Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of longitudinal bacterial carriage studies accounting for sensitivity of swabbing: an application to Neisseria meningitidis

Longitudinal carriage studies of colonizing bacteria such as Neisseria meningitidis can provide important insights into the transmission dynamics of these organisms. Carriage is detected by culturing from a nasopharyngeal swab, but the sensitivity of this technique is low and varies between studies. This paper applies a statistical method for estimating the sensitivity of swabbing, infection rate, recovery rate and initial prevalence of carriage to three longitudinal carriage studies of N. meningitidis. These parameters and 95% confidence intervals were estimated using maximum likelihood techniques. The sensitivity of swabbing was estimated to be 60–83% and this should be taken into account when interpreting carriage studies. The estimates of force of infection and recovery rates seem to be consistent with estimates from more traditional methods. Differences in the parameter estimates between datasets may be due to differences in study design. This method could be used to assist in the design of future carriage studies.
A Generalized-Laguerre--Fourier--Hermite Pseudospectral Method for Computing the Dynamics of Rotating Bose--Einstein Condensates

A time-splitting generalized-Laguerre–Fourier–Hermite pseudospectral method is proposed for computing the dynamics of rotating Bose–Einstein condensates (BECs) in two and three dimensions. The new numerical method is based on the following: (i) the use of a time-splitting technique for decoupling the nonlinearity; (ii) the adoption of polar coordinates in two dimensions and cylindrical coordinates in three dimensions such that the angular rotation term becomes constant coefficient; and (iii) the construction of eigenfunctions for the linear operator by properly scaling the generalized-Laguerre, Fourier, and Hermite functions. The new method enjoys the following properties: (i) it is explicit, time reversible, and time transverse invariant; (ii) it conserves the position density and is spectrally accurate in space and second-order or fourth-order accurate in time; and (iii) it solves the problem in the original whole space instead of in a truncated artificial computational domain. The method is also extend.
Creating False Memories

n 1986 Nadean Cool, a nurse’ s aidein Wisconsin, sought therapy fr oma psychiatrist to help her cope withher reaction to a traumatic event expe -rienced by her daughter. During thera-py, the psychiatrist used hypnosis andother suggestive techniques to dig outburied memories of abuse that Coolherself had allegedly experienced. In theprocess, Cool became convinced thatshe had repressed memories of havingbeen in a satanic cult, of eating babies,of being raped, of having sex with ani-mals and of being forced to watch themurder of her eight-year -old friend. Shecame to believe that she had mor e than120 personalities
Hilbert's 14th problem and Cox rings

Our main result is the description of generators of the total coordinate ring of the blow-up of $\mathbb{P}^n$ in any number of points that lie on a rational normal curve. As a corollary we show that the algebra of invariants of the action of a two-dimensional vector group introduced by Nagata is finitely generated by certain explicit determinants. We also prove the finite generation of the algebras of invariants of actions of vector groups related to T-shaped Dynkin diagrams introduced by Mukai.
Biological stoichiometry of Daphnia growth: An ecophysiological test of the growth rate hypothesis

The growth rate hypothesis (GRH) proposes that variation in organism C: P and N: P ratios reflects variation in P content associated with altered allocation to P‐rich ribosomal RNA under different growth rates. We tested the GRH by examining the effects of food quantity and stoichiometric quality (differing carbon : nitrogen : phosphorus [C :N: P] ratios) on juvenile growth and chemical composition (C :N: P, RNA, and DNA contents) of two species of Daphnia (D. galeata, D. pulicaria). Daphnia in P‐limited experiments were fed saturating and limiting concentrations of food (Scenedesmus acutus) of high P (C: P = 110 ± 7.3), medium P (456 ± 20.7), and low P (934 ± 23.6), and in an N‐limited experiment D. pulicaria was fed saturating concentrations of high N (C:N = 6.31 ± 0.35), medium 1 and medium 2 (9.0 ± 0.42; 15.0 ± 0.49, respectively), and low N (18.22 ± 0.56) food. In P‐limited experiments, both Daphnia species grew fastest under P‐rich, high food conditions and grew slowest under P‐deficient, low food conditions, showing effects of both food quality and quantity. Daphnia body percentage P, C: P, N: P, and percentage RNA were tightly correlated with growth rates, and RNA contributed a significant fraction of total body P (48.8% [62.0%]). This strong three‐way (growth‐RNA‐P) set of correlations supports the GRH. In the N‐limited experiment, food C:N had a moderate effect on Daphnia growth. While there was a good linear correlation between P and RNA, growth rate was uncorrelated with RNA content and P content, suggesting that the three‐way coupling of growth, RNA, and P content is broken under N limitation of growth, but more data for these conditions are needed. These data help in delineating the physiological conditions under which the GRH holds and may be useful in interpreting variation in body stoichiometry of zooplankton from field and lab studies.
Adaptive Distributional Extensions to DFR Ranking

Divergence From Randomness (DFR) ranking models assume that informative terms are distributed in a corpus differently than non-informative terms. Different statistical models (e.g. Poisson, geometric) are used to model the distribution of non-informative terms, producing different DFR models. An informative term is then detected by measuring the divergence of its distribution from the distribution of non-informative terms. However, there is little empirical evidence that the distributions of non-informative terms used in DFR actually fit current datasets. Practically this risks providing a poor separation between informative and non-informative terms, thus compromising the discriminative power of the ranking model. We present a novel extension to DFR, which first detects the best-fitting distribution of non-informative terms in a collection, and then adapts the ranking computation to this best-fitting distribution. We call this model Adaptive Distributional Ranking (ADR) because it adapts the ranking to the statistics of the specific dataset being processed each time. Experiments on TREC data show ADR to outperform DFR models (and their extensions) and be comparable in performance to a query likelihood language model (LM).
In-Fiber Mach–Zehnder Interferometer Based on Double Cladding Fibers for Refractive Index Sensor

An in-fiber Mach-Zehnder interferometer (MZI) was fabricated and characterized for solution refractive index (RI) sensors. The MZI consists of two cascade double cladding fibers (DCFs) in a standard single mode fiber (SMF). The DCFs serve as the in-fiber couplers which split and combine light propagating in the core and the outer cladding region. Since the cladding mode is excited, the interference spectrum is sensitive to the ambient RI variation. Within the RI range from 1.3333 to 1.4535, the sensor characteristics were characterized. The sensitivity of 31 nm/RIU and 823 nm/RIU were obtained for the lower RI (1.34) and the higher RI (1.44), respectively. With the mass-producing of DCF and the easy fabrication process of the sensor head, the proposed in-fiber MZI is a potential alternative for the RI sensor application.
A 2 GHz effective sampling frequency K-Delta-1-Sigma analog-to-digital converter

As CMOS technology scales to nanometer dimensions, analog-to-digital converter (ADC) design has become increasingly more challenging. This is mainly due to the increased transistor leakage currents, process variations, and poor matching. The K-Delta-1-Sigma (KD1S) modulator was proposed as a practical solution for designing high-speed ADCs in nanometer CMOS processes. This paper presents an 8-path KD1S modulator with an effective sampling frequency of 2 GHz derived from a 250 MHz input clock. The simulation results confirm the true first-order noise shaping of the modulator. The simulated SNR is 44.95 dB and the simulated SNDR is 44.41 dB corresponding to Neff = 7.17 bits with a conversion bandwidth of 15.625 MHz.
Mycelium composites: A review of engineering characteristics and growth kinetics

Mycelium composites comprise of networks of filamentous hyphae, utilising biological growth rather than expensive energy intensive manufacturing processes to convert low-cost organic wastes into economically viable and environmentally friendly materials. Although generally characterised as polymer grade foams and used primarily for limited packaging and construction applications, the mechanical performance of these materials varies significantly and is governed by hyphal architecture, cell wall composition, composite constituents and growth kinetics which are in turn influenced by inherent and exogenous factors. A range of potential applications have been proposed including acoustic dampers, super absorbents, paper, textiles, structural and electronic parts. Limited research, inconclusive data and the proposed applications and feasibility suggest that further investigation is warranted.
Formulation and Evaluation of Self Nanoemulsifying Drug Delivery System of Nifedipine

Oral route is the most preferred route of drug administration due to its easy accessibility, intake, and wide range of choices making it economical. Currently, greater than 60% of marketed drugs are oral products. Over 90% of therapeutic compounds given orally areknown to possess oral bioavailability limitations. Therefore, there is a need to explore various approaches that can be used to improve oral drug bioavailability besides using physical and chemical means. The objective of this study is to prepare a formulation i.e. self microemulsifying drug delivery system (SMEDDS) of nifedipine with the intention to improve the increase dissolution rate (solubility). This will ensure the quick absorption and uniform bioavailability of nifedipine. Selection of oils, surfactants and co-surfactants was done by determining % transparency and on the basis of compatibility studies by FTIR spectra analysis. Different SMEDDS formulation were prepared of different ratio of oil:surfactantmix (1:9,2:8,3:7,4:6,5:5,6:4,7:3,8:2,9:1) and different ratio of surfactants : cosurfactants. Pseudo ternary phase diagram were constructed by water titration method to obtain a particle microemulsion region (on the basis of clarity and transparency). The formulation B-I was optimized because of maximum transparency (87.35%) and maximum % drug entrapment (95.32%). The average droplet size and zeta potential was found 86.05 and -0.189. The solubility of nifedipine increase in SMEDDS formulation upto72.17%. From in vitro dissolution study it was proved that SMEDDS formulation releases drug at faster rate, thus the objective of increase solubility and hence the better dissolution rate for uniform bioavailability via SMEDDS formulation of nifedipine was successfully achieved.
Assimilation of seasonal chlorophyll and nutrient data into an adjoint three‐dimensional ocean carbon cycle model: Sensitivity analysis and ecosystem parameter optimization

An adjoint method is applied to a three‐dimensional global ocean biogeochemical cycle model to optimize the ecosystem parameters on the basis of SeaWiFS surface chlorophyll observation. We showed with identical twin experiments that the model simulated chlorophyll concentration is sensitive to perturbation of phytoplankton and zooplankton exudation, herbivore egestion as fecal pellets, zooplankton grazing, and the assimilation efficiency parameters. The assimilation of SeaWiFS chlorophyll data significantly improved the prediction of chlorophyll concentration, especially in the high‐latitude regions. Experiments that considered regional variations of parameters yielded a high seasonal variance of ecosystem parameters in the high latitudes, but a low variance in the tropical regions. These experiments indicate that the adjoint model is, despite the many uncertainties, generally capable to optimize sensitive parameters and carbon fluxes in the euphotic zone. The best fit regional parameters predict a global net primary production of 36 Pg C yr−1, which lies within the range suggested by Antoine et al. (1996). Additional constraints of nutrient data from the World Ocean Atlas showed further reduction in the model‐data misfit and that assimilation with extensive data sets is necessary.
Sensorimotor supremacy: Investigating conscious and unconscious vision by masked priming

According to the sensorimotor supremacy hypothesis, conscious perception draws on motor action. In the present report, we will sketch two lines of potential development in the field of masking research based on the sensorimotor supremacy hypothesis. In the first part of the report, evidence is reviewed that masked, invisible stimuli can affect motor responses, attention shifts, and semantic processes. After the review of the corresponding evidence – so-called masked priming effects – an approach based on the sensorimotor supremacy hypothesis is detailed as to how the question of a unitary mechanism of unconscious vision can be pursued by masked priming studies. In the second part of the report, different models and theories of backward masking and masked priming are reviewed. Types of models based on the sensorimotor hypothesis are discussed that can take into account ways in which sensorimotor processes (reflected in masked priming effects) can affect conscious vision under backward masking conditions.
Transmembrane Tumor Necrosis Factor Controls Myeloid-Derived Suppressor Cell Activity via TNF Receptor 2 and Protects from Excessive Inflammation during BCG-Induced Pleurisy

Pleural tuberculosis (TB) is a form of extra-pulmonary TB observed in patients infected with Mycobacterium tuberculosis. Accumulation of myeloid-derived suppressor cells (MDSC) has been observed in animal models of TB and in human patients but their role remains to be fully elucidated. In this study, we analyzed the role of transmembrane TNF (tmTNF) in the accumulation and function of MDSC in the pleural cavity during an acute mycobacterial infection. Mycobacterium bovis BCG-induced pleurisy was resolved in mice expressing tmTNF, but lethal in the absence of tumor necrosis factor. Pleural infection induced MDSC accumulation in the pleural cavity and functional MDSC required tmTNF to suppress T cells as did pleural wild-type MDSC. Interaction of MDSC expressing tmTNF with CD4 T cells bearing TNF receptor 2 (TNFR2), but not TNFR1, was required for MDSC suppressive activity on CD4 T cells. Expression of tmTNF attenuated Th1 cell-mediated inflammatory responses generated by the acute pleural mycobacterial infection in association with effective MDSC expressing tmTNF and interacting with CD4 T cells expressing TNFR2. In conclusion, this study provides new insights into the crucial role played by the tmTNF/TNFR2 pathway in MDSC suppressive activity required during acute pleural infection to attenuate excessive inflammation generated by the infection.
Efficacy and safety of liposomal amphotericin B (AmBisome) for visceral leishmaniasis in endemic developing countries.

Reported are the results of a study to determine the efficacy and safety of liposomal amphotericin B (AmBisome) for treating visceral leishmaniasis (kala-azar) in several developing countries where the disease is endemic (Brazil, India, and Kenya). At each study site, sequential cohorts of 10 patients each were treated with AmBisome at a dose of 2 mg.kg-1.day-1 (2 MKD). The first cohort received regimen 1:2 MKD on days 1-6 and day 10 (total dose: 14 mg/kg). If the efficacy with this regimen was satisfactory, a second cohort received regimen 2:2 MKD on days 1-4 and 10 (total dose: 10 mg/kg); and a third cohort received regimen 3:2 MKD on days 1, 5, and 10 (total dose: 6 mg/kg). In India, regimens 1, 2, and 3 (which were studied concurrently) each cured 100% of 10 patients. In Kenya, regimen 1 cured all 10 patients, regimen 2 cured 90% of 10 patients, but regimen 3 cured only 20% of 5 patients. In Brazil, regimen 1 was only partially curative: 5 of 13 patients (62%). Therefore, 15 patients were administered regimen 4 (2 MKD for 10 consecutive days; total dose, 20 mg/kg) and 13 patients were cured (83%). These results suggest that for the treatment of kala-azar the following doses of AmBisome should be administered: in India and Kenya, 2 mg/kg on days 1-4 and day 10; and in Brazil, 2 mg/kg on days 1-10.
Validation of the Addenbrooke’s Cognitive Examination for Detecting Early Alzheimer’s Disease and Mild Vascular Dementia in a German Population

We assessed the diagnostic accuracy of the German version of the Addenbrooke’s Cognitive Examination (ACE) in identifying early Alzheimer’s disease (AD) and mild vascular dementia (VaD) in comparison with the conventional Mini-Mental State Examination (MMSE). The study refers to 50 patients with mild dementia of AD, 26 patients with mild dementia of vascular etiology and to 54 cognitively normal subjects. The ACE and MMSE were validated against an expert diagnosis based on a comprehensive diagnostic workup. Statistical analysis was performed using the receiver operator characteristics method. The optimal cut-off score for the ACE for detecting dementia in patients with early AD was 85/86, which had a sensitivity of 93% and a specificity of 86%. The optimal cut-off for the ACE for the identification of dementia in patients with mild VaD was also 85/86 and it had a sensitivity of 93% and a specificity of 100%. The ĸ values imply a substantial agreement between the diagnoses made by the ACE and the MMSE. The German version of the ACE is a short and practical but accurate test battery for the identification of AD and VaD, assessing a broad range of cognitive functions and providing a wide profile of cognitive functions/dysfunctions.
Correction to ‘Neural systems for landmark-based wayfinding in humans’

[ Phil. Trans. R. Soc. B . 369 , 20120533. (Published 23 December 2013) ([doi:10.1098/rstb.2012.0533][2])][2] The publisher regrets that the reference list is incorrectly numbered. The references between 1–25 and 50–62 are correct, but references 26–49 should appear as follows. 1. 26.1.
Effects of vaccinia virus anti-inflammatory protein 35K and TIMP-1 gene transfers on vein graft stenosis in rabbits.

BACKGROUND Vein graft stenosis is a common problem after bypass surgery. Vein grafts are ideal targets for gene therapy because transduction can be made ex vivo before grafting. Since chemokines and inflammatory factors are involved in vein graft thickening, we tested a hypothesis that the vaccinia virus anti-inflammatory protein 35K which can sequester CC-chemokines, can reduce vein graft thickening in vivo. MATERIALS AND METHODS We used adenovirus-mediated gene transfer (1x10(9) pfu/ml) of 35K and compared its effects on reducing stenosis in a rabbit jugular vein graft model with tissue inhibitor of metalloproteinase-1 (TIMP-1) and LacZ control gene. TIMP-1 was used in this study because it has previously been shown to inhibit vein graft stenosis in other model systems. The expression of transgenes in the transduced segments was confirmed by RT-PCR. Vein grafts were analyzed using immunohistological and morphometric methods at the three-day time-point and at two-week and four-week time-points. RESULTS It was found that the anti-inflammatory protein 35K was an efficient factor in reducing neointima formation at the two-week time-point, indicating that inflammatory factors play an important role in vein graft stenosis. At the four-week time-point, 35K still showed a reduced accumulation of macrophages. TIMP-1 also tended to reduce neointimal thickening at the two-week time-point as compared to LacZ. CONCLUSION It was found that 35K is an efficient factor in reducing neointima formation, macrophage accumulation and proliferation in rabbit vein grafts after adenoviral ex vivo gene transfer.
Big Bang - Big Crunch optimization algorithm hybridized with local directional moves and application to target motion analysis problem

Big Bang - Big Crunch (BB-BC) optimization algorithm relies on one of the theories of the evolution of the universe; namely, the Big Bang and Big Crunch Theory [1]. It was proposed as a novel optimization method in 2006 and is shown to be capable of quick convergence. In this work, local search moves are injected in between the original “banging” and “crunching” phases of the optimization algorithm. These phases preserve their structures; but the representative point (“best” or “fittest” point) attained after crunching phase of the iteration is modified with local directional moves using the previous representative points. This hybridization scheme smoothens the path going to optima and decreases the process time for reaching the global minima. The results over benchmark test functions have proven that BB-BC Algorithm enhanced with local directional moves has provided more accuracy with the same computation time or for the same number of function evaluations. As a real world case study, the newly proposed routine is applied in target motion analysis problem where the basic parameters defining the target motion is estimated through noise corrupted measurement data.
Living Crystals of Light-Activated Colloidal Surfers

Light On Clusters From schools of fish to bacterial colonies, large-scale phenomena—such as swarming or pattern formation—are ubiquitous. In such systems, there is a continuing question as to the relative importance of "intelligence" (biology) of the agents versus purely physical effects. Working with synthetic colloids, Palacci et al. (p. 936) show that self-organized clustering can be switched on and off to form crystals that dissolve when the light source is turned off. The particles consist of a hematite cube partly encapsulated in a polymeric sphere that is able to catalyze chemical reactions when exposed to light. The self-assembly behavior results from a combination of propelling forces, osmotic effects, and coupling between colloidal and tracer particles. Light-catalyzed reactions drive the far-from-equilibrium crystallization of colloids that couple to tracer particles. Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional "living crystals," which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles.
In the rough: in-field evaluation of an autonomous vehicle for golf course maintenance

Maintenance is a time consuming and expensive task for any golf course or driving range manager. For a golf course the primary tasks are grass mowing and maintenance (fertilizer and herbicide spreading), while for a driving range mowing, maintenance and ball collection are required. All these tasks require an operator to drive a vehicle along paths, which are generally predefined. This paper presents some preliminary in-field testing results for an automated tractor vehicle performing golf ball collection on an actual driving range, and mowing on difficult unstructured terrain.