Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting the Dynamics of Protein Abundance

Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA–protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency. The software and data used in this research are available at http://bioinf.scmb. uq.edu. au/proteinabundance/.
Effects of parameters on the accuracy and precision of ultrasound-based local pulse wave velocity measurement: a simulation study

Quantification of arterial stiffness, such as pulse wave velocity (PWV), is increasingly used in the risk assessment of cardiovascular disease. Pulse wave imaging (PWI) is an emerging ultrasound-based technique to noninvasively measure the local PWV instead of the global PWV, as in conventional methods. In PWI, several key parameters, including the frame rate of ultrasound imaging, motion estimation rate (MER), number of scan lines, image width, PWV value, and sonographic signal-to-noise ratio (SNRs), play an important but still unclear role in the accuracy and precision of PWV measurement. In this study, computer simulations were performed to investigate the fundamental effects of these parameters on the PWV measurement. The pulse waveform was estimated by speckle tracking on ultrasound RF signals acquired at a frame rate of 2083 Hz from a location on the common carotid artery of a healthy subject. By applying different time delays on the estimated waveform based on specific PWI parameters, the pulse waveforms at others locations were simulated. Ultrasound RF signals of the artery during the pulse wave propagation were generated from a 2-D convolutional image formation model. The PWI technique was applied to estimate the PWV at different values of frame rate, MER, number of scan lines, image width, PWV, and SNRs. The performance of the PWV estimation was evaluated by measuring the relative error, coefficient of variation (CV) and coefficient of determination (R2). The results showed that PWVs could be correctly measured when the frame rate was higher than a certain value (i.e., minimum frame rate), below which the estimated error increased rapidly. The minimum frame rate required for PWV estimation was found to increase with the value of PWV. An optimal MER was found (i.e., about 200 Hz) and allowed better performance of PWV measurement. The CV of PWV estimation decreased and R2 increased with number of scan lines and image width, indicating that the performance of the PWV estimation could be improved with a larger number of scan lines and image width. For a given sufficiently high frame rate, a higher PWV value was found to deteriorate the PWV estimation, as indicated by an increasing CV and decreasing R2. The simulation results were in good agreement with the theoretical analysis. Finally, high-quality PWV estimation could be obtained as long as the SNRs was higher than about 30 dB. The quantitative effects of the key parameters obtained from this study might provide important guidelines for parameter optimization in ultrasound-based local PWV measurement in vivo.
Activation of the Raf‐1/MEK/ERK cascade by bile acids occurs via the epidermal growth factor receptor in primary rat hepatocytes

Bile acids have been reported to activate several different cell signaling cascades in rat hepatocytes. However, the mechanism(s) of activation of these pathways have not been determined. This study aims to determine which bile acids activate the Raf‐1/MEK/ERK cascade and the mechanism of activation of this pathway. Taurodeoxycholic acid (TDCA) stimulated (+235%) the phosphorylation of p74 Raf‐1 in a time (5 to 20 minutes) and concentration‐dependent (10 to 100 μmol/L) manner. Raf‐1 and ERK activities were both significantly increased by most bile acids tested. Deoxycholic acid (DCA) was the best activator of ERK (3.6‐fold). A dominant negative Ras (N17) construct expressed in primary hepatocytes prevented the activation of ERK by DCA. The epidermal growth factor receptor (EGFR)‐specific inhibitor (AG1478) significantly inhibited (∼81%) the activation of ERK by DCA. DCA rapidly (30 to 60 seconds) increased phosphorylation of the EGFR (∼2‐fold) and Shc (∼4‐fold). A dominant negative mutant of the EGFR (CD533) blocked the ability of DCA to activate ERK. In conclusion, these results show that DCA activates the Raf‐1/MEK/ERK signaling cascade in primary hepatocytes primarily via an EGFR/Ras‐dependent mechanism.
Pharmacodynamic effects of standard dose prasugrel versus high dose clopidogrel in non-diabetic obese patients with coronary artery disease

Summary Increased body weight is independently associated with impaired clopidogrel pharmacodynamic (PD) response. Prasugrel has more potent PD effects compared with clopidogrel, although its PD effects in obese patients are unknown. The aim of this prospective, randomised, study was to compare the PD effects of standard-dose prasugrel [60 mg loading dose (LD)/10 mg daily maintenance dose (MD)] with highdose clopidogrel (900 mg LD/150 mg daily MD) in non-diabetic obese [body mass index (BMI) ≥30 kg/m2] patients, with coronary artery disease (CAD) on aspirin therapy. PD assessments (baseline, 2 hours post-LD and 6 ± 2 days after MD) were conducted using four platelet function assays, and the platelet reactivity index (PRI) assessed by VASP was used for sample size estimation. A total of 42 patients with a BMI of 36.42 ± 5.6 kg/m2 completed the study. There were no differences in baseline PD measures between groups. At 2 hours post-LD, prasugrel was associated with lower PRI compared with clopidogrel (24.3 ± 5.5 vs 58.7 ± 5.7, p≤0.001), with consistent findings for all assays. At one-week, PRI values on prasugrel MD were lower than clopidogrel MD without reaching statistical significance (34.7 ± 5.8 vs 42.9 ± 5.8, p=0.32), with consistent findings for all assays. Accordingly, rates of high on-treatment platelet reactivity were markedly reduced after prasugrel LD, but not after MD. In conclusion, in non-diabetic obese patients with CAD, standard prasugrel dosing achieved more potent PD effects than high-dose clopidogrel in the acute phase of treatment, but this was not sustained during maintenance phase treatment. Whether an intensified prasugrel regimen is required in obese patients warrants investigation.
Facilitating Activation of the Peroneus Longus: Electromyographic Analysis of Exercises Consistent With Biomechanical Function

Bellew, JW, Frilot, CF, Busch, SC, Lamothe, TV, and Ozane, CJ. Facilitating activation of the peroneus longus: Electromyographic analysis of exercises consistent with biomechanical function. J Strength Cond Res 24(2): 442-446, 2010-Exercises for the ankle are often used to improve sport performance through balance and stability or to prevent or recover from ankle injury. Ankle training programs often include exercises for the primary muscle of the lateral ankle, the peroneus longus (PL). However, many exercises for the PL are non-weight bearing and unidirectional. However, data from biomechanical studies show that peak activity of the PL occurs neither in non-weight-bearing nor during uniplanar movements. This lack of congruency may limit the effectiveness of PL training. Exercises more consistent with the biomechanical function of the PL may increase the efficacy of ankle training. This study examined and compared the electromyographic (EMG) activity of the PL during 2 exercises that specifically address the known biomechanical function of the PL and a traditional non-weight-bearing unidirectional PL exercise. Twenty healthy college-aged men and women (age 24.8 ± 2.7 years) without history of ankle injury were examined in a single-session repeated measures design. The average root means square (RMS) values of the PL during each of the 3 exercises were measured and compared to assess for differences in magnitude of muscular activity. The RMS activity of the PL was significantly greater (p < 0.05) in each of the biomechanically correct exercises when compared with the conventional exercise. However, no significant difference was noted in EMG activity between the 2 biomechanical exercises. This study provides evidence for increased activity from the PL during 2 exercises that more accurately reflect its biomechanical function. Use of these exercises when training the PL for sports performance or rehabilitation may increase the effectiveness of ankle training programs that include PL activity.
Intersecting Oppressions: Racial-Ethnic Stratification in Domestic Work and Implications for Identity-Based Organizing

This article reports on a survey of 410 Colorado domestic workers, which demonstrates that race/ethnicity and national origin are more powerful predictors of workplace oppression than gender or class. An “intersectionality” framework explores how a hierarchy of oppressions divides female domestic workers from their female employers, and from each other, suggesting challenges to domestic worker organizing along gender or class lines, in that both professional women and white domestic workers benefit from racialized hierarchies within domestic work. These findings suggest associational “identity politics” organizing as a productive strategy to highlight the unique experiences of racially and ethnically subordinate domestic workers and to build on existing community networks of nonwhite immigrant workers, thus establishing an identity-based foundation of mutual strength and political power from which domestic women of color can reach out to build majoritarian alliances for change. MAIDS AND MA’AMS: GENDER DISCORD As the “feminization of migration” increasingly characterizes transnational labor flows (Lyons, 2004a, 2004b; Maher, 2004; Moras, 2008a), domestic workers
Background Television as an Inhibitor of Performance on Easy and Difficult Homework Assignments

Two experiments were conducted to investigate the effects of two types of background television programs on students' performance on easy and difficult homework assignments. In both experiments, students in Grade 8 (Experiment 1: N = 90; Experiment 2: N = 144) were matched on reading proficiency. Subsequently, the participants were randomly assigned to one of three experimental conditions in which they did homework with (a) a Dutch-language soap opera, (b) English-language music videos, or (c) no television in the background. The execution of homework was hindered only when it was combined with watching a soap opera. The distraction effect of the soap opera was expressed either in a performance decrement (Experiment 1) or in an extension of performance time (Experiment 2).
Repressive coping and cardiovascular reactivity to novel and recurrent stress

ABSTRACT Background and objectives: Repressors tend to report less negative emotion and to describe challenges as less stressful, yet tend to exhibit higher rates of cardiovascular disease. While repressive coping has been shown to be associated with exaggerated physiological reactivity to novel stress, we sought to establish if elevated responses persisted across repeated exposure. Design and methods: In a sample of 86 healthy female adults, a verbal-autonomic response dissociation index of repressive coping was computed. Participants were exposed to two consecutive stress tasks, with analyses based on comparisons of consecutive stress responses. Results: Analysis of covariance demonstrated significant differences across the study on diastolic blood pressure and cardiac output, as a function of repressive coping. Repressors showed elevated reactions to both stress tasks; however, cardiac output responses to the second task were more muted indicating that repressive coping was associated with successful adaptation to recurrent stress. Nevertheless, repressive copers maintained an exaggerated cardiovascular responses to recurrent stress. Conclusions: The present study identifies that repressive coping may be associated with increased risk of cardiovascular disease development through elevated cardiovascular reactions to both novel and recurrent stress.
Why Can't We Resolve the Research Issue in Public Administration?

Nearly 50 years ago, in a now classic issue of the Public Administration Review, Robert Hutchins and William Mosher debated whether schools should be established to train people in public administration. Hutchins, then president of the University of Chicago, took a negative view. He argued that public administration is too variable a field to lend itself to systematic exploration. Mosher, then dean of the Maxwell School at Syracuse University, argued in the affirmative. His words are worth recalling:
Role of D-ribose as a cometabolite in D-xylose metabolism by Saccharomyces cerevisiae

The influence of D-ribose as a cosubstrate on the uptake and metabolism of the non-growth substrate D-xylose by Saccharomyces cerevisiae ATCC 26602 was investigated. Xylose was taken up by means of low- and high-affinity glucose transport systems. In cells exposed for 2 days to a mixture of xylose and ribose, only the high-affinity system could be detected. Glucose strongly inhibited the transport of xylose by both systems. Starvation or exposure to either xylose or ribose resulted in inactivation of xylose transport, which did not occur in the presence of a mixture of ribose and xylose. A constitutive non-glucose-repressible NADPH2-dependent xylose reductase with a specific activity of ca. 5 mU/mg of protein that converted xylose to xylitol was present in a glucose-grown culture. No activity converting xylitol to xylulose or vice versa was found in crude extracts. Both xylose and ribose were converted to their corresponding polyols, xylitol and ribitol, as indicated by 13C nuclear magnetic resonance spectroscopy. Furthermore, ethanol was detected, and this implied that pathways for the complete catabolism of xylose and ribose exist. However, the NADPH2 required for the conversion of xylose to xylitol is apparently not supplied by the pentose phosphate pathway since the ethanol produced from D-[1-13C]xylose was labelled only in the C-2 position. Acetic acid was produced from ribose and may assist in the conversion of xylose to xylitol by cycling NADPH2.
Cardiac output and its distribution through capillaries and A-V shunts in diving seals.

Regional blood flow and cardiac output were determined by distribution of radioactive microspheres injected via catheter into the left ventricle during experimental diving and recovery in juvenile spotted seals (Phoca vitulina largha) and grey seals (Halichoerus grypus). Cardiac output was 9.7 L/min before diving, declined 90% during submersion and increased to 12.1 L/min after 40 s of recovery. Left ventricular myocardial perfusion declined from 179 +/- 24 (21) to 25 +/- 2 (6) ml/min . 100 g at 2 min submersion, and measured 23 +/- 3 (8) after 10 min of submersion. Cerebral cortical flow was reduced from a pre-dive value of 115 +/- 3 (15) to 40 +/- 5 (3) and 49 +/- 6 (3) at 2 and 5 min of diving, respectively, but increased to 253 +/- 14 (4) ml/min . 100 g at 10 min along with elevated PCO2 (84 torr) and lowered pH (7.10) in arterial blood. It remained at that level in recovery. Brain stem perfusion after 10 min submersion was still identical with control, but increased to 275% of control in recovery. Adrenal flow decreased to 34 and 27% of control at 2 and 5 min of diving, respectively. Recovery flow after 10 min of diving was 200% of control. Liver, kidney, fat, skin, and stomach were ischemic throughout the dive. Recovery flow increased slowly in these tissues. Skeletal muscle (M. psoas) was perfused at a low rate. (3 ml/min . 100 g) pre-dive and was ischemic during diving. Recovery muscle perfusion was variable at different sites (from 5 to 105 ml/min . 100 g). Pre-dive pulmonary capillary perfusion was 58 +/- 8 (9) ml/min . 100 g, decreased to 7 +/- 0 (3) ml/min . 100 g min of submersion, and had increased to 50% of pre-dive value after 40 s of recovery from a 10 min dive. Conclusions are: (1) previous information from implanted flow transducers was confirmed, (2) detailed data for discrete tissues elaborate the concept of selective redistribution of cardiac output in diving seals, (3) non-uniform reperfusion contributes to the maintenance of arterial pressure during recovery, and (4) substantial A-V shunting of cardiac output took place in the first 2-5 min of the dive, when total capillary/nutritive flow was low. Late in the dive, however, CO was routed through systemic capillaries mainly in the cerebral circulation and less than 15% through A-V shunts.
Evidence for increased myofibrillar mobility in desmin-null mouse skeletal muscle.

Quantitative electron microscopy was used to characterize the longitudinal mobility of myofibrils during muscle extension to investigate the functional roles of skeletal muscle intermediate filaments. Extensor digitorum longus fifth toe muscles from wild-type (+/+) and desmin-null (des -/-) animals were passively stretched to varying lengths, and the horizontal displacement of adjacent Z-disks in neighboring myofibrils (Deltax(myo)) and average sarcomere length (SL) were calculated. At short SL (<2.20 microm), wild-type and desmin-null Deltax(myo) were not significantly different, although there was a trend towards greater Z-disk misalignment in muscles from knockout animals (Deltax(myo) 0.34+/-0.04 microm versus 0.22+/-0.09 microm; P>0.2; means +/- S.E. M. ). However, at higher SL (>2.90 microm), muscles from knockout animals displayed a dramatically increased Deltax(myo) relative to wild-type muscles (0.49+/-0.10 microm versus 0.25+/-0.07 microm; P<0.05). The results, which establish a maximum extension of the desmin network surrounding the Z-disk, provide what we believe to be the first quantitative estimation of the functional limits of the desmin intermediate filament system in the presence of an intact myofibrillar lattice. The existence of a limit on the extension of desmin suggests a mechanism for the recruitment of desmin into a network of force transmission, whether as a longitudinal load bearer or as a component in a radial force-transmission system.
Circuit simulation model for ferrite core inductor taking into account dynamic magnetic loss

The purpose of this study is to develop a precise-loss circuit simulation model for ferrite inductors and transformers used in power converters. The power loss in ferrite is mainly due to the magnetic losses of hysteresis and dynamic magnetic losses. The B-H loop becomes narrower with decreasing excitation frequency. However, even at frequencies lower than 1 kHz, the B-H loop exhibits a certain minimum width. This loop is referred to as the DC hysteresis loop or simply the hysteresis loop. The dynamic magnetic loss is obtained by subtracting the hysteresis loss from the B-H loop area measured at a frequency above 1–10 kHz. Magnetic field intensity, Hf, causing the dynamic magnetic loss is defined as (dB/dt)A, f, where kf is the dynamic magnetic loss parameter. Hf is obtained as a function of B and dB/dt from the measured B-H loops under rectangular waveform voltage excitation. Using the Hf data, we simulated B- H loops under sinusoidal waveform voltage excitation where the instantaneous value of dB/dt changes at every moment in time. The simulated and experimental results were in good agreement. The results of the present study contribute to the development of a precise-loss nonlinear simulation circuit model for ferrite-applied magnetic devices. The model can be used in the design of power electronics.
Are low-productive exporters marginal exporters? Evidence from Germany

A stylized fact from the emerging literature on the micro-econometrics of international trade and a central implication of the heterogeneous firm models from the new new trade theory is that exporters are more productive than non-exporters. It is argued that this exporter-productivity premium is due to extra cost of exporting that can be covered profitably by more productive firms only. Germany is a case in point - exporting firms from manufacturing industries are more productive than non-exporting firms from the same 4-digit industry both on average and over the whole productivity distribution. However, many firms from the lower end of this distribution are exporters. This paper report that these low-productivity exporters are not marginal exporters defined according to the share of exports in total sales, or export participation over time, or the number of goods exported, or the number of countries exported to.
Effect of Hypophysectomy on Corticotropin-Releasing Hormone and Adrenocorticotropin Immunoreactivities in the Rat Adrenal Gland

It has previously been shown that rat adrenal zona medullaris possesses an interleukin-1 beta (IL-1 beta)-responsive peripheral branch of the CRH/ACTH system that duplicates the hypothalamopituitary central one (Mazzocchi et al., Mol. Cell. Neurosci. 4: 267, 1993). The intraadrenal content of corticotropin-releasing hormone (CRH) and adrenocorticotropin (ACTH) immunoreactivities (ir), as well as IL-1 beta-stimulated release of CRH-ir and ACTH-ir, increased in relation to the number of days elapsed from hypophysectomy; the effect of hypophysectomy required at least 48 h to become significant and reached its maximum after 72 h. The action of IL-1 beta on ACTH-ir release was annulled by simultaneous exposure to alpha-helical-CRH, an antagonist of CRH. ACTH infusion, at a rate restoring a normal blood level of the hormone, prevented the effect of hypophysectomy on intraadrenal concentrations of both CRH-ir and ACTH-ir; similarly, the hypophysectomy-evoked rise in intraadrenal ACTH-ir content was completely annulled by treating hypophysectomized rats with CRH or dexamethasone. Taken together our findings suggest that the elimination of the central branch of CRH/ACTH system induces a marked increase in the activity of the intraadrenal peripheral one. The hypothesis is advanced that the hypophysectomy-induced lowering of circulating ACTH and the consequent drop in the production of adrenal glucocorticoids enhances, via a classic negative feedback mechanism, gene expression of CRH and ACTH in adrenal medullary chromaffin cells.