaxation therapy (meditation) in Myanmar. LIMITATIONS Limitations of this study were the cross-sectional design study, the small number of hospitals included, the limitation of patients to nursing staff, and the omission from the questionnaire of questions regarding body height and weight, working situation, family background, trauma history, sports activity history, smoking history, psychological/character tests, QOL, and pain levels of patients. CONCLUSION The prevalence of chronic pain was significantly lower in Myanmar than in Japan or Thailand. With regard to the site and treatment of chronic pain, no clear tendencies were observed between countries, suggesting that frequency and the character of chronic pain differ from country to country around the world.
Modeling click-through based word-pairs for web search

Statistical translation models and latent semantic analysis (LSA) are two effective approaches to exploit click-through data for web search ranking. This paper presents two document ranking models that combine both approaches by explicitly modeling word-pairs. The first model, called PairModel, is a monolingual ranking model based on word pairs that are derived from click-through data. It maps queries and documents into a concept space spanned by these word pairs. The second model, called Bilingual Paired Topic Model (BPTM), uses bilingual word pairs and jointly models a bilingual query-document collection. This model maps queries and documents in multiple languages into a lower dimensional semantic subspace. Experimental results on web search task show that they significantly outperform the state-of-the-art baseline models, and the best result is obtained by interpolating PairModel and BPTM.
The Role of Religious Values : Young Christians ’ Opinions towards Tattoos

Since the 1960s tattooing has become increasingly popular in mainstream American society (Rubin, 1988; Schildkrout, 2004). Explanations for this phenomenon include expressing individuality and gaining acceptance into a subculture (Blanchard, 1991; Gagne & Orend, 2009). Although research has demonstrated that spirituality can influence tattooing practices (Caplan, 2000; Swartz, 2006), few studies explore the intersection between Christian beliefs and tattoos (Scheinfeld, 2007). My research focused on the relationship between tattooing practices and the changing values of 18 to 30 year old active Christians in Greenville, NC. For this study, an active Christian was defined as a person who participates in his or her faith community at least three times per month. A class project during a previous semester facilitated the proposal development, including a literature review of tattoos and Christianity and the design of the data collection instrument, asking questions on personal faith, Bible verse interpretations, tattoo stereotypes, tattoo symbolism, and opinions about tattoos. Data were collected using a semi-structured interview instrument which asked open-ended questions, including free-listing tasks (Bernard, 2011; Brewer, 2002). To increase comparability, all informants were recruited from the same non-denominational Christian organization in Greenville, NC (Bernard, 2011). A quota sample was employed to reflect differences by gender and preference for tattoos (Bernard, 2011). Interviews were recorded and transcribed. The resulting text was coded using a grounded theory approach, logging discoveries about frequencies and co-occurrences of themes to establish similarities and differences between study participants (Bernard, 2011). A model of young Christian’s beliefs and values that suggests possible reasons for the choice for or against a tattoo was discussed.
Blockade of vascular endothelial growth factor receptor-3 signaling inhibits fibroblast growth factor-2-induced lymphangiogenesis in mouse cornea

Vascular endothelial growth factor receptor-3 (VEGFR-3) is a major mediator of lymphangiogenesis. Recently, VEGFR-3 ligands, VEGF-C, and VEGF-D were reported to promote tumor lymphangiogenesis and lymphatic metastasis, and these processes were inhibited by blocking of the VEGFR-3-signaling pathway. Here, we have adapted the mouse corneal angiogenesis assay to study potential lymphangiogenic factors and inhibitors. Immunohistochemical analysis with lymphatic endothelial markers showed that VEGF-C induces lymphatic as well as blood vessel growth in the cornea. By contrast, VEGF induced angiogenesis but not lymphangiogenesis. Fibroblast growth factor-2 (FGF-2) stimulated both lymphangiogenesis and angiogenesis. FGF-2 up-regulated VEGF-C expression in vascular endothelial and perivascular cells. Furthermore, administration of blocking anti-VEGFR-3 antibodies inhibited the FGF-2-induced lymphangiogenesis. These findings show that VEGFR-3 can mediate lymphangiogenesis induced by other growth factors. Because increased expression of FGF-2 and VEGF-C has been associated with lymphatic metastasis, our results provide a potential strategy for the inhibition of lymphatic metastasis in cancer therapy.
Encoding Organizational Source and Associative Source under Incidental and Intentional Learning Conditions

The present study aimed at providing a plausible answer for the controversy whether organizational source or associative source could be encoded in a more automatic manner through incidental learning. In the experiment, subjects were asked to learn organizational and associative sources under incidental or intentional learning conditions. It turned out that only associative source accuracy increased when subjects were instructed to intentionally learn that source, which implied that associative source might be encoded in a more effortful way, whereas processing of organizational source might be performed incidentally.
16 S rRNA Sequencing An integrated research solution for bacterial identification using 16 S rRNA sequencing on the Ion PGM TM System with Ion Reporter

• Three reference query options classify individual reads via alignment to either the premium curated MicroSEQ® ID or curated Greengenes databases as well as an optimal two-step alignment that utilizes both databases Introduction Understanding the diversity of bacterial communities, in almost any environment, has been greatly facilitated by rapid advances in nextgeneration sequencing (NGS) technologies and associated bioinformatics approaches. Research using 16S ribosomal RNA (rRNA) sequencing is a fast, inexpensive profiling technique based on variation in the bacterial 16S rRNA gene. This method has a wide range of uses, including the characterization of bacterial populations, taxonomical analysis, and species identification. For example, the Ion PGMTM System was used to characterize bacterial communities important for research in human health using archived samples from a diversity of sites including the mouth [1, 2], airway [3, 4], diabetic mycetoma (or “Madura foot”) [5], meconium [6], the hands of healthcare workers [7], brain abscesses [8], and the human and murine intestinal tract [9, 10, 11, 12]. 16S rRNA Sequencing
Suppressive effects of trihexyphenidyl on methamphetamine‐induced dopamine release as measured by in vivo microdialysis

Abuse of methamphetamine (MAP) and cocaine causes severe medical and social problems throughout the world. Our previous study found that trihexyphenidyl (THP), a muscarinic cholinergic receptor antagonist, specifically suppressed the rewarding properties of MAP but not of cocaine, as measured by conditioned place preference in mice. The present study examined using in vivo microdialysis whether THP differentially affects the extracellular dopamine (DA) levels in the nucleus accumbens and striatum of mice injected with MAP and cocaine in comparison with another antimuscarinic agent, scopolamine (SCP). In addition, locomotor activity was simultaneously measured during microdialysis. In vivo microdialysis experiments revealed that during the initial hour after injection of MAP (1 mg/kg) DA levels increased up to 698% in the nucleus accumbens and 367% in the striatum as compared to the basal level. These increases were reduced to 293% in the nucleus accumbens and 207% in the striatum by treatment with 5 mg/kg THP. However, SCP (3 mg/kg) had no effect on the increases in extracellular DA levels in both regions after MAP injection. Cocaine (10 mg/kg) increased DA levels during the initial hour to 254% in the nucleus accumbens and 220% in the striatum as compared to the basal level. These increases were unaffected by treatment with either THP or SCP. On the contrary, both THP and SCP enhanced the locomotor‐stimulant action of MAP and cocaine. These results, together with our previous finding, suggest that THP may specifically antagonize the rewarding properties of MAP through suppression of DA release in the mesolimbic area without retarding locomotor activity. Synapse 49:47–54, 2003. © 2003 Wiley‐Liss, Inc.
Assessing Fit of Alternative Unidimensional Polytomous IRT Models Using Posterior Predictive Model Checking

This article explored the application of the posterior predictive model checking (PPMC) method in assessing fit for unidimensional polytomous item response theory (IRT) models, specifically the divide-by-total models (e.g., the generalized partial credit model). Previous research has primarily focused on using PPMC in model checking for unidimensional and multidimensional IRT models for dichotomous data, and has paid little attention to polytomous models. A Monte Carlo simulation was conducted to investigate the performance of PPMC in detecting different sources of misfit for the partial credit model family. Results showed that the PPMC method, in combination with appropriate discrepancy measures, had adequate power in detecting different sources of misfit for the partial credit model family. Global odds ratio and item total correlation exhibited specific patterns in detecting the absence of the slope parameter, whereas Yen’s Q1 was found to be promising in the detection of misfit caused by the constant category intersection parameter constraint across items.
Flow Cytometric FRET Analysis of ErbB Receptor Tyrosine Kinase Interaction

The homologous and heterologous interaction of members of the epidermal growth factor (EGF)–related receptor tyrosine kinase (RTK) family (ErbB or HER family receptors) upon ligand binding is the initial key event in signal transduction by these receptors. In addition to the availability of their respective ligands, the relative expression level of the four ErbB receptors triggers receptor cross‐activation, which determines signal diversification and the cells' biological response. However, the function of ErbB receptors and their ligands appears highly complex, and its impact on cell growth and proliferation of normal and tumor cells is incompletely understood. Flow cytometric fluorescence resonance energy transfer (FRET) measurements facilitate the quantitative analysis of receptor interaction. This unit delineates the cell‐by‐cell analysis of epidermal growth factor receptor (EGFR, ErbB1, HER1) and ErbB2 (HER2) receptor interaction in ErbB2‐overexpressing BT474 and SK‐BR‐3 breast cancer cell lines, using a dual‐laser flow cytometer. ReFlex software–based quantification of energy transfer efficiency (E) directly reflects the amount of receptor interaction. Curr. Protocol. Cytom. 45:12.14. 1‐12.14. 19. © 2008 by John Wiley & Sons, Inc.
Sonocrystallization: The Use of Ultrasound for Improved Industrial Crystallization

An overview of the application of power ultrasound to crystallization of organic molecules, and the equipment developed in recent years in which sonocrystallization and sonochemistry may be carried out at industrial scale, is presented. It includes both results from the research and development programs carried out by us and a survey of developments in the field more generally. The most important effect of ultrasound on crystallization is the induction of nucleation and the principal benefits derived from an ability to manipulate this effect. The reported effects of ultrasound on crystal nucleation and growth have been briefly reviewed, and examples are given of physical properties of the products having been manipulated by varying and controlling the insonation regime. New applications, directions, and developments have been identified. Developments in scale-up methods and available equipment have also been reviewed. It is the availability of robust large-scale equipment that has been critical to establi.
Physical Activity, Tumor PTGS2 Expression, and Survival in Patients with Colorectal Cancer

Background: Higher levels of physical activity are associated with lower colorectal carcinoma incidence and mortality, perhaps through influencing energy balance, cellular prosta7 systemic inflammation. Although evidence suggests interactive effects of energetics, sedentary lifestyle, and tumor CTNNB1 (β-catenin) or CDKN1B (p27) status on colon cancer prognosis, interactive effects of physical activity and tumor PTGS2 (the official symbol for COX-2) status on clinical outcome remain unknown. Methods: Using molecular pathological epidemiology database of 605 stage I–III colon and rectal cancers in two prospective cohort studies (the Nurse's Health Study and the Health Professionals Follow-up Study), we examined patient survival according to postdiagnosis physical activity and tumor PTGS2 status (with 382 PTGS2-positive and 223 PTGS2-negative tumors by immunohistochemistry). Cox proportional hazards models were used to calculate colorectal cancer-specific mortality HR, adjusting for clinical and other tumor variables including microsatellite instability status. Results: Among PTGS2-positive cases, compared with the least active first quartile, the multivariate HRs (95% confidence interval) were 0.30 (0.14–0.62) for the second, 0.38 (0.20–0.71) for the third, and 0.18 (0.08–0.41) for the fourth quartile of physical activity level (Ptrend = 0.0002). In contrast, among PTGS2-negative cases, physical activity level was not significantly associated with survival (Ptrend = 0.84; Pinteraction = 0.024, between physical activity and tumor PTGS2 status). Conclusions: Postdiagnosis physical activity is associated with better survival among patients with PTGS2-positive tumors but not among patients with PTGS2-negative tumors. Impact: Immunohistochemical PTGS2 expression in colorectal carcinoma may serve as a predictive biomarker in pathology practice, which may predict stronger benefit from exercise. Cancer Epidemiol Biomarkers Prev; 22(6); 1142–52. ©2013 AACR.
Phonological Distance Measures*

Abstract Phonological distance can be measured computationally using formally specified algorithms. This work investigates two such measures, one developed by Nerbonne and Heeringa (1997) based on Levenshtein distance (Levenshtein, 1965) and the other an adaptation of Dunning's (1994) language classifier that uses maximum likelihood distance. These two measures are compared against naïve transcriptions of the speech of paediatric cochlear implant users. The new measure, maximum likelihood distance, correlates highly with Levenshtein distance and naïve transcriptions; results from this corpus are easier to obtain since cochlear implant speech has a lower intelligibility than the usually high intelligibility of the speech of a different dialect.
p53-dependent association between cyclin G and the B' subunit of protein phosphatase 2A

We and others previously showed that cyclin G is a transcriptional target of the p53 tumor suppressor protein. However, cellular proteins which might form a complex with cyclin G have not yet been identified. To gain insight into the biological role of cyclin G, we used the yeast two-hybrid screen and isolated two mouse cDNAs encoding cyclin G-interacting proteins. Interestingly, both positive cDNAs encoded B' regulatory subunits of protein phosphatase 2A (PP2A). One clone encodes B'alpha, while the other clone codes for a new member of the B' family, B'beta. B'beta is 70% identical to other members of the B' family. B'alpha associated both in vitro and in vivo with cyclin G but not with the other mammalian cyclins. Furthermore, cyclin G formed a complex with B'alpha only after induction of p53 in p53 temperature-sensitive cell lines. These results indicate that cyclin G forms a specific complex with the B' subunit of PP2A and that complex formation is regulated by p53. Potential roles for the cyclin G-B' complex in p53-mediated pathways are discussed.
Process‐Improvement Cost Model for the Emergency Department

EXECUTIVE SUMMARY The objective of this report is to present a simplified, activity‐based costing approach for hospital emergency departments (EDs) to use with Lean Six Sigma cost‐benefit analyses. The cost model complexity is reduced by removing diagnostic and condition‐specific costs, thereby revealing the underlying process activities' cost inefficiencies. Examples are provided for evaluating the cost savings from reducing discharge delays and the cost impact of keeping patients in the ED (boarding) after the decision to admit has been made. The process‐improvement cost model provides a needed tool in selecting, prioritizing, and validating Lean process‐improvement projects in the ED and other areas of patient care that involve multiple dissimilar diagnoses.