Miracle-dz/UniFAR-FTUs huggingface dataset:
Project Management and Workflow Analysis of Agile Manufacturing

Agile manufacturing (AM) is a typical concurrent and collaborative way between different enterprises and different departments in order to meet market requirement for time, cost and quality as soon as possible. From the point of view, AM is special project management. Agile manufacturing and project management (PM) have many same characteristics. The characteristics and relations of AM and PM are discussed firstly. The resources of the manufacturing enterprise alliances have characteristics such as autonomous, distributed, heterogeneous, dynamic, and so on. Therefore, the PM of AM is different from traditional PM. Secondly, a typical workflow of agile manufacturing is illustrated. Then the architecture of PM of agile manufacturing is proposed and analyzed, which includes some key technologies to support good project management. Combining the automation and standards of the workflow with the PM of high quality is a good solution to agile manufacturing. Finally, the technologies of information exchange and communication mechanism are introduced.
Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway

The TOL plasmid upper pathway operon encodes enzymes involved in the catabolism of aromatic hydrocarbons such as toluene and xylenes. The regulator of the gene pathway, the XylR protein, exhibits a very broad effector specificity, being able to recognize as effectors not only pathway substrates but also a wide variety of mono- and disubstituted methyl-, ethyl-, and chlorotoluenes, benzyl alcohols, and p-chlorobenzaldehyde. Benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase, two upper pathway enzymes, exhibit very broad substrate specificities and transform unsubstituted substrates and m- and p-methyl-, m- and p-ethyl-, and m- and p-chloro-substituted benzyl alcohols and benzaldehydes, respectively, at a high rate. In contrast, toluene oxidase only oxidizes toluene, m- and p-xylene, m-ethyltoluene, and 1,2,4-trimethylbenzene [corrected], also at a high rate. A biological test showed that toluene oxidase attacks m- and p-chlorotoluene, albeit at a low rate. No evidence for the transformation of p-ethyltoluene by toluene oxidase has been found. Hence, toluene oxidase acts as the bottleneck step for the catabolism of p-ethyl- and m- and p-chlorotoluene through the TOL upper pathway. A mutant toluene oxidase able to transform p-ethyltoluene was isolated, and a mutant strain capable of fully degrading p-ethyltoluene was constructed with a modified TOL plasmid meta-cleavage pathway able to mineralize p-ethylbenzoate. By transfer of a TOL plasmid into Pseudomonas sp. strain B13, a clone able to slowly degrade m-chlorotoluene was also obtained.
A Behavioral Modification of Popular Option Pricing Models

In incomplete markets, risk judgments regarding options are necessary as options cannot be replicated by using the underlying stock and the risk-free asset. How are such risk judgments formed? Underlying stock risk is a natural starting point for call option risk as the two assets pay off in the same states, and call option volatility is a scaled-up version of the underlying stock volatility. However, using underlying stock volatility as a starting point and attempting to scaleup appropriately exposes investors to anchoring bias, which lowers the risk-premium demanded on a call option. I show that anchoring-influenced option prices always lie within no-arbitrage bounds in incomplete markets. Modified versions of Black-Scholes, Heston, and Bates models are put forward. Modified models show improvements across several dimensions, while capturing several option-return puzzles. Two novel predictions arising from the modification are also empirically supported.
Phosphorylation of the UL31 Protein of Herpes Simplex Virus 1 by the US3-Encoded Kinase Regulates Localization of the Nuclear Envelopment Complex and Egress of Nucleocapsids

ABSTRACT Herpes simplex virus 1 nucleocapsids bud through the inner nuclear membrane (INM) into the perinuclear space to obtain a primary viral envelope. This process requires a protein complex at the INM composed of the UL31 and UL34 gene products. While it is clear that the viral kinase encoded by the US3 gene regulates the localization of pUL31/pUL34 within the INM, the molecular mechanism by which this is accomplished remains enigmatic. Here, we have determined the following. (i) The N terminus of pUL31 is indispensable for the protein's normal function and contains up to six serines that are phosphorylated by the US3 kinase during infection. (ii) Phosphorylation at these six serines was not essential for a productive infection but was required for optimal viral growth kinetics. (iii) In the presence of active US3 kinase, changing the serines to alanine caused the pUL31/pUL34 complex to aggregate at the nuclear rim and caused some virions to accumulate aberrantly in herniations of the nuclear membrane, much as in cells infected with a US3 kinase-dead mutant. (iv) The replacement of the six serines of pUL31 with glutamic acid largely restored the smooth distribution of pUL34/pUL31 at the nuclear membrane and precluded the accumulation of virions in herniations whether or not US3 kinase was active but also precluded the optimal primary envelopment of nucleocapsids. These observations indicate that the phosphorylation of pUL31 by pUS3 represents an important regulatory event in the virion egress pathway that can account for much of pUS3's role in nuclear egress. The data also suggest that the dynamics of pUL31 phosphorylation modulate both the primary envelopment and the subsequent fusion of the nascent virion envelope with the outer nuclear membrane.
Docking ligands onto binding site representations derived from proteins built by homology modelling.

Due to the abundant sequence information available from genome projects, an increasing number of structurally unknown proteins, homologous to examples of known 3D structure, will be discovered as new targets for drug design. Since homology models do not provide sufficient accuracy to apply common drug design tools, a new approach, DragHome, has been developed to dock ligands into such approximate protein models. DragHome combines information from homology modelling with ligand data, used by and derived from 3D quantitative structure-activity relationships (QSAR). The binding-site of a model-built protein is analysed in terms of putative ligand interaction sites and translated via Gaussian functions into a functional binding-site description represented by physico-chemical properties. Ligands to be docked onto these binding-site representations are similarly translated into a description based on Gaussian functions. The docking is computed by optimising the overlap between the functional description of the binding site and the ligand, generating multiple solutions. For a set of different ligands, these solutions are ranked according to the internal similarity consistance among the various ligands in the binding modes obtained from docking. DragHome has been validated at examples for which crystal structures are available: structurally distinct thrombin inhibitors were docked onto models of thrombin generated from serine proteases of 28 to 40 % sequence identity, yielding ligand binding modes with an average RMS deviation of 1.4 A. Mostly the near-native solutions are ranked best. Molecular flexibility of ligands can be considered in terms of pre-calculated multiple conformers. DragHome has been used to automatically generate an alignment of 88 thrombin inhibitors, for which a significant 3D QSAR model could be derived. The contribution maps resulting from this analysis can be interpreted with respect to the surrounding protein model. They highlight inconsistencies and deficiencies present in the model. In future developments, this information could be fed back into a subsequent modelling step to improve the protein model.
Robust object pose estimation with point clouds from vision and touch

We present a study of object pose estimation performed with hybrid visuo-tactile sensing in mind. We propose that a tactile sensor can be treated as a source of dense local geometric information, and hence consider it to be a point cloud source analogous to an RGB-D camera. We incorporate the tactile geometric information directly into a conventional point-cloud-based articulated object tracker based on signed-distance functions. This tracker runs at 12 Hz using an online depth reconstruction algorithm for the GelSight tactile sensor and a modified second-order update for the tracking algorithm. The tracker provides robust pose estimates of small objects throughout manipulation, even when the objects are occluded by the robot’s end effector. To address limitations in this tracker, we additionally present a formulation of the underlying point-cloud correspondence problem as a mixed-integer convex program, which we efficiently solve to optimality with an off-the-shelf branch and bound solver. We show that reasoning about object pose estimation in this way allows natural extension to point-to-mesh correspondence, multiple object estimation, and outlier rejection without losing the ability to obtain a globally optimal solution. We probe the extent to which rich problem-specific formulations typically tackled with unreliable nonlinear optimization can be rigorously treated in a global optimization framework. Thesis Supervisor: Russ Tedrake Title: Professor of Electrical Engineering and Computer Science
Reducing bacterial counts in dental unit waterlines: distilled water vs. antimicrobial agents.

BACKGROUND This study evaluated five chemical disinfectants to compare their abilities to improve dental unit waterline quality and assess their effects, if any, on the biofilm layer. METHODS Sixty new dental units, with a closed-circuit water system, were used to compare microbial levels in DUWLs treated with five antimicrobials: Listerine, Bio 2000, Rembrandt, Dentosept, and sodium fluoride to a control group of sterile distilled water alone over a six-week period. For all units, the waterlines were filled with solution, left overnight, and then flushed for 30 seconds with sterile distilled water the following morning prior to patient treatment. Waterlines were examined for biofilm buildup using scanning electron microscopy and colony-forming-unit counts. RESULTS The sodium fluoride and the four chemical antimicrobials reduced the microbial count to 200 cfu/ml or less. Only samples taken from dental units receiving the control treatment (distilled water with no added antimicrobial) failed to meet ADA's stated goal. Examination of the SEMs revealed an apparent decrease in the biofilm mass but not elimination, despite repeated treatment with the four antimicrobial materials. CONCLUSIONS Even in a closed-circuit water system, distilled water alone cannot reduce microbial contamination of dental treatment water from dental unit waterlines to the 200 cfu/ml ADA stated goal. However, water treated with Listerine mouthrinse, Rembrandt mouthrinse, Bio 2000, 0.5 percent sodium fluoride and Dentosept, did meet the microbial reduction goal. The biofilm apparently was reduced in volume, but not entirely eliminated. CLINICAL SIGNIFICANCE The ADA goal of a maximum of 200 cfu/ml was achieved using any of five chemical antimicrobials and distilled water in a closed-water system. Despite the successful reduction in microbial contamination of the dental treatment water, the biofilm was not completely eliminated. Biofilm elimination and prevention would be needed through some other means.
Quantitative Risk Estimation for a Legionella pneumophila Infection Due to Whirlpool Use

Quantitative microbiological risk assessment was used to quantify the risk associated with the exposure to Legionella pneumophila in a whirlpool. Conceptually, air bubbles ascend to the surface, intercepting Legionella from the traversed water. At the surface the bubble bursts into dominantly noninhalable jet drops and inhalable film drops. Assuming that film drops carry half of the intercepted Legionella, a total of four (95% interval: 1–9) and 4.5×104 (4.4×104 – 4.7×104) cfu/min were estimated to be aerosolized for concentrations of 1 and 1,000 legionellas per liter, respectively. Using a dose‐response model for guinea pigs to represent humans, infection risks for active whirlpool use with 100 cfu/L water for 15 minutes were 0.29 (∼0.11–0.48) for susceptible males and 0.22 (∼0.06–0.42) for susceptible females. A L. pneumophila concentration of ≥1,000 cfu/L water was estimated to nearly always cause an infection (mean: 0.95; 95% interval: 0.9–∼1). Estimated infection risks were time‐dependent, ranging from 0.02 (0–0.11) for 1‐minute exposures to 0.93 (0.86–0.97) for 2‐hour exposures when the L. pneumophila concentration was 100 cfu/L water. Pool water in Dutch bathing establishments should contain <100 cfu Legionella/L water. This study suggests that stricter provisions might be required to assure adequate public health protection.
Enoxaparin Use in Pregnancy: State of the Art

Low-molecular-weight heparin is the anticoagulant of choice in pregnancy. Enoxaparin has been increasingly used over the past 20 years in pregnant women at risk of thrombosis and pregnancy complications. The main indications are prophylaxis of venous thromboembolism and prevention of pregnancy loss in thrombophilic women. Other indications include treatment of venous thromboembolism, prophylaxis of arterial thrombosis in pregnant women with mechanical heart valves and prevention of late gestational complication such as pre-eclampsia and intrauterine growth restriction. Enoxaparin does not cross the placenta and is safe for the fetus. Maternal side effects are uncommon and include mild localized allergic reactions in 2% and increased bleeding in 2%, which is dose dependent. Heparin-induced thrombocytopenia is very rare and bone resorption is not clinically relevant. The mechanisms of action of enoxaparin in pregnancy are multiple and include anti-factor Xa (anti-Xa) activity in maternal circulation, tissue factor pathway inhibitor release from endothelial cells and trophoblasts at the placental level as well as anti-inflammatory effects.
Proportional Hazards Regression in Epidemiologic Follow-up Studies: An Intuitive Consideration of Primary Time Scale

In epidemiologic cohort studies of chronic diseases, such as heart disease or cancer, confounding by age can bias the estimated effects of risk factors under study. With Cox proportional-hazards regression modeling in such studies, it would generally be recommended that chronological age be handled nonparametrically as the primary time scale. However, studies involving baseline measurements of biomarkers or other factors frequently use follow-up time since measurement as the primary time scale, with no explicit justification. The effects of age are adjusted for by modeling age at entry as a parametric covariate. Parametric adjustment raises the question of model adequacy, in that it assumes a known functional relationship between age and disease, whereas using age as the primary time scale does not. We illustrate this graphically and show intuitively why the parametric approach to age adjustment using follow-up time as the primary time scale provides a poor approximation to age-specific incidence. Adequate parametric adjustment for age could require extensive modeling, which is wasteful, given the simplicity of using age as the primary time scale. Furthermore, the underlying hazard with follow-up time based on arbitrary timing of study initiation may have no inherent meaning in terms of risk. Given the potential for biased risk estimates, age should be considered as the preferred time scale for proportional-hazards regression with epidemiologic follow-up data when confounding by age is a concern.
The Genetic Epidemiology of Self-Esteem

Background Previous studies on self-esteem have focused exclusively on its psychosocial determinants. The goal of the present study is to clarify genetic v. environmental determinants of self-esteem. Method Participants were Caucasian women sampled from the Virginia Twin Register: 363 pairs of MZ and 238 pairs of DZ twins were available from the first wave of the study, and 430 pairs of MZ and 308 pairs of DZ twins from the second. Self-esteem was assessed with the Rosenberg's Self-Esteem Scale. Results Using univariate twin analyses of self-esteem and a repeated measurement twin model, we found that self-esteem is a moderately heritable trait (heritability = 52% in the repeated measurement model); environmental influences are also very important, and are probably mostly not shared by members of a twin pair. Conclusions Aetiological models of self-esteem which examine only psychosocial factors are incomplete; genetic factors need to be integrated.
Fast Circular Tomography Device for Cardiac Imaging: Image Deflection Mechanism and Evaluation

A circular tomography system for cardiac imaging is described and measurements of the detector system are presented. Fast tomographic motion is obtained with a custom-made rotating focal spot X-ray tube combined with servo-operated scanning mirrors that deflect the optical image between a large field of view image intensifier and television camera. The motion of the deflection mirrors is locked in frequency and phase to the position of the focal spot with precision analog electronics. Initial measurements on the system components indicate that circular tomograms of the beating heart can be obtained in 1/60 s at rates as high as 30/s. Image degradation due to focal spot tracking error is minimal; however, the optical temporal lag of a P-20 type image intensifier output phosphor results in a factor of three contrast loss for millimeter-sized objects. A linear system analysis in conjunction with the measured temporal step response of the phosphor is in good agreement with the magnitude of this contrast loss.
Improving the accessibility of the EHR system with a fuzzy hierarchy of contexts

Improving the accessibility to the information stored in the Electronic Health Records (EHRs) and the usability of the Hospital Information Systems (HISs), is an important issue to solve currently, due to the great impact that they have in the quality of the attention given to the patients. Having the most useful information for the present assistance act easily and quickly available means better informed decisions and less time required for the consultation. In this paper we propose an improvement of the contextualized access to the EHR based on the definition of a fuzzy hierarchy over the contexts, that provides the system with a better accessibility to the data. Not only in the usual medical situations, but also for the cases in which the information most relevant corresponds to several contexts (like patients with several pathologies or medical trials), or the cases when the context is not defined in the system (like in the interoperability problem).
Crime and Unemployment Insurance in the Great Recession

Crime fell sharply in the United States during the Great Recession, at a time of deep economic decline. This was a puzzle: crime is expected to rise, not fall, when unemployment rises. Using a novel identification strategy, I show that unemployment insurance (UI) benefit extensions can account for part of the puzzle, explaining why crime did not rise. The higher propensity to commit crime associated with higher joblessness was mitigated by the fact that UI was more generous, replacing a larger portion of pre-unemployment income for a longer time. I use exogenous variation provided by different state-level UI extension rules in the length of benefits to identify the impact of unemployment benefits on crime. I estimate that in places with an additional $1,000 rise in UI per unemployed person crime would have been 1.5% higher were it not for the extensions. UI extensions can account up to half of the reason why crime did not rise.
Describing complex cells in primary visual cortex: a comparison of context and multifilter LN models

Receptive field (RF) models are an important tool for deciphering neural responses to sensory stimuli. The two currently popular RF models are multifilter linear-nonlinear (LN) models and context models. Models are, however, never correct, and they rely on assumptions to keep them simple enough to be interpretable. As a consequence, different models describe different stimulus-response mappings, which may or may not be good approximations of real neural behavior. In the current study, we take up two tasks: 1) we introduce new ways to estimate context models with realistic nonlinearities, that is, with logistic and exponential functions, and 2) we evaluate context models and multifilter LN models in terms of how well they describe recorded data from complex cells in cat primary visual cortex. Our results, based on single-spike information and correlation coefficients, indicate that context models outperform corresponding multifilter LN models of equal complexity (measured in terms of number of parameters), with the best increase in performance being achieved by the novel context models. Consequently, our results suggest that the multifilter LN-model framework is suboptimal for describing the behavior of complex cells: the context-model framework is clearly superior while still providing interpretable quantizations of neural behavior. NEW & NOTEWORTHY We used data from complex cells in primary visual cortex to estimate a wide variety of receptive field models from two frameworks that have previously not been compared with each other. The models included traditionally used multifilter linear-nonlinear models and novel variants of context models. Using mutual information and correlation coefficients as performance measures, we showed that context models are superior for describing complex cells and that the novel context models performed the best.
Blood metabolism study on protection of residual renal function of hemodialysis patients by traditional Chinese medicine Kidney Flaccidity Compound.

In recent years, metabolomics using high-performance liquid chromatography (UPLC) has been used to study the metabolic profiles in plasma, urine, stool and tissue in animal model of chronic kidney disease (CKD). In the previous work, we found that traditional Chinese medicine (TCM) "Kidney Flaccidity Compound" (KFC) based on "kidney flaccidity theory" can improve renal function and quality of life of patients with kidney disease. This study aimed to investigate the metabolic profiles in peripheral blood of hemodialysis patients administrated by KFC for 1.5 and 3 months and explore the potential metabolic mechanism using UPLC. Results showed that 121 metabolites were different between KFC 3-months group and untreated control, of which 75 were significantly upregulated and 46 were significantly downregulated. In the 1.5-months treatment group, there were 365 metabolites, of which 164 were significantly upregulated and 192 downregulated. There were 6 metabolites and 15 metabolites upregulated 3-fold in 3-months and 1.5-months KFC treatment group, respectively. In addition, more than 60 new metabolites were identified in the peripheral blood in KFC treated patients, including two potential diagnostic markers MGDG 30:8 and 2-(hydroxymethyl)-6-[[(1R,4S) -2,2,4-trimethyl-3-oxabicyclo[2.2. 2]octan-5-yl]oxy]oxane-3,4,5-triol. The pathway enrichment analysis showed thce differential metabolites mainly enriched in Arginine and proline metabolism, Urea cycle, Tyrosine metabolism, Methionine metabolism, Tricarboxylic acid cycle, and Androgen and estrogen metabolism. The findings are helpful to reveal the mechanism of KFC protects CKD, and to provide a new strategy for recovery renal function in hemodialysis patients.