Miracle-dz/UniFAR-FTUs huggingface dataset:
Streptococcus sanguinis Class Ib Ribonucleotide Reductase

Background: Class Ib ribonucleotide reductase (RNR) is an essential enzyme for aerobic growth of S. sanguinis. Results: Its manganese form is 3.5-fold more active than the iron form when assayed with NrdH and thioredoxin reductase. Conclusion: This specific activity is the highest reported to date for the class Ib RNR. Significance: Our studies suggest why manganese is important in streptococcal pathogenesis. Streptococcus sanguinis is a causative agent of infective endocarditis. Deletion of SsaB, a manganese transporter, drastically reduces S. sanguinis virulence. Many pathogenic organisms require class Ib ribonucleotide reductase (RNR) to catalyze the conversion of nucleotides to deoxynucleotides under aerobic conditions, and recent studies demonstrate that this enzyme uses a dimanganese-tyrosyl radical (MnIII2-Y•) cofactor in vivo. The proteins required for S. sanguinis ribonucleotide reduction (NrdE and NrdF, α and β subunits of RNR; NrdH and TrxR, a glutaredoxin-like thioredoxin and a thioredoxin reductase; and NrdI, a flavodoxin essential for assembly of the RNR metallo-cofactor) have been identified and characterized. Apo-NrdF with FeII and O2 can self-assemble a diferric-tyrosyl radical (FeIII2-Y•) cofactor (1.2 Y•/β2) and with the help of NrdI can assemble a MnIII2-Y• cofactor (0.9 Y•/β2). The activity of RNR with its endogenous reductants, NrdH and TrxR, is 5,000 and 1,500 units/mg for the Mn- and Fe-NrdFs (Fe-loaded NrdF), respectively. X-ray structures of S. sanguinis NrdIox and MnII2-NrdF are reported and provide a possible rationale for the weak affinity (2.9 μm) between them. These streptococcal proteins form a structurally distinct subclass relative to other Ib proteins with unique features likely important in cluster assembly, including a long and negatively charged loop near the NrdI flavin and a bulky residue (Thr) at a constriction in the oxidant channel to the NrdI interface. These studies set the stage for identifying the active form of S. sanguinis class Ib RNR in an animal model for infective endocarditis and establishing whether the manganese requirement for pathogenesis is associated with RNR.
Pronunciation instruction in English as a foreign language contexts : a review of goals and best practices

With the spread of English as an international language, near native-like accuracy is no longer regarded as a necessary goal for the pronunciation class. This Report discusses the current status and goals of pronunciation instruction in ESL and EFL contexts. Second, it reviews research findings supporting the new focus on intelligibility, and examines instructors’ pedagogical challenges and opinions on how to teach English pronunciation. Third, it evaluates Korean textbooks currently used to teach English pronunciation in Korea and discusses how instructional materials and resources can enhance oral proficiency in EFL contexts. Lastly, it presents a list of pedagogical implications and suggests a best practices approach to English pronunciation instruction in EFL contexts.
The American Community Survey: Warmer (More Current), but Fuzzier (Less Precise) than the Decennial Census

Abstract The American Community Survey, which will replace data many planners rely on from the decennial Census long form, is finally in progress. The first nationwide data for places of 65,000 or more was released in the summer of 2006. It has several interesting implications for planning. On the one hand, more current data will eliminate many of the inaccuracies introduced by projection-based updates of stale census data. On the other, smaller sample sizes will mean we will have less precise estimates. Because the ACS will use averaged rather than point-in-time data, it will measure slightly different things than the decennial census. Finally, planners should be alert to the opportunities they will have to improve local data quality by improving the address file from which the sample is drawn.
Prevalence and clinical correlates of white coat hypertension in chronic kidney disease.

BACKGROUND The role of white coat hypertension (WCH) in the poor control of blood pressure (BP) in chronic kidney disease (CKD) is ill defined. METHODS We measured systolic clinical (CBP) and ambulatory blood pressure (ABP) in 290 consecutive patients with non-dialysis CKD [glomerular filtration rate (GFR) <60 ml/min/1.73 m(2)]. We defined normotension (NOR) if CBP and daytime ABP <130 mmHg, sustained hypertension (SH) when both BP >or=130 mmHg, WCH if only daytime ABP <130 mmHg, and masked hypertension (MH) when only CBP <130 mmHg. RESULTS NOR patients were 15.5%, WCH 31.7%, SH 46.9% and MH 5.9%. Due to the high prevalence of WCH, achievement of BP target (<130 mmHg) was more than doubled by daytime ABP than CBP (47.2 vs 21.4%). WCH was characterized by prevalence of diabetes (31.5%), left ventricular hypertrophy (LVH; 50.0%) and CBP values (146 +/- 12 mmHg) lower than in SH (41.9%, 71.3% and 158 +/- 18 mmHg) but greater than in NOR (17.8%, 37.8% and 118 +/- 7 mmHg). Among patients with CBP >or=130 mmHg, the independent risk of having SH rather than WCH increased in the presence of higher CBP [Odds ration (OR) 1.61, 95% confidence intervals (CI) 1.29-2.02], LVH (OR 1.94, 95% CI 1.03-3.63) and proteinuria (OR 3.12, 95% CI 1.31-7.43). In the WCH group, 24 h, daytime and nighttime ABP were 118 +/- 7/68 +/- 8, 120 +/- 7/71 +/- 8 and 112 +/- 12/63 +/- 9 mmHg, respectively. CONCLUSIONS In CKD, WCH is highly prevalent and can be predicted in the absence of higher CBP, LVH and proteinuria. In these patients, pursuing a low BP target may not be safe because of the risk of cardio-renal hypoperfusion especially at nighttime.
Scheduled exposures to a novel environment with a running‐wheel differentially accelerate re‐entrainment of mice peripheral clocks to new light–dark cycles

Effects of scheduled exposures to novel environment with a running‐wheel were examined on re‐entrainment to 8 h shifted light–dark (LD) cycles of mouse circadian rhythms in locomotor activity and clock gene, Per1, expression in the suprachiasmatic nucleus (SCN) and peripheral tissues. Per1 expression was monitored by a bioluminescence reporter introduced into mice. The animals were exposed to the novel environment for 3 h from the shifted dark onset for four cycles and released into constant darkness. In the phase‐advance shift, the circadian rhythm in locomotor activity fully re‐entrained in the exposed group, whereas it was in transients in the control. On the other hand, the circadian rhythm of Per1 expression in the SCN almost completely re‐entrained in both the control and exposed groups. In the skeletal muscle and lung, the circadian rhythm fully re‐entrained in the exposed group, whereas the rhythms in the control did not. In the phase‐delay shift, the circadian rhythms in locomotor activity and Per1 expression almost completely re‐entrained in both groups. These findings indicate that the scheduled exposures to novel environment with a running‐wheel differentially accelerate the re‐entrainment of the mouse peripheral clocks to 8 h phase‐advanced LD cycles.
Spanning the scales of mechanical metamaterials using time domain simulations in transformed crystals, graphene flakes and structured soils

We begin with a brief historical survey of discoveries of quasi-crystals and graphene, and then introduce the concept of transformation crystallography, which consists of the application of geometric transforms to periodic structures. We consider motifs with three-fold, four-fold and six-fold symmetries according to the crystallographic restriction theorem. Furthermore, we define motifs with five-fold symmetry such as quasi-crystals generated by a cut-and-projection method from periodic structures in higher-dimensional space. We analyze elastic wave propagation in the transformed crystals and (Penrose-type) quasi-crystals with the finite difference time domain freeware SimSonic. We consider geometric transforms underpinning the design of seismic cloaks with square, circular, elliptical and peanut shapes in the context of honeycomb crystals that can be viewed as scaled-up versions of graphene. Interestingly, the use of morphing techniques leads to the design of cloaks with interpolated geometries reminiscent of Victor Vasarely’s artwork. Employing the case of transformed graphene-like (honeycomb) structures allows one to draw useful analogies between large-scale seismic metamaterials such as soils structured with columns of concrete or grout with soil and nanoscale biochemical metamaterials. We further identify similarities in designs of cloaks for elastodynamic and hydrodynamic waves and cloaks for diffusion (heat or mass) processes, as these are underpinned by geometric transforms. Experimental data extracted from field test analysis of soil structured with boreholes demonstrates the application of crystallography to large scale phononic crystals, coined as seismic metamaterials, as they might exhibit low frequency stop bands. This brings us to the outlook of mechanical metamaterials, with control of phonon emission in graphene through extreme anisotropy, attenuation of vibrations of suspension bridges via low frequency stop bands and the concept of transformed meta-cities. We conclude that these novel materials hold strong applications spanning different disciplines or across different scales from biophysics to geophysics.
Economic Analysis of Infrastructure Investment and Irrigation Budget Issues in a Southwestern U.S. Water Utility

The three chapters of this dissertation investigate two policy issues faced by water utilities: infrastructure investment and water budget programs. Water utilities have infrastructure that is deteriorating at an increasing rate, necessitating higher rates of investment from ratepayers. At the same time utilities must improve their management of existing water supplies in order to postpone the need to procure water supplies with a higher marginal cost. Water budgets are a way to manage scarce water resources more efficiently. The first chapter focuses on customer preferences for infrastructure investments. Individuals are willing-to-pay to have fewer outages at home, shorter average outage lengths, greater advance notification, more urban greenspace
Physiology and Pathophysiology of Physical Inactivity Does physical inactivity cause nonalcoholic fatty liver disease ?

Rector RS, Thyfault JP. Does physical inactivity cause nonalcoholic fatty liver disease? J Appl Physiol 111: 1828–1835, 2011. First published May 12, 2011; doi:10.1152/japplphysiol.00384. 2011. —While physical activity represents a key element in the prevention and management of many chronic diseases, we and others believe that physical inactivity is a primary cause of obesity and associated metabolic disorders. Unfortunately, accumulating evidence suggests that we have engineered physical activity out of our normal daily living activity. One such consequence of our sedentary and excessive lifestyle is nonalcoholic fatty liver disease (NAFLD), which is now considered the most common cause of chronic liver disease in Westernized societies. In this review, we will present evidence that physical inactivity, low aerobic fitness, and overnutrition, either separately or in combination, are an underlying cause of NAFLD.
Left Ventricular Functional Parameters and Geometric Patterns in Korean Adults on Coronary CT Angiography with a 320-Detector-Row CT Scanner

Objective To assess the normal reference values of left ventricle (LV) functional parameters in Korean adults on coronary CT angiography (CCTA) with a 320-detector-row CT scanner, and to analyze sex-related differences and correlations with various clinical characteristics. Materials and Methods This study retrospectively enrolled 172 subjects (107 men and 65 women; age, 58 ± 10.9 years; body surface area [BSA], 1.75 ± 0.2 m2) who underwent CCTA without any prior history of cardiac disease. The following parameters were measured by post-processing the CT data: LV volume, LV functional parameters (ejection fraction, stroke volume, cardiac output, etc.), LV myocardial mass, LV inner diameter, and LV myocardial thickness (including septal wall thickness [SWT], posterior wall thickness [PWT], and relative wall thickness [RWT = 2 × PWT / LV inner diameter]). All of the functional or volumetric parameters were normalized using the BSA. The general characteristics and co-morbidities for the enrolled subjects were recorded, and the correlations between these factors and the LV parameters were then evaluated. Results The LV myocardial thickness (SWT, 1.08 ± 0.18 cm vs. 0.90 ± 0.17 cm, p < 0.001; PWT, 0.91 ± 0.15 cm vs. 0.78 ± 0.10 cm, p < 0.001; RWT, 0.38 ± 0.08 cm vs. 0.33 ± 0.05 cm, p < 0.001), LV volume (LV end-diastolic volume, 112.9 ± 26.1 mL vs. 98.2 ± 21.0 mL, p < 0.001; LV end-systolic volume, 41.7 ± 14.7 mL vs. 33.7 ± 12.2 mL, p = 0.001) and mass (145.0 ± 29.1 g vs. 107.9 ± 20.0 g, p < 0.001) were significantly greater in men than in women. However, these differences were not significant after normalization using BSA, except for the LV mass (LV mass index, 79.6 ± 14.0 g/m2 vs. 66.2 ± 11.0 g/m2, p < 0.001). The cardiac output and ejection fraction were not significantly different between the men and women (cardiac output, 4.3 ± 1.0 L/min vs. 4.2 ± 0.9 L/min, p = 0.452; ejection fraction, 63.4 ± 7.7% vs. 66.4 ± 7.6%, p = 0.079). Most of the LV parameters were positively correlated with BSA, body weight, and total Agatston score. Conclusion This study provides sex-related reference values and percentiles for LV on cardiac CT and should assist in interpreting results.
Wrist Pain, Distal Radial Physeal Injury, and Ulnar Variance in Young Gymnasts: Does a Relationship Exist? *

Background Chronic wrist pain affects up to 79% of young gymnasts. Distal radial growth plate injury and positive ulnar variance have also been reported in this population. Hypothesis There is a relationship between wrist pain, radiographic findings of distal radial growth plate injury, and ulnar variance in skeletally immature young gymnasts. Study Design Cross-sectional study. Methods Fifty-nine gymnasts (28 girls and 31 boys; average age, 9.3 years) completed a questionnaire detailing training and wrist pain symptoms. Each received a wrist examination, grip strength measurement, and bilateral wrist radiographs. Results Wrist pain was reported by 56% of the gymnasts (33 of 59), with 45% (15 of 33) describing pain of at least 6 months’ duration. Factors significantly associated with wrist pain included higher skill level, older age, and more years of training. For those between 10 and 14 years of age, 83% had wrist pain, compared with 44% for those outside of that age range. Fifty-one percent of the gymnasts (30 of 59) had findings of stress injury to the distal radial physis of at least a grade 2; 7% (4) had frank widening of the growth plate. Wrist pain prevalence was significantly related to the grade of radiographic injury. Mean ulnar variance was significantly more positive than established norms. Ulnar variance was not associated with wrist pain or radiographic injury of the distal radial physis. Conclusions Radiographic findings of distal radial physeal injury are associated with wrist pain among young nonelite gymnasts.
Hyposomatomedinemia in quadriplegic men.

Many studies have shown that vigorous exercise acutely stimulates growth hormone (GH) release but the relative contribution of daily physical activity to maintaining the GH/somatomedin C (SmC) axis is not known. It has been reported that basal and post-exercise plasma SmC values are higher in physically conditioned young men than in sedentary men of similar age. To assess the effect of severe inactivity on the plasma SmC level, basal concentrations of this hormone were measured in patients with quadriplegia (QP) resulting from spinal cord injury (SCI). Venous blood samples were obtained after overnight fast in 41 QP men, ages 24-66, and compared with 119 healthy men of similar ages. Nonparametric analysis of variance showed SmC to be significantly lower in QP than in healthy men (p < .007). Plasma SmC below 0.35 U/ml in adults usually indicates little or no GH secretion by the pituitary gland. In QP, 46% of plasma SmC values were < 0.35 U/ml compared to 24% in the healthy group (p < .02). In both groups, an inverse relationship of SmC and increasing age was observed (p < .01). The data suggest that severe inactivity or SCI tend to cause hyposomatomedinemia. The latter endocrine alteration may contribute to the decrease in lean body mass and muscle atrophy of QP patients, and add further functional impairment to the original neurologic deficit. In addition, hyposomatomedinemia could increase the tendency for pressure sore formation and osteoporosis in SCI patients.
Clinical and microbiological factors associated with early patient mortality from methicillin-resistant Staphylococcus aureus bacteremia

Background/Aims Methicillin-resistant Staphylococcus aureus bacteremia (MRSAB) is a major bloodstream infection with a high mortality rate. Identification of factors associated with early mortality in MRSAB patients would be useful for predicting prognosis and developing new therapeutic options. Methods A prospective cohort of MRSAB patients was examined between August 2008 and June 2011. Early and late mortality was defined as death within 2 and 28 days of blood culture, respectively. The clinical and microbiological characteristics in the early and late mortality and survival groups were compared. Risk factors associated with severe sepsis or septic shock were also investigated. Results A total of 385 adult MRSAB patients whose S. aureus isolates were available were enrolled; of these patients, 25 patients (6.5%) and 50 (13%) died early and late, respectively. Compared with both the late-mortality group and the survival group, severe sepsis or septic shock was a statistically significant independent risk factor associated with early mortality. Rapidly or ultimately fatal McCabe and Jackson classification (adjusted odds ratio [aOR], 1.94; 95% confidence interval [CI], 1.25 to 3.02) and pneumonia (aOR, 2.04; 95% CI, 1.03 to 4.02) were independently associated with severe sepsis or septic shock. A vancomycin minimum inhibitory concentration (MIC) ≥ 1.5 μg/mL was associated with a reduced incidence of severe sepsis or septic shock (aOR, 0.53; 95% CI, 0.34 to 0.84). Conclusions Severity of illness seems to be the most important risk factor associated with early mortality in MRSAB. Although vancomycin MIC was not independently associated with early mortality, reduced vancomycin susceptibility appears to be linked to reduced disease severity.
Temporary Migration and Bilateral Trade Flows

Empirical evidence on migration and trade has established that permanent migration promotes trade. This finding has been interpreted as proof for the role of migrants in reducing trade-related transaction costs such as contract enforcement costs or information costs. This paper contributes to improving our understanding of trade-related transaction costs by analysing empirically whether temporary migrants, like permanent migrants, have an impact on bilateral trade flows. Temporary migrants can be expected to be less integrated in the host country than permanent migrants. At the same time, their knowledge of the home country can, on average, be expected to be more up-to-date. Our findings therefore give insights as to the relative importance of knowledge on the host and the home country for trade-related transaction costs. Using a gravity approach in our empirical analysis, we find that temporary migration has a positive and significant effect on trade and that temporary migration tends to have a stronger and more significant effect on both imports and exports than permanent migration. Interestingly, the role of temporary migrants in reducing trade costs does not appear to be associated with their skills.
Statistical design of double EWMA controller

The double exponentially weighted moving average (dEWMA) feedback controller is a popular run-by-run (RbR) control scheme for adjusting certain semi-conductor manufacturing process with a linear drift. Del Castillo (IIE Trans. 1999; 31:1157) introduced an interesting state-space representation of the process output of this control scheme, and then the long-term stability conditions of this closed-loop system can be derived. The results; however, are very restricted to the case when the process disturbance follows a white noise series or an IMA(1, q) series. For a general process disturbance such as an ARIMA(p, d, q) model, it is not easy to obtain a state-space representation of the process output of this controller. Hence, some statistical properties (such as stability conditions and process yield) of this controller cannot be addressed by using the state-space theory. To overcome this difficulty, this paper first proposed an analytical expression for the process output of this dEWMA controller. Then the stability conditions and the optimal discount factors of this control scheme (based on the criterion of minimizing the average process fallout rate) can be obtained successfully. Finally, we also address some concluding remarks at the end of this paper.
Comparison of the dissemination and implementation of standardized public health nursing competencies in academic and practice settings.

OBJECTIVES To assess the use of the "Core Competencies for Public Health Professionals" standards in practice and academic work settings by public health nurses (PHNs), and to determine differences between practitioners and faculty. DESIGN Nonexperimental, descriptive study using a cross-sectional survey. SAMPLE Three public health nursing (PHN) organizations sent invitations to all members. A total of 334 (18.7%) from an estimated 1,786 members completed the survey. MEASUREMENTS The investigators developed a 17-item web-based survey with open- and closed-ended responses, using Rogers' diffusion of innovations as a theoretical framework. RESULTS Respondents are equally familiar with the competencies for public health professionals disseminated by the Council on Linkages and for PHNs by the Quad Council of Public Health Nursing Organizations (Quad Council). Two thirds of PHNs are aware of the competencies after only 2 years, primarily from professional PHN organizations. Faculty are adopting and using the competencies at a significantly faster rate than practitioners. CONCLUSIONS Faculty and practitioners who use the competencies value them, and rarely discontinued their use after adoption. Efforts to promote diffusion among faculty and especially practitioners need to continue. Professional organizations can actively provide and share examples of useable formats and best practices associated with the competencies.
Curiosity-Driven Exploration by Self-Supervised Prediction

In many real-world scenarios, rewards extrinsic to the agent are extremely sparse, or absent altogether. In such cases, curiosity can serve as an intrinsic reward signal to enable the agent to explore its environment and learn skills that might be useful later in its life. We formulate curiosity as the error in an agent's ability to predict the consequence of its own actions in a visual feature space learned by a self-supervised inverse dynamics model. Our formulation scales to high-dimensional continuous state spaces like images, bypasses the difficulties of directly predicting pixels, and, critically, ignores the aspects of the environment that cannot affect the agent. The proposed approach is evaluated in two environments: VizDoom and Super Mario Bros. Three broad settings are investigated: 1) sparse extrinsic reward; 2) exploration with no extrinsic reward; and 3) generalization to unseen scenarios (e.g. new levels of the same game).