Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic modeling of Saccharomyces cerevisiae using the optimal control of homeostasis: a cybernetic model definition.

A model is presented to describe the observed behavior of microorganisms that aim at metabolic homeostasis while growing and adapting to their environment in an optimal way. The cellular metabolism is seen as a network with a multiple controller system with both feedback and feedforward control, i.e., a model based on a dynamic optimal metabolic control. The dynamic network consists of aggregated pathways, each having a control setpoint for the metabolic states at a given growth rate. This set of strategies of the cell forms a true cybernetic model with a minimal number of assumptions. The cellular strategies and constraints were derived from metabolic flux analysis using an identified, biochemically relevant, stoichiometry matrix derived from experimental data on the cellular composition of continuous cultures of Saccharomyces cerevisiae. Based on these data a cybernetic model was developed to study its dynamic behavior. The growth rate of the cell is determined by the structural compounds and fluxes of compounds related to central metabolism. In contrast to many other cybernetic models, the minimal model does not consist of any assumed internal kinetic parameters or interactions. This necessitates the use of a stepwise integration with an optimization of the fluxes at every time interval. Some examples of the behavior of this model are given with respect to steady states and pulse responses. This model is very suitable for describing semiquantitatively dynamics of global cellular metabolism and may form a useful framework for including structured and more detailed kinetic models.
A comparative study of acquisition schemes for diffusion tensor imaging using MRI.

This study has investigated the effects of the selection of the diffusion-weighted (DW) gradient directions on the precision of a diffusion tensor imaging (DTI) experiment. The theoretical analysis provided a quantitative framework in which the noise performance of DTI schemes could be assessed objectively and for the development of novel DTI schemes, which employ multiple DW gradient directions. This generic framework was first applied to the examination of two commonly used DTI schemes, which employed 6 DW gradient directions and hitherto were used indiscriminately under the sole condition of noncollinearity. It was then used to design and assess a novel 12-DW-gradient-direction DTI protocol, which employed the same total number of DW acquisitions as the two conventional schemes (12). This theoretical investigation was then corroborated using rigorous simulation and DTI experiments on both an isotropic phantom and a healthy human brain. Both the theoretical and the experimental analysis demonstrated that the two conventional schemes showed a significantly different noise performance and that use of the new multiple-DW-gradient-direction scheme clearly improved the precision of the DTI measurements.
Equimolar mixture of nitroux oxyde and oxygen during post‐operative physiotherapy in patients with cerebral palsy: A randomized, double‐blind, placebo‐controlled study

The administration of an equimolar mixture of nitrous oxide and oxygen (N2O) is recommended during painful procedures. However, the evaluation of its use during physiotherapy after surgery has not been reported, although pain may hamper physiotherapy efficiency. This study investigated whether the use of N2O improves the efficacy of post‐operative physiotherapy after multilevel surgery in patients with cerebral palsy.
Three Lessons for Creating a Knowledge Base to Enable Explanation, Reasoning and Dialog

Our work is driven by the hypothesis that, for a program to answer questions, explain the answers, and engage in a dialog just as a human does, it must have an explicit representation of knowledge. Such explicit representations naturally occur in many situations such as in designs created by engineers, software requirements created in a unified modeling language or process flow diagrams created for a manufacturing process. Automated approaches based on natural language processing have progressed on tasks such as named entity recognition, fact extraction and relation learning, but they cannot generate expressive representations with high accuracy. In this paper, we report on our effort to systematically curate a knowledge base (KB) for a substantial fraction of a biology textbook. Although this experience and the process inherently offer insights, three aspects are especially instructive for the future development of KBs both by manual and by automatic methods: (1) Consider imposing a simplifying abstract structure on natural language sentences so that the surface form is closer to the target logical form to be extracted. (2) Adopt an upper ontology that is strongly motivated and influenced by natural language. (3) Develop a set of syntactic and semantic guidelines that captures how the conceptual distinctions in the ontology may be realized in natural language. Because this representation has effectively enabled reasoning, explanation and dialog, it gives a concrete target for what should be learned by automated methods.
Semi-Supervised Learning of Sequence Models with Method of Moments

We propose a fast and scalable method for semi-supervised learning of sequence models, based on anchor words and moment matching. Our method can handle hidden Markov models with feature-based log-linear emissions. Unlike other semi-supervised methods, no decoding passes are necessary on the unlabeled data and no graph needs to be constructed— only one pass is necessary to collect moment statistics. The model parameters are estimated by solving a small quadratic program for each feature. Experiments on part-of-speech (POS) tagging for Twitter and for a low-resource language (Malagasy) show that our method can learn from very few annotated sentences.
Longitudinal mapping of cortical thickness and clinical outcome in children and adolescents with attention-deficit/hyperactivity disorder.

CONTEXT Data from a previous prospective study of lobar volumes in children with attention-deficit/hyperactivity disorder (ADHD) are reexamined using a measure of cortical thickness. OBJECTIVE To determine whether regional differences in cortical thickness or cortical changes across time characterize ADHD and predict or reflect its clinical outcome. DESIGN, SETTING, AND PARTICIPANTS Longitudinal study of 163 children with ADHD (mean age at entry, 8.9 years) and 166 controls recruited mainly from a local community in Maryland. Participants were assessed with magnetic resonance imaging. Ninety-seven patients with ADHD (60%) had 2 or more images and baseline and follow-up clinical evaluations (mean follow-up, 5.7 years). MAIN OUTCOME MEASURES Cortical thickness across the cerebrum. Patients with ADHD were divided into better and worse outcome groups on the basis of a mean split in scores on the Children's Global Assessment Scale and persistence/remission of DSM-IV-defined ADHD. RESULTS Children with ADHD had global thinning of the cortex (mean reduction, -0.09 mm; P=.02), most prominently in the medial and superior prefrontal and precentral regions. Children with worse clinical outcome had a thinner left medial prefrontal cortex at baseline than the better outcome group (-0.38 mm; P=.003) and controls (-0.25 mm; P=.002). Cortical thickness developmental trajectories did not differ significantly between the ADHD and control groups throughout except in the right parietal cortex, where trajectories converged. This normalization of cortical thickness occurred only in the better outcome group. CONCLUSIONS Children with ADHD show relative cortical thinning in regions important for attentional control. Children with a worse outcome have "fixed" thinning of the left medial prefrontal cortex, which may compromise the anterior attentional network and encumber clinical improvement. Right parietal cortex thickness normalization in patients with a better outcome may represent compensatory cortical change.
Senior Officer Decision Making in the Canadian Forces

Framework In the call for proposals, the Canadian Forces Leadership Institute’s (CFLI) question related to the topic of decision-making was as follows: Decision-making: How do senior leaders make decisions? Because decision-making is such a fundamental aspect of leadership, there is a need to better understand decision making within both an organizational setting and while experiencing extreme or adverse circumstances. Explorations could include: strategic decision making; enhancing decision making skills outside the experiential model; generalizability to flag and general officers; implications for group/team decision making; and/or a review of the relevant literatures. In response, the contribution of the paper will be to consider the problem of senior officer decision-making through multiple lenses of contemporary management literature. This exercise will unfold in three general parts: -discussion of the general theoretical progression of decision making thought in the management literature -creating a model of CF senior officer decision making, informed by selections from this this theory -consideration of managerial implications and suggestions for future research for the CF within this domain
Diagnostic performance of an electronic nose, fractional exhaled nitric oxide, and lung function testing in asthma.

BACKGROUND Analysis of exhaled breath by biosensors discriminates between patients with asthma and healthy subjects. An electronic nose consists of a chemical sensor array for the detection of volatile organic compounds (VOCs) and an algorithm for pattern recognition. We compared the diagnostic performance of a prototype of an electronic nose with lung function tests and fractional exhaled nitric oxide (FENO) in patients with atopic asthma. METHODS A cross-sectional study was undertaken in 27 patients with intermittent and persistent mild asthma and in 24 healthy subjects. Two procedures for collecting exhaled breath were followed to study the differences between total and alveolar air. Seven patients with asthma and seven healthy subjects participated in a study with mass spectrometry (MS) fingerprinting as an independent technique for assessing between group discrimination. Classification was based on principal component analysis and a feed-forward neural network. RESULTS The best results were obtained when the electronic nose analysis was performed on alveolar air. Diagnostic performance for electronic nose, FENO, and lung function testing was 87.5%, 79.2%, and 70.8%, respectively. The combination of electronic nose and FENO had the highest diagnostic performance for asthma (95.8%). MS fingerprints of VOCs could discriminate between patients with asthma and healthy subjects. CONCLUSIONS The electronic nose has a high diagnostic performance that can be increased when combined with FENO. Large studies are now required to definitively establish the diagnostic performance of the electronic nose. Whether this integrated noninvasive approach will translate into an early diagnosis of asthma has to be clarified. TRIAL REGISTRATION EUDRACT https://eudralink.emea. europa.eu; Identifier: 2007-000890-51; and clinicaltrials.gov; Identifier: NCT00819676.
Unusual room-temperature compressive plasticity in nanocrystal-toughened bulk copper-zirconium glass

Cast Cu50Zr50 alloy rods with a diameter of 1 mm have been found to consist of a glassy phase containing fine crystalline particles with a size of about 5 nm. They have a glass transition temperature T g of 675 K, and a large supercooled-liquid region extending 57 K above T g. The rods exhibit a high yield strength of 1860 MPa and a Young's modulus of 104 GPa. Because they contain a dispersion of embedded nanocrystals, the as-cast bulk metallic glass rods can sustain a compressive plastic strain at room temperature of more than 50%, an exceptional value which is explicable by compensation of any shear softening by nanocrystal coalescence and pinning of shear bands.
Placement-Proximity-Based Voltage Island Grouping Under Performance Requirement

High power consumption not only leads to short battery life for hand-held devices but also causes on-chip thermal and reliability problems in general. As power consumption is proportional to the square of supply voltage, reducing supply voltage can significantly reduce power consumption. Multi-supply voltage (MSV) has previously been introduced to provide finer grain power and performance tradeoff. In this paper, we propose a methodology on top of a set of algorithms to exploit nontrivial voltage island boundaries for optimal power versus design-cost tradeoff under performance requirement. Our algorithms are efficient, robust, and error-bounded and can be flexibly tuned to optimize for various design objectives (e.g., minimal power within a given number of voltage islands, or minimal fragmentation in voltage islands within a given power bound) depending on the design requirement. Our experiment on real industry designs shows a tenfold improvement of our method over current logical-boundary-based industry approach.
Single-dose azithromycin for the treatment of cholera in adults.

BACKGROUND Single-dose azithromycin is effective in the treatment of severe cholera in children, but its effectiveness in adults has not been evaluated. METHODS We conducted a double-blind, randomized trial comparing the equivalence of azithromycin and ciprofloxacin (each given in a single 1-g dose of two 500-mg tablets) among 195 men with severe cholera caused by Vibrio cholerae O1 or O139. Patients were hospitalized for five days. A stool culture was performed daily. Primary outcome measures were clinical success (the cessation of watery stools within 48 hours after drug administration) and bacteriologic success (the inability to isolate V. cholerae after 48 hours). RESULTS Therapy was clinically successful in 71 of 97 patients receiving azithromycin (73 percent) and in 26 of 98 patients receiving ciprofloxacin (27 percent) (P<0.001) and bacteriologically successful in 76 of 97 patients receiving azithromycin (78 percent) and in 10 of 98 patients receiving ciprofloxacin (10 percent) (P<0.001). Patients who were treated with azithromycin had a shorter duration of diarrhea than did patients treated with ciprofloxacin (median, 30 vs. 78 hours); a lower frequency of vomiting (43 percent vs. 67 percent); fewer stools (median, 36 vs. 52); and a lower stool volume (median, 114 vs. 322 ml per kilogram of body weight). The median minimal inhibitory concentration of ciprofloxacin for the 177 isolates of V. cholerae O1 was 0.25 mug per milliliter, which was 11 to 83 times as high as that in previous studies at this site. CONCLUSIONS Single-dose azithromycin was effective in the treatment of severe cholera in adults. The lack of efficacy of ciprofloxacin may result from its diminished activity against V. cholerae O1 strains currently circulating in Bangladesh. (ClinicalTrials.gov number, NCT00229944.).
Biochemical and morphological evidence that the insulin receptor is internalized with insulin in hepatocytes

There is morphological and biochemical evidence that insulin is internalized in hepatocytes. The present study was designed to investigate the fate of the insulin receptor itself, subsequently to the initial binding step of the hormone to the hepatocyte plasma membrane. The insulin receptor was labeled with a 125I-photoreactive insulin analogue (B2[2-nitro,4-azidophenylacetyl]des-PheB1-insulin). This photoprobe was covalently coupled to the receptor by UV irradiation of hepatocytes after an initial binding step of 2-4 h at 15 degrees C. At this temperature, only limited (approximately 20%) internalization of the ligand occurred. In a second step, hepatocytes were resuspended in insulin-free buffer and further incubated for 2-4 h at 37 degrees C. After h at 37 degrees C, no significant radioactivity could be detected in non-UV-irradiated cells, whereas 12-15 % of the radioactivity initially bound remained associated to UV-irradiated cells. Morphological analysis after electron microscopy revealed that approximately 70% of this radioactivity was internalized and preferentially associated with lysosomal structures. SDS PAGE analysis under reducing conditions revealed that most of the radioactivity was associated with a 130,000-dalton band, previously identified as the major subunit of the insulin receptor in a variety of tissues. Internalization of the labeled insulin-receptor complex at the end of the 37 degrees C incubation was further demonstrated by its inaccessibility to trypsin. Conversely, at the end of the association step, the receptor (also characterized as a predominant 130,000-dalton species) was localized on the cell surface since it was cleaved by trypsin. We conclude that in hepatocytes the insulin receptor is internalized with insulin.
Structure activity relationship of phenolic acid inhibitors of α-synuclein fibril formation and toxicity

The aggregation of α-synuclein (α-syn) is considered the key pathogenic event in many neurological disorders such as Parkinson's disease (PD), dementia with Lewy bodies and multiple system atrophy, giving rise to a whole category of neurodegenerative diseases known as synucleinopathies. Although the molecular basis of α-syn toxicity has not been precisely elucidated, a great deal of effort has been put into identifying compounds that could inhibit or even reverse the aggregation process. Previous reports indicated that many phenolic compounds are potent inhibitors of α-syn aggregation. The aim of the present study was to assess the anti-aggregating effect of gallic acid (GA) (3,4,5-trihydroxybenzoic acid), a benzoic acid derivative that belongs to a group of phenolic compounds known as phenolic acids. By employing an array of biophysical and biochemical techniques and a cell-viability assay, GA was shown not only to inhibit α-syn fibrillation and toxicity but also to disaggregate preformed α-syn amyloid fibrils. Interestingly, GA was found to bind to soluble, non-toxic oligomers with no β-sheet content, and to stabilize their structure. The binding of GA to the oligomers may represent a potential mechanism of action. Additionally, by using structure activity relationship data obtained from fourteen structurally similar benzoic acid derivatives, it was determined that the inhibition of α-syn fibrillation by GA is related to the number of hydroxyl moieties and their position on the phenyl ring. GA may represent the starting point for designing new molecules that could be used for the treatment of PD and related disorders.
WebStage: an active media enhanced World Wide Web browser

The World Wide Web provides us with enormous opportunities to obtain global information. However, conventional browsers are time-intensive, requiring many operations with attendant mental concentration, to view the Web pages. This can ofien discourage people from seeking access to the Web. In this paper, we present an “active” Web browser, named “WebStage”. Unlike conventional browsers, it displays Web pages using a television metaphor to encourage “passive” users to access the Web.
A beyond near-infrared response in a wide-bandgap ZnO/ZnSe coaxial nanowire solar cell by pseudomorphic layers

Wide-bandgap semiconductors are potential materials for photovoltaic (PV) devices in solution-based applications because of their higher stability compared with narrow-bandgap semiconductors. However, these materials are poor absorbers of photons in the solar spectrum and yield modest conversion efficiencies. Here we show how this problem can be solved by the growth and control of pseudomorphic crystals in type-II wide-bandgap ZnO/ZnSe coaxial nanowires. Light absorption of coaxial nanowires under critical strains significantly extended beyond the near-infrared region to cover up to 94% of the solar power. The photocurrent response of the nanowire solar cell was markedly enhanced in visible and infrared regions with a threshold of approximately 0.9 eV, accounting for more than 35% of the conversion efficiency. This work paves the way for stable and efficient PV devices based on wide-bandgap semiconductors.
Coarse Grained Simulation of Lipid Membrane and Triblock Copolymers

We investigated the interaction between DPPC (Dipalmitoyl phosphatidylcholine) bilayer and polyethylene oxide‐polypropylene oxide‐polyethylene oxide (PEO‐PPO‐PEO) triblock copolymers using coarse grained simulation. We simulated two systems of DPPC bilayer and PEO‐PPO‐PEO triblock copolymer containing different mole fractions, and simulated DPPC vesicle with the copolymers. We found different adsorption mechanisms of triblock copolymers depending on concentration. And we also observed docking process between a lipid vesicle and a micelle of the copolymers.
A detailed cost model for concurrent use with hardware/software co-design

Hardware/software co-design methodologies generally focus on the prediction of system performance or co-verification of system functionality. This study extends this conventional focus through the development of a methodology and software tool that evaluates system (hardware and software) development, fabrication, and testing costs (dollar costs) concurrent with hardware/software partitioning in a co-design environment. Based on the determination of key metrics such as gate count and lines of software, a new tool called Ghost, evaluates software and hardware development, fabrication, packaging and testing costs. Ghost enables optimization of hardware/software partitioning as a function of specific combinations of hardware foundries and software development environments.
Copy Number Variation of TLR-7 Gene and its Association with the Development of Systemic Lupus Erythematosus in Female Patients from Yucatan Mexico

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the production of autoantibodies against self-antigens, which occurs most often in women between 15 and 40 years of age. The innate immunity is involved in the pathogenesis of SLE through TLR-7. Genetic factors such as copy number variation (CNV) of target genes may contribute to disease development, but this possible risk has not yet been studied in SLE patients from Yucatan, Mexico. The CNV of TLR-7 gene was determined by quantitative polymerase chain reaction assay using TaqMan probes in 80 SLE women and 150 control subjects. The results showed that 10% of SLE patients exhibited more than two copies of TLR-7 gene, whereas no mRNA overexpression was detected. These data suggested that increased CNV of the TLR-7 gene in Yucatan SLE women can be a risk factor for this disease.
Surface Modification of Carbon Nanotubes with an Enhanced Antifungal Activity for the Control of Plant Fungal Pathogen

The addition of surface functional groups to multi-walled carbon nanotubes (MWCNTs) expands their application in engineering, materials, and life science. In the study, we explored the antifungal activities of MWCNTs with different surface groups against an important plant pathogenic fungi Fusarium graminearum. All of the OH-, COOH-, and NH2-modified MWCNTs showed enhanced inhibition in spore elongation and germination than the pristine MWCNTs. The length of spores decreased by almost a half from 54.5 μm to 28.3, 27.4, and 29.5 μm, after being treated with 500 μg·mL−1 MWCNTs-COOH, MWCNTs-OH, and MWCNTs-NH2 separately. Furthermore, the spore germination was remarkably inhibited by surface-modified MWCNTs, and the germination rate was only about 18.2%, three times lower than pristine MWCNTs. The possible antifungal mechanism of MWCNTs is also discussed. Given the superior antifungal activity of surface modified MWCNTs and the fact that MWCNTs can be mass-produced with facile surface modification at low cost, it is expected that this carbon nanomaterial may find important applications in plant protection.