Miracle-dz/UniFAR-FTUs huggingface dataset:
Apparent Entropy of Cellular Automata

A radius-r one-dimensional cellular automaton (CA) is an infinite sequence of identical finite-state machines (indexed by Ÿ) called cells. Each finite-state machine is in a state and these states change simultaneously according to a local transition function: the following state of the machine is related to its own state as well as the states of its 2r neighbors. A configuration of an automaton is the function which associates to each cell a state. We can thus define a global transition function from the set of all the configurations to itself which associates the following configuration after one step of computation. Recently, a lot of articles proposed classifications of CAs [5, 8, 13] but the canonical reference is still Wolfram’s empirical classification [14] which has resisted numerous attempts of formalization. Among the latest attempts, some are based on the mathematical definitions of chaos for dynamical systems adapted to CAs thanks to Besicovitch topology [2, 6] and [11] introduces the almost everywhere sensitivity to initial conditions for this topology and compares this notion with information propagation formalization. As in [8], this notion does not really classify the CA but the CA for a measure. This gives, for instance, a tool to understand fluid flow phenomenon modeled by CA: we can now say that the CA is not almost everywhere sensitive to initial conditions (and thus almost everywhere not sensitive) for small fluid speed and almost everywhere sensitive for high fluid speed. It appears that almost everywhere sensitivity, although close to, does not really match Wolfram’s intuitive idea of chaos. To better understand
Comparison of 2 Correction Methods for Absolute Values of Esophageal Pressure in Subjects With Acute Hypoxemic Respiratory Failure, Mechanically Ventilated in the ICU

BACKGROUND: A recent trial showed that setting PEEP according to end-expiratory transpulmonary pressure (Ppl,ee) in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) might improve patient outcome. Ppl,ee was obtained by subtracting the absolute value of esophageal pressure (Pes) from airway pressure an invariant value of 5 cm H2O. The goal of the present study was to compare 2 methods for correcting absolute Pes values in terms of resulting Ppl,ee and recommended PEEP. METHODS: Measurements collected prospectively from 42 subjects with various forms of acute hypoxemic respiratory failure receiving mechanical ventilation in ICU were analyzed. Pes was measured at PEEP (Pes,ee) and at relaxation volume of the respiratory system Vr (Pes,Vr), obtained by allowing the subject to exhale into the atmosphere (zero PEEP). Two methods for correcting Pes were compared: Talmor method (Ppl,ee,Talmor = Pes,ee – 5 cm H2O), and Vr method (Pes,ee,Vr = Pes,ee – Pes,Vr). The rationale was that Pes,Vr was a more physiologically based correction factor than an invariant value of 5 cm H2O applied to all subjects. RESULTS: Over the 42 subjects, median and interquartile range of Pes,ee and Pes,Vr were 11 (7–14) cm H2O and 8 (4–11) cm H2O, respectively. Ppl,ee,Talmor was 6 (1–8) cm H2O, and Pes,ee,Vr was 2 (1–5) cm H2O (P = .008). Two groups of subjects were defined, based on the difference between the 2 corrected values. In 28 subjects Ppl,ee,Talmor was ≥ Pes,ee,Vr (7 [5–9] cm H2O vs 2 [1–5] cm H2O, respectively), while in 14 subjects Pes,ee,Vr was > Ppl,ee,Talmor (2 [0–4] cm H2O vs −1 [−3 to 2] cm H2O, respectively). Ppl,ee,Vr was significantly greater than Ppl,ee,Talmor (7 [5–11] cm H2O vs 5 [2–7] cm H2O) in the former, and significantly lower in the latter (1 [−2 to 6] cm H2O vs 6 [4–9] cm H2O). CONCLUSIONS: Referring absolute Pes values to Vr rather than to an invariant value would be better adapted to a patient's physiological background. Further studies are required to determine whether this correction method might improve patient outcome.
Understory plant community dynamics in southwestern ponderosa pine forest restoration

The research in this dissertation focused on three major components related to understory plant community dynamics in southwestern ponderosa pine forest restoration in northern Arizona. Our first goal was to compare different understory plant monitoring sampling techniques and sampling sizes. Our results illustrated that the sampling technique chosen for monitoring herbaceous and shrub species richness and foliar cover in restoration studies can greatly influence the ability to detect change. We found that large area sampling techniques were the most effective at capturing species richness and rare and exotic species. Our second goal was to quantify the effect of restoration tree thinning
Changes in themes over time from medical student journaling.

CONTEXT There has been little exploration of journaling in medical student education. OBJECTIVE To document the themes on which medical students reflect during training. DESIGN We evaluated journals kept by primary care medical students to identify prominent themes and determine change or constancy in themes over time. We looked at third-year medical students participating in a required primary care clerkship in a university-affiliated, community-based family medicine residency program with a rural catchment area. INTERVENTION During 1994-1996 and 2001-2003, students were asked to keep weekly journals reflecting on their thoughts and feelings regarding "topical content, course processes and methods, and personal reflections on becoming a doctor. " Faculty evaluated journals to identify change or constancy in themes over time. RESULTS Prominent themes included gender issues, professional identity emergence, career choice, and rural practice, the experience of learning, the experience of relating to patients, and the nature of medical practice. CONCLUSIONS We found both constancy and change in student journal themes over time. Changes in journal themes appeared to correlate with outside events and educational trends, including increased attention to reflective practice, changing demographics in medicine and the increasing acceptance of female physicians, and personal life events.
Towards a fuzzy-based multi-classifier selection module for activity recognition applications

Performing activity recognition using the information provided by the different sensors embedded in a smartphone face limitations due to the capabilities of those devices when the computations are carried out in the terminal. In this work a fuzzy inference module is implemented in order to decide which classifier is the most appropriate to be used at a specific moment regarding the application requirements and the device context characterized by its battery level, available memory and CPU load. The set of classifiers that is considered is composed of Decision Tables and Trees that have been trained using different number of sensors and features. In addition, some classifiers perform activity recognition regardless of the on-body device position and others rely on the previous recognition of that position to use a classifier that is trained with measurements gathered with the mobile placed on that specific position. The modules implemented show that an evaluation of the classifiers allows sorting them so the fuzzy inference module can choose periodically the one that best suits the device context and application requirements.
Sudden Exposure to Solar UV-B Radiation Reduces Net CO2 Uptake and Photosystem I Efficiency in Shade-Acclimated Tropical Tree Seedlings1

Tree seedlings developing in the understory of the tropical forest have to endure short periods of high-light stress when tree-fall gaps are formed, and direct solar radiation, including substantial UV light, reaches the leaves. In experiments simulating the opening of a tree-fall gap, the response of photosynthesis in leaves of shade-acclimated seedlings (Anacardium excelsum,Virola surinamensis, and Calophyllum longifolium) to exposure to direct sunlight (for 20–50 min) was investigated in Panama (9°N). To assess the effects of solar UV-B radiation (280–320 nm), the sunlight was filtered through plastic films that selectively absorbed UV-B or transmitted the complete spectrum. The results document a strong inhibition of CO2assimilation by sun exposure. Light-limited and light-saturated rates of photosynthetic CO2 uptake by the leaves were affected, which apparently occurred independently of a simultaneous inhibition of potential photosystem (PS) II efficiency. The ambient UV-B light substantially contributed to these effects. The photochemical capacity of PSI, measured as absorbance change at 810 nm in saturating far-red light, was not significantly affected by sun exposure of the seedlings. However, a decrease in the efficiency of P700 photooxidation by far-red light was observed, which was strongly promoted by solar UV-B radiation. The decrease in PSI efficiency may result from enhanced charge recombination in the reaction center, which might represent an incipient inactivation of PSI, but contributes to thermal dissipation of excessive light energy and thereby to photoprotection.
Sliding mode adaptive state observation for time-delay uncertain nonlinear systems

In this paper a method to design robust adaptive sliding mode observers (ASMO) for a class of nonlinear time- delay systems with uncertainties, is proposed. The objective is to achieve insensitivity and robustness of the proposed sliding mode observer to matched disturbances. A novel systematic design method is synthesized to solve matching conditions and compute observer stabilizing gains. The Lyapunov-Krasovskii theorem is employed to prove the ultimate stability with arbitrary boundedness radius of the estimation error of the proposed filter. Finally, the ability of ASMO for fault reconstruction is studied.
Consequences of Preset Pitch Angle on Cross-Flow Turbine Hydrodynamics

The energy conversion efficiency of a straight-bladed cross-flow turbine is examined experimentally. The preset pitch angle of the turbine blades is shown to have a large impact on turbine performance for two and four-bladed turbines over the range of tip-speed ratios tested. The optimal preset pitch angle was found to be 6◦ for both turbines and nearly all tipspeed ratios. The nominal (apparent) angle of attack in the foil frame of reference is shown to depend only on tip-speed ratio and preset pitch angle if induced velocities are neglected. Turbine performance trends are described via a critical nominal angle of attack, hypothesized to be important during dynamic stall of the foil. Interaction of the foil with a leading edge vortex generated during the dynamic stall process is proposed as an explanatory mechanism for other turbine performance trends. Other hydrodynamic factors possibly influencing turbine performance are discussed briefly. Keywords— Hydrokinetic Energy, Cross-Flow Turbine, Pitch Angle, Tip-Speed Ratio, Dynamic Stall, Vortex Dynamics
Multicenter Evaluation of the Performance Characteristics of the NucliSens HIV-1 QT Assay Used for Quantitation of Human Immunodeficiency Virus Type 1 RNA

ABSTRACT The analytical performance of the NucliSens HIV-1 QT assay, a highly sensitive test based on nucleic acid sequence-based amplification technology, was evaluated in a multicenter trial. Assay specificity was evaluated with 502 plasma (EDTA) specimens from human immunodeficiency virus type 1 (HIV-1)-seronegative volunteer donors. No HIV-1 RNA was reported in any of the donor specimens. Analytical sensitivity and reproducibility were estimated with panels prepared from a high-titer well-characterized HIV-1 RNA stock (5.84 × 108 RNA copies/ml). The assay's dynamic range was linear from 106 to 101 HIV-1 RNA copies, with a lower detectable limit of 25 copies/ml and a 95% detection rate of 176 copies/ml. Sensitivity of the assay to detect HIV-1 RNA in clinical specimens from patients (n = 101) and in commercially available or prepared panels (n = 24) was compared with NASBA HIV-1 RNA QT (an earlier version of NucliSens HIV-1 QT) and with the Food and Drug Administration-approved standard and ultrasensitive AMPLICOR HIV-1 MONITOR, version 1.0, assays. Detection of HIV-1 RNA was reproducible over a 5-log range (mean standard deviation = 0.15 log). The NucliSens and the standard AMPLICOR assays were equivalent in detection of HIV-1 RNA (concentration, 103 to 105 copies/ml) in 57 clinical specimens. The NucliSens assay was more sensitive in detecting HIV-1 RNA at lower concentrations (≤102 copies/ml) (44 of 44) than either the standard AMPLICOR test (12 of 19) or the NASBA assay (10 of 25). A 25% increase in HIV-1 RNA detection frequency with panels was observed with the NucliSens assay (23 of 24) compared with the standard AMPLICOR test (17 of 24). The new assay was highly specific and demonstrated good sensitivity with a broad linear dynamic range.
New realities in aircraft design and manufacture

Considers how Boeing Computer Services in Seattle is developing two real-time applications-one in virtual reality, the other in what the company calls augmented reality, aimed at putting more information directly in front of the engineers designing aircraft and the manufacturing workers who build them. Boeing's virtual reality project plans to import aircraft CAD data to a VR environment where engineers in helmet-mounted displays can explore the aircraft long before any manufacturing begins. Boeing (like other aircraft manufacturers) have switched to performing aircraft checks on a CAD system, moving a human figure on-screen to check access. <<ETX>>
Modeling Single-Neuron Dynamics and Computations: A Balance of Detail and Abstraction

The fundamental building block of every nervous system is the single neuron. Understanding how these exquisitely structured elements operate is an integral part of the quest to solve the mysteries of the brain. Quantitative mathematical models have proved to be an indispensable tool in pursuing this goal. We review recent advances and examine how single-cell models on five levels of complexity, from black-box approaches to detailed compartmental simulations, address key questions about neural dynamics and signal processing.
Efficient Generation of Functional Dopaminergic Neurons from Human Induced Pluripotent Stem Cells Under Defined Conditions

Human induced pluripotent stem cells (iPSCs) reprogrammed from somatic cells represent a promising unlimited cell source for generating patient‐specific cells for biomedical research and personalized medicine. As a first step, critical to clinical applications, we attempted to develop defined culture conditions to expand and differentiate human iPSCs into functional progeny such as dopaminergic neurons for treating or modeling Parkinson's disease (PD). We used a completely defined (xeno‐free) system that we previously developed for efficient generation of authentic dopaminergic neurons from human embryonic stem cells (hESCs), and applied it to iPSCs. First, we adapted two human iPSC lines derived from different somatic cell types for the defined expansion medium and showed that the iPSCs grew similarly as hESCs in the same medium regarding pluripotency and genomic stability. Second, by using these two independent adapted iPSC lines, we showed that the process of differentiation into committed neural stem cells (NSCs) and subsequently into dopaminergic neurons was also similar to hESCs. Importantly, iPSC‐derived dopaminergic neurons were functional as they survived and improved behavioral deficits in 6‐hydroxydopamine‐leasioned rats after transplantation. In addition, iPSC‐derived NSCs and neurons could be efficiently transduced by a baculoviral vector delivering episomal DNA for future gene function study and disease modeling using iPSCs. We also performed genome‐wide microarray comparisons between iPSCs and hESCs, and we derived NSC and dopaminergic neurons. Our data revealed overall similarity and visible differences at a molecular level. Efficient generation of functional dopaminergic neurons under defined conditions will facilitate research and applications using PD patient‐specific iPSCs. STEM CELLS 2010;28:1893–1904
Fuzzy optimization for detecting enzyme targets of human uric acid metabolism

MOTIVATION Mathematical modeling and optimization have been used for detecting enzyme targets in human metabolic disorders. Such optimal drug design methods are generally differentiated as two stages, identification and decision-making, to find optimal targets. We developed a unified method named fuzzy equal metabolic adjustment to formulate an optimal enzyme target design problem for drug discovery. The optimization framework combines the identification of enzyme targets and a decision-making strategy simultaneously. The objectives of this algorithm include evaluations of the therapeutic effect of target enzymes, the adverse effects of drugs and the minimum effective dose (MED). RESULTS An existing generalized mass action system model of human uric acid (UA) metabolism was used to formulate the fuzzy optimization method for detecting two types of enzymopathies: hyperuricemia caused by phosphoribosylpyrophosphate synthetase (PRPPS) overactivity and Lesch-Nyhan syndrome. The fuzzy objectives were set so that the concentrations of the metabolites were as close as possible to the healthy levels. The target design included a diet control of ribose-5-phospahate (R5P). The diet control of R5P served as an extra remedy to reduce phosphate uptake entering the purine metabolic pathway, so that we could obtain a more satisfactory treatment than obtained for those without a diet control. Moreover, enhancing UA excretion resulted in an effective treatment of hyperuricemia caused by PRPPS overactivity. This result correlates with using probenecid and benbromazone, which are uricosuric agents present in current clinical medications. By contrast, the Lesch-Nyhan syndrome required at least three enzyme targets to cure hyperuricemia.
Central Pulse Pressure and Mortality in End-Stage Renal Disease

Damage of large arteries is a major factor in the high cardiovascular morbidity and mortality of patients with end-stage renal disease (ESRD). Increased aortic pulse wave velocity (PWV) and brachial pulse pressure (PP) are the principal arterial markers of cardiovascular mortality described in these patients. Whether central (carotid) PP and brachial-carotid PP amplification may predict all-cause (including cardiovascular) mortality has never been investigated. A cohort of 180 patients with ESRD who were undergoing hemodialysis was studied between January 1990 and March 2000. The mean duration of follow-up was 52±36 months (mean±SD). Mean age at entry was 51.5±16.3 years. Seventy deaths occurred, including both cardiovascular and noncardiovascular fatal events. At entry, patients underwent carotid PP measurements (pulse wave analysis), echocardiography, and aortic PWV (Doppler ultrasonography), together with standard clinical and biochemical analyses. On the basis of Cox analyses, after adjustment of age, time on dialysis before inclusion, and previous cardiovascular events, 3 factors emerged as predictors of all-cause mortality: carotid PP, brachial/carotid PP, and aortic PWV. Adjusted hazard ratios for 1-SD increments were 1.4 (1.1 to 1.8) for carotid PP, 0.5 (0.3 to 0.8) for brachial/carotid PP, and 1.3 (1.0 to 1.7) for PWV. Brachial blood pressure, including PP, had no predictive value for mortality after adjustment. These results provide the first direct evidence that in patients with ESRD, the carotid PP level and, mostly, the disappearance of PP amplification are strong independent predictors of all-cause (including cardiovascular) mortality.
What do we mean by prediction in language comprehension?

ABSTRACT We consider several key aspects of prediction in language comprehension: its computational nature, the representational level(s) at which we predict, whether we use higher-level representations to predictively pre-activate lower level representations, and whether we “commit” in any way to our predictions, beyond pre-activation. We argue that the bulk of behavioural and neural evidence suggests that we predict probabilistically and at multiple levels and grains of representation. We also argue that we can, in principle, use higher-level inferences to predictively pre-activate information at multiple lower representational levels. We suggest that the degree and level of predictive pre-activation might be a function of its expected utility, which, in turn, may depend on comprehenders’ goals and their estimates of the relative reliability of their prior knowledge and the bottom-up input. Finally, we argue that all these properties of language understanding can be naturally explained and productively explored within a multi-representational hierarchical actively generative architecture whose goal is to infer the message intended by the producer, and in which predictions play a crucial role in explaining the bottom-up input.
Comparison of decentralized time slot allocation strategies for asymmetric traffic in TDD systems

Recently, wireless multimedia services have been growing because of the spread of various wireless applications. Hence, time division duplex (TDD) systems and their crossed-slot interference problems in a cellular environment have been attracting growing interests. Considering large signaling overhead between cells, decentralized time slot allocation (TSA) strategy is suitable for practical implementation. Thus, Fixed-TSA strategy which fixes the same ratio of uplink and downlink time slots in all cells is adopted in commercial WiBro systems (IEEE802.16e Mobile WiMax) to mitigate the crossed-slot interference. However, the Fixed-TSA strategy reduces the flexibility in time slot allocation due to a strong constraint set by a predefined boundary. Moreover, the mathematical derivation of the optimal value for the predefined boundary has not been presented yet. In this paper, we propose two decentralized TSA strategies. The first one is Enhanced Fixed-TSA strategy, which dynamically adapts the predefined boundary of the conventional Fixed-TSA strategy according to traffic conditions. The second one is region-based Decentralized Time Slot Allocation (RED-TSA) strategy, which utilizes partial location information of MSs to reduce crossedslot interference. We fully analyze the proposed TSA strategies in terms of new call blocking probability, average bit error probability, and the overall system throughput. Numerical results show that the proposed RED-TSA strategy provides the highest system throughput by compromising both new call blocking performance and average bit error performance, whereas it requires additional location information and complicated computation. On the contrary, the proposed Enhanced Fixed-TSA strategy requires reasonable computational complexity while it provides almost the same system throughput with that of the proposed RED-TSA strategy. In a nutshell, the proposed Enhanced Fixed- TSA strategy is more appropriate for the practical systems. Moreover, it can be directly applied to the current commercial WiMax/WiBro systems with minimum changes.