Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Expression-based Analysis of Metabolism

Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM). We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such “history-dependent” sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques.
Individual differences at high perceptual load: The relation between trait anxiety and selective attention

Attentional control theory (Eysenck et al., 2007) posits that taxing attentional resources impairs performance efficiency in anxious individuals. This theory, however, does not explicitly address if or how the relation between anxiety and attentional control depends upon the perceptual demands of the task at hand. Consequently, the present study examined the relation between trait anxiety and task performance using a perceptual load task (Maylor & Lavie, 1998). Sixty-eight male college students completed a visual search task that indexed processing of irrelevant distractors systematically across four levels of perceptual load. Results indicated that anxiety was related to difficulty suppressing the behavioural effects of irrelevant distractors (i.e., decreased reaction time efficiency) under high, but not low, perceptual loads. In contrast, anxiety was not associated with error rates on the task. These findings are consistent with the prediction that anxiety is associated with impairments in performance efficiency under conditions that tax attentional resources.
The epidemiology of fractures in England

Introduction: Fractures are a considerable public health burden in the United Kingdom but information on their epidemiology is limited. Objective: This study aims to estimate the true annual incidence and lifetime prevalence of fractures in England, within both the general population and specific groups, using a self-report methodology. Methods: A self-report survey of a nationally representative general population sample of 45 293 individuals in England, plus a special boost sample of 10 111 drawn from the ethnic minority population. Results: The calculated fracture incidence is 3.6 fractures per 100 people per year. Lifetime fracture prevalence exceeds 50% in middle-aged men, and 40% in women over the age of 75 years. Fractures occur with reduced frequency in the non-white population: this effect is seen across most black and minority ethnic groups. Conclusions: This study suggests that fractures in England may be more common than previously estimated, with an overall annual fracture incidence of 3.6%. Age-standardised lifetime fracture prevalence is estimated to be 38.2%. Fractures are more commonplace in the white population.
Dimensions and Validation of Perceived Message Sensation Value Scale for Print Messages

OF DISSERTATION DIMENSIONS AND VALIDATION OF PERCEIVED MESSAGE SENSATION VALUE SCALE FOR PRINT MESSAGES The purpose of this research project was to develop a reliable and valid scale to assess the perceived message sensation value (PMSV) of print messages. The goal of this project was accomplished by conducting two studies. Study one involved collecting 397 undergraduate students’ responses to one high and one low sensation value anti-smoking message, while for study two, 284 undergraduate students’ responses to one high and one low sensation value anti-crystal meth message were collected. The results of the studies highlighted that the PMSV of a print message can be assessed using three dimensions (emotional arousal, novelty, and dramatic impact) and 12 items. Additionally, the newly developed PMSV scale for print messages remained stable across sensation-seeking levels and two different sets of anti-drug messages. Analysis of the data collected also provided support for the convergent, divergent, and predictive validity of the PMSV scale for print messages. Furthermore, from the data it can be inferred that PMSV is an important element that contributes to perceived message effectiveness and attitude towards the ad. The findings associated with this research project also suggest that both high and low sensation seekers preferred high over low sensation value print messages. Lastly, the implications of the PMSV scale for print messages were addressed.
Blood and urinary measures of hydration status during progressive acute dehydration.

PURPOSE To determine whether: a) plasma osmolarity (Posm) is sensitive to small incremental changes in hydration status, b) urine specific gravity (Usg) can accurately identify a state of euhydration, c) Usg is a sensitive indicator of a change in hydration status, and d) Usg correlates with Posm. METHODS Euhydrated (Posm = 288 +/- 4 mOsm.L-1) subjects (N = 12) were dehydrated by 5% of their body weight via exercise in the heat (40 degrees C, 20% RH). Posm, urine osmolarity (Uosm), and Usg were measured at 1%, 3%, and 5% dehydration, and 30 and 60 min of recovery (rec). Subjects consumed water in recovery equal to their loss of body weight. RESULTS Posm increased incrementally with each successive increase in percent body weight loss (%BWL). Usg was not significantly different from baseline until 3% BML. Uosm was not significantly different from baseline until 5% BWL. Usg correlated moderately (r = 0.46, P > 0.10) with Posm but reasonably well (r = 0.68, P < 0.02) with Uosm. CONCLUSIONS Posm accurately identifies a state of euhydration and is sensitive to changes in hydration status during acute dehydration and rehydration. Usg and Uosm are also sensitive to changes in hydration status but lag behind during periods of rapid body fluid turnover and therefore correlate only moderately with Posm during acute dehydration.
Clinical aspects of upper gastrointestinal bleeding associated with the use of nonsteroidal antiinflammatory drugs

Objective:The aim of this study was to compare the clinical features of major upper gastrointestinal bleeding among patients exposed to nonsteroidal antiinflammatory drugs (NSAID) and those not taking these drugs.Methods:Using data from a multicenter international case-control study designed to evaluate the role of drugs in the etiology of major upper gastrointestinal bleeding (UGIB), patients with a confirmed first episode of major UGIB were divided into two groups: those exposed to NSAIDs during the week before the onset of bleeding, and those not exposed. The groups were compared according to age and sex, clinical appearance and site of the bleeding, preceding symptoms, and requirement for transfusion and acute surgery.Results:The median age was significantly higher and the proportion of women was slightly higher among the NSAID users. There was no significant difference between users and nonusers according to the clinical presentation, the site of the bleeding, or the frequency of preceding symptoms. Forty percent in each group had no symptoms before the onset of bleeding. Slightly more NSAID users received blood transfusions, although the same median amount of blood per transfusion was given in both groups. There was no difference in the frequency of surgical intervention.Conclusions:There are no important differences in the clinical presentation of major UGIB according to whether or not an individual is an NSAID user. An important finding is the frequent absence of preceding symptoms in patients with major UGIB, regardless of NSAID use.
Optic disc size and progression of visual field damage in patients with normal-tension glaucoma

Purpose Our goal was to evaluate the influence of optic disc size on the progression of visual field damage in patients with normal-tension glaucoma (NTG). Subjects and methods Eighty-two eyes of 82 NTG patients who had been receiving topical antiglaucoma medications and followed-up for more than 4 years were enrolled in this study. The patients were allocated to two groups, according to the mean size of their optic discs. The data were analyzed using regression analysis, based on the Cox proportional hazard model. Results The probability of visual field stability was significantly lower in eyes with large discs than in those with small discs (log rank test, P = 0.007). Progression of visual field damage was significantly associated with the optic disc area (hazard ratio [HR]: 1.812, P = 0.018), occurrence of disc hemorrhage (HR: 2.116, P = 0.028), and intraocular pressure reduction ratio (HR: 0.957, P = 0.014). Conclusion The optic disc area correlates with progression of visual field damage in patients with NTG.
Engineering of a Water-Soluble Plant Cytochrome P450, CYP73A1, and NMR-Based Orientation of Natural and Alternate Substrates in the Active Site1

CYP73A1 catalyzes cinnamic acid hydroxylation, a reaction essential for the synthesis of lignin monomers and most phenolic compounds in higher plants. The native CYP73A1, initially isolated from Jerusalem artichoke (Helianthus tuberosus), was engineered to simplify purification from recombinant yeast and improve solublity and stability in the absence of detergent by replacing the hydrophobic N terminus with the peptitergent amphipathic sequence PD1. Optimized expression and purification procedures yielded 4 mg engineered CYP73A1 L–1 yeast culture. This water-soluble enzyme was suitable for 1H-nuclear magnetic resonance (NMR) investigation of substrate positioning in the active site. The metabolism and interaction with the enzyme of cinnamate and four analogs were compared by UV-visible and 1H-NMR analysis. It was shown that trans-3-thienylacrylic acid, trans-2-thienylacrylic acid, and 4-vinylbenzoic acid are good ligands and substrates, whereas trans-4-fluorocinnamate is a competitive inhibitor. Paramagnetic relaxation effects of CYP73A1-Fe(III) on the 1H-NMR spectra of cinnamate and analogs indicate that their average initial orientation in the active site is parallel to the heme. Initial orientation and distances of ring protons to the iron do not explain the selective hydroxylation of cinnamate in the 4-position or the formation of single products from the thienyl compounds. Position adjustments are thus likely to occur during the later steps of the catalytic cycle.
Evicting cuckoo nestlings from the nest: a new anti-parasitism behaviour

As avian brood parasitism usually reduces hosts' reproductive success, hosts often exhibit strong defence mechanisms. While such host defences at the egg stage (especially egg rejection) have been extensively studied, defence mechanisms at the nestling stage have been reported only recently. We found a previously unknown anti-parasitism behaviour in the large-billed Gerygone, which is a host species of the little bronze-cuckoo, a host-evicting brood parasite. The hosts forcibly pulled resisting nestlings out of their nests and dumped them. Although it has been suggested that defence mechanisms at the nestling stage may evolve when host defence at the egg stage is evaded by the parasite, the studied host seems to lack an anti-parasitism strategy at the egg stage. This suggests that the evolutionary pathway may be quite different from those of previously studied cuckoo–host systems. Future research on this unique system may give us new insights into the evolution of avian brood parasitism.
Amino‐terminal deletion of heparin‐binding epidermal growth factor‐like growth factor4−127 stimulates cell proliferation but lacks insulin‐like activity

Abstract. Heparin‐binding epidermal growth factor‐like growth factor (HB‐EGF) Northern analysis demonstrated a novel 0.8‐kb liver‐specific HB‐EGF transcript in addition to the endogenous 2.5‐kb HB‐EGF full‐length transcript present in kidney, lung and liver tissues. Reverse transcriptase‐polymerase chain reaction screening of liver RNA suggests that the 0.8‐kb HB‐EGF transcript lacks at least a portion of the amino‐terminal EGF‐like domain. In light of these data, we have constructed a human HB‐EGF cDNA (HB‐EGFΔN) which lacks 373 bp, encoding the majority of the extracellular EGF‐like domain, while maintaining the ectodomain ‘shedding’ site, transmembrane and cytoplasmic domains. Objective: The goal of this study is to characterize the ability of HB‐EGFΔN to (i) stimulate cell proliferation and (ii) determine whether down‐regulation of insulin‐like growth factor‐binding protein (IGFBP)‐3 and ‐4 mRNA is regulated by soluble, mature HB‐EGF or HB‐EGF C. Materials and methods: HB‐EGFΔN encodes nucleotides +1–10 of exon 1 linked to nucleotides 383–627 of the carboxy‐terminal portion of exon 3 through exon 5. Results: Expression of HB‐EGFΔN in mouse fibroblasts (MLC) resulted in 6.5‐ and 8‐kDa HB‐EGF immunoreactive proteins, stimulated tyrosine phosphorylation of p42 kDa and cell proliferation in MLC, but lacked the ability to bind EGF receptors. Finally, HB‐EGFΔN failed to down‐regulate IGFBP‐3 and ‐4 mRNA when expressed in normal rat kidney cells. Conclusions: These findings demonstrate that amino‐terminally truncated, membrane‐bound form of HB‐EGF stimulates cell proliferation but lacks insulin‐like signalling, suggesting that insulin‐like signalling is mediated by soluble, mature HB‐EGF binding to EGF receptors.
End-to-end Optimized Image Compression

We describe an image compression method, consisting of a nonlinear analysis transformation, a uniform quantizer, and a nonlinear synthesis transformation. The transforms are constructed in three successive stages of convolutional linear filters and nonlinear activation functions. Unlike most convolutional neural networks, the joint nonlinearity is chosen to implement a form of local gain control, inspired by those used to model biological neurons. Using a variant of stochastic gradient descent, we jointly optimize the entire model for rate-distortion performance over a database of training images, introducing a continuous proxy for the discontinuous loss function arising from the quantizer. Under certain conditions, the relaxed loss function may be interpreted as the log likelihood of a generative model, as implemented by a variational autoencoder. Unlike these models, however, the compression model must operate at any given point along the rate-distortion curve, as specified by a trade-off parameter. Across an independent set of test images, we find that the optimized method generally exhibits better rate-distortion performance than the standard JPEG and JPEG 2000 compression methods. More importantly, we observe a dramatic improvement in visual quality for all images at all bit rates, which is supported by objective quality estimates using MS-SSIM.
Elderly patients' reports of physical restraint experiences in intensive care units.

BACKGROUND Use of physical restraints has undesirable sequelae. As they weigh the risks and benefits of protocols for reducing the use of restraints, staff members in intensive care units, where restraints are most used in hospitals, need to know how well elderly patients remember being restrained and how patients perceive the use of restraints. OBJECTIVES To estimate the proportion of patients who remember being restrained, describe the experience from the patients' perspectives, and describe any distress caused by use of restraints within the overall experience of being in the intensive care unit. METHODS Transcripts of semistructured, audiotaped interviews of patients who had been in the medical or surgical intensive care unit in any of 3 eastern and midwestern medical centers were analyzed by question and for overall themes. RESULTS Six patients (40%) remembered some aspect of being restrained but did not report great distress. Patients accepted restraints as needed because of the lack of alternatives. Patients reported remembering that they should not perform certain behaviors but being unable to stop themselves. Patients cited hallucinations and intubation as major stressors in the intensive care unit. Patients' continuing health problems after discharge from the intensive care unit severely limited recruitment of subjects. CONCLUSIONS Patients do not remember great distress specifically related to the use of restraints, but the overall situation leading to use of restraints is disturbing if remembered. The discovery of methods to reduce the distress of intubation and hallucinations could decrease use of restraints.
Differences exist across insurance schemes in China post-consolidation

Background In China, the basic insurance system consists of three schemes: the UEBMI (Urban Employee Basic Medical Insurance), URBMI (Urban Resident Basic Medical Insurance), and NCMS (New Cooperative Medical Scheme), across which significant differences have been observed. Since 2009, the central government has been experimenting with consolidating these schemes in selected areas. This study examines whether differences still exist across schemes after the consolidation. Methods A survey was conducted in the city of Suzhou, collecting data on subjects 45 years old and above with at least one inpatient or outpatient treatment during a period of twelve months. Analysis on 583 subjects was performed comparing subjects’ characteristics across insurance schemes. A resampling-based method was applied to compute the predicted gross medical cost, OOP (out-of-pocket) cost, and insurance reimbursement rate. Results Subjects under different insurance schemes differ in multiple aspects. For inpatient treatments, subjects under the URBMI have the highest observed and predicted gross and OOP costs, while those under the UEBMI have the lowest. For outpatient treatments, subjects under the UEBMI and URBMI have comparable costs, while those under the NCMS have much lower costs. Subjects under the NCMS also have a much lower reimbursement rate. Conclusions Differences still exist across schemes in medical costs and insurance reimbursement rate post-consolidation. Further investigations are needed to identify the causes, and interventions are needed to eliminate such differences.
Die bispektrale Analyse unterscheidet das Narkose-EEG nicht von einem linearen Zufallsprozeß. Bispectral Analysis does not Differentiate Between Anaesthesia EEG and a Linear Random Process

Bispectral analysis of the electroencephalogram (EEG) has been used to monitor depth of anaesthesia. In the majority of publications this has involved the use of the so called BIS-Index TM (Aspect Medical Systems, Inc.). The exact relationship of this index to such bispectral parameters as the bispectrum and bicoherence has not yet been reported. If the EEG is considered as a linear random process, bicoherence is trivial, i.e. it is independent of the EEG frequency. The aim of this study was to determine the proportion of EEG epochs with non-trivial bicoherence during isoflurane/N20 anaesthesia. We reanalyzed 25.5 hours of digitalised EEG signal from 9 patients undergoing gynaecological surgery. The test developed by Hinich for Gaussian distribution and linearity was then applied. The test was validated using various synthetic surrogate data: Gaussian random data, the z-component of the Lorenz attractor, the phase randomized EEG and the phase randomized z-component of the Lorenz attractor. The percentage of epochs (8.192 s, 1024 data points) with non-trivial bicoherence was: Lorenz data 95.4%, phase randomized Lorenz data 9.4%, synthetic Gaussian data 14.8%, original EEG 9.1%, phase randomized EEG 5.1%. The original EEG data were not found to contain a higher percentage of epochs with non-trivial bicoherence than the phase randomized data and the synthetic Gaussian data. We conclude that bispectral analysis does not substantially add to the information obtained with other methods of quantitative EEG analysis.
Continuous Conditional Dependency Network for Structured Regression

Structured regression on graphs aims to predict response variables from multiple nodes by discovering and exploiting the dependency structure among response variables. This problem is challenging since dependencies among response variables are always unknown, and the associated prior knowledge is non-symmetric. In previous studies, various promising solutions were proposed to improve structured regression by utilizing symmetric prior knowledge, learning sparse dependency structure among response variables, or learning representations of attributes of multiple nodes. However, none of them are capable of efficiently learning dependency structure while incorporating non-symmetric prior knowledge. To achieve these objectives, we proposed Continuous Conditional Dependency Network (CCDN) for structured regression. The intuitive idea behind this model is that each response variable is not only dependent on attributes from the same node, but also on response variables from all other nodes. This results in a joint modeling of local conditional probabilities. The parameter learning is formulated as a convex optimization problem and an effective sampling algorithm is proposed for inference. CCDN is flexible in absorbing non-symmetric prior knowledge. The performance of CCDN on multiple datasets provides evidence of its structure recovery ability and superior effectiveness and efficiency as compared to the state-of-the-art alternatives.
Mothers' Attributions in Reminiscing Conversations About Children's Successes and Failures: Connections With Children's Self-Evaluations

Effects of feedback on children's self-evaluations are well established, yet little is known about how parents talk with children about everyday successes and failures, despite the importance of parent-child reminiscing in children's psychological understanding. We examine mothers' attributions and performance evaluations in conversations about their 5-year-olds' (N = 80) success and failure experiences, and connections between conversations and children's self-evaluations. Conversations differed for success and failure: Mothers were equally likely to make internal-person, internal-process, or external attributions for successes, but were most likely to make an evaluation. For failures, mothers were equally likely to make internal-process or external attributions, or evaluations. Internal-person attributions for success and external attributions were associated with negative self-evaluations. However, children expressed fewer negative self-evaluations when mothers made internal-process attributions for failure, or positively evaluated the success. Results support the experimental literature and extend it to external attributions, which were common in mothers' framing and linked to negative self-evaluations.