Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Combinations of Pre-erythrocytic Plasmodium falciparum Malaria Vaccines

Despite substantial progress in the control of Plasmodium falciparum infection due to the widespread deployment of insecticide-treated bed nets and artemisinin combination therapies, malaria remains a prolific killer, with over half a million deaths estimated to have occurred in 2013 alone. Recent evidence of the development of resistance to treatments in both parasites and their mosquito vectors has underscored the need for a vaccine. Here, we use a mathematical model of the within-host dynamics of P. falciparum infection, fit to data from controlled human malaria infection clinical trials, to predict the efficacy of co-administering the two most promising subunit vaccines, RTS,S/AS01 and ChAd63-MVA ME-TRAP. We conclude that currently available technologies could be combined to induce very high levels of sterile efficacy, even in immune-naive individuals.
Double dissociation of letter and category fluency following left frontal and temporal lobe lesions

Background: A number of studies have suggested that temporal cortex is critical for the ability to generate exemplars belonging to a particular semantic category (i.e., category fluency), while frontal cortex is critical for generating words beginning with a particular letter (i.e., letter or phonemic fluency). However, previous studies have often focused on relative, quantitative differences in performance across groups of patients and primarily in the oral domain. Aims: The current study analysed verbal fluency data from two individuals with chronic aphasia, one with a large left temporal lobe lesion and a severe Wernicke's aphasia, and a second individual with a large left frontal lobe lesion and a moderately severe non-fluent aphasia. The goal of the study was to do both qualitative and quantitative analyses of letter and category fluency performance in these two individuals across oral and written fluency domains. Methods & Procedures: Participants were administered both oral and written versions of letter fluency (FAS) and category fluency conditions (fruits, animals, and supermarket items). Participants were given 90 seconds to generate as many items as possible, and their responses were scored for both overall output, as well as qualitative structure using a clustering analysis. Outcomes & Results: The individual with an extensive temporal lobe lesion generated a large number of exemplars on the letter fluency task. Some of these items were neologisms (e.g., frest, anth, and swink), but remarkably all adhered to the phonological constraints of the task. However, this individual was very poor at generating items belonging to semantic categories. In contrast, the individual with a large frontal lesion generated many exemplars on the category fluency task but only two items on the letter fluency task. The same pattern was replicated in the written domain in both individuals, and results from the clustering analysis paralleled these quantitative findings. Conclusions: This report describes two individuals with aphasia who exhibited a double dissociation between letter and category fluency performance in both oral and written domains. The current findings provide further evidence for the notion that left frontal cortex is critical for word retrieval based on phonology, while left temporal cortex is critical for word retrieval based on semantics. The findings have implications for the types of strategies that may be most effective in individuals with lesions to these brain regions critical for word retrieval.
Factors Influencing Internalization of Organizational Mission Among Frontline Staff of the YMCA of San Francisco

iv Vita Auctoris . v Acknowledgements . vi List of Tables . vii List of Appendices . viii Chapter One: Introduction . 1 Chapter Two: Review of the Literature . 12 Chapter Three: Methodology . 22 Chapter Four: Results . 31 Chapter Five: Summary and Conclusions . 47 References . 57 Appendices . 60
Fragile X Mental Retardation Protein Regulates the Levels of Scaffold Proteins and Glutamate Receptors in Postsynaptic Densities*

Functional absence of fragile X mental retardation protein (FMRP) causes the fragile X syndrome, a hereditary form of mental retardation characterized by a change in dendritic spine morphology. The RNA-binding protein FMRP has been implicated in regulating postsynaptic protein synthesis. Here we have analyzed whether the abundance of scaffold proteins and neurotransmitter receptor subunits in postsynaptic densities (PSDs) is altered in the neocortex and hippocampus of FMRP-deficient mice. Whereas the levels of several PSD components are unchanged, concentrations of Shank1 and SAPAP scaffold proteins and various glutamate receptor subunits are altered in both adult and juvenile knock-out mice. With the exception of slightly increased hippocampal SAPAP2 mRNA levels in adult animals, altered postsynaptic protein concentrations do not correlate with similar changes in total and synaptic levels of corresponding mRNAs. Thus, loss of FMRP in neurons appears to mainly affect the translation and not the abundance of particular brain transcripts. Semi-quantitative analysis of RNA levels in FMRP immunoprecipitates showed that in the mouse brain mRNAs encoding PSD components, such as Shank1, SAPAP1–3, PSD-95, and the glutamate receptor subunits NR1 and NR2B, are associated with FMRP. Luciferase reporter assays performed in primary cortical neurons from knock-out and wild-type mice indicate that FMRP silences translation of Shank1 mRNAs via their 3′-untranslated region. Activation of metabotropic glutamate receptors relieves translational suppression. As Shank1 controls dendritic spine morphology, our data suggest that dysregulation of Shank1 synthesis may significantly contribute to the abnormal spine development and function observed in brains of fragile X syndrome patients.
Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils

Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here, we use a molecular profiling technique (T‐RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize vs. potato), soil type (sand vs. clay‐textured soils) and habitat (plant root vs. bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species‐poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive ‘loss’ from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass‐cropping history together explained 32% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a ‘bottleneck effect’ on AMF communities through increased stochastic effects under environmental stress.
STATE-WIDE TAXATION OF COMMERCIAL AND INDUSTRIAL PROPERTY FOR EDUCATION

Using a behavioral model of the education expenditure decision, we simulate the education expenditure effects in the Boston SMSA of state-wide taxation of commercial and industrial property with the proceeds distributed back to school districts as state aid for education. Although this proposal has been advocated primarily on equity grounds, the simulations show that removal of business property from the local tax base available for education would have adverse distributional effects on the pattern of education expenditures across communities in the Boston SMSA. The precise effects on expenditure levels, revenue flows, and tax rates depend on the particular state aid formula employed.
Operator-Valued Norms

We introduce two kinds of operator-valued norms. One of them is an $L(H)$-valued norm. The other one is an $L(C(K))$-valued norm. We characterize the completeness with respect to a bounded $L(H)$-valued norm. Furthermore, for a given Banach space $\textbf{B}$, we provide an $L(C(K))$-valued norm on $\textbf{B}$. and we introduce an $L(C(K))$-valued norm on a Banach space satisfying special properties.
A new hierarchical approach for simultaneous control of multi-joint powered prostheses

Advanced upper-limb prostheses capable of actuating multiple degrees of freedom (DOF) are now commercially available. Pattern recognition based algorithms that use surface electromyography (EMG) signals measured from residual muscles show great promise as multi-DOF controllers. Unfortunately, current pattern recognition systems are limited to sequential control of each DOF. This study introduces a hierarchy of linear discriminant analysis (LDA) classifiers arranged to provide simultaneous DOF control. This approach and two other simultaneous control strategies were evaluated using healthy subjects controlling up to four DOFs, where any two DOFs could be controlled simultaneously. The new hierarchical approach was the most promising with classification errors at or below 15% on average for discrete and combined motions. The classification performance was significantly better (p <; 0.05) than using a single LDA classifier trained to recognize both discrete and combined motions or classifying each DOF using a set of parallel classifiers. The high accuracy of the hierarchical approach suggests that pattern recognition techniques can be extended to permit simultaneous control, potentially allowing amputees to produce more fluid, life-like movements, ultimately increasing their quality of life.
End-to-End Rate Control in Communication Networks Considering User-Level Satisfactions

In this paper, we consider a rate control problem in communication networks based on the network utility maximization framework. To accurately model the satisfaction of a user to its service, we propose a new concept of the utility function, which is called a user-level utility junction, considering both transmitting and receiving sessions of a user together. We then formulate an optimization problem for rate control with user-level utility functions and develop a distributed rate control algorithm.
The distance to NGC 5904 (M 5) via the subdwarf main sequence fitting method

We present a determination of the distance modulus of the globular cluster NGC 5904 (M 5), obtained by means of the subdwarf main-sequence fitting on the (V,V −I) color-magnitude diagram. The subdwarf sample has been selected from the HIPPARCOS catalog in a metallicity range homogeneous with the cluster ((Fe/H) �− 1.1). Both the cluster and the subdwarfs have been observed with the same telescope+instrument+filters setup (namely, ESO-NTT equipped with the SUSI2 camera), in order to preserve homogeneity and reduce systematic uncertainties. A set of archival HST data has then been used to obtain a deep and precise ridge line. These have been accurately calibrated in the ground photometric system by using the NTT data and used to fit the cluster distance modulus. By adopting the most commonly accepted values for the reddening, E(B − V) = 0.035 and 0.03, we obtain respectively µ0 = 14.44± 0.09± 0.07 and µ0 = 14.41± 0.09± 0.07, in agreement with recent determinations.
The ‘Densitometric Image Analysis Software’ and Its Application to Determine Stepwise Equilibrium Constants from Electrophoretic Mobility Shift Assays

Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad) and the Intelligent or Advanced Quantifier (Bio Image) do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the ‘Densitometric Image Analysis Software’ has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs). For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub. ac.be.
Evidence for “Chain Reaction” in the Time Profiles of Gamma-Ray Bursts

Although the time profiles of gamma-ray bursts (GRBs) show extremely diverse behavior, their average statistical properties such as the average peak-aligned profile and the autocorrelation function show simple stretched exponential behavior. This could indicate that the diversity of all bursts is just due to different random realizations of the same simple stochastic process where the process is scale invariant in time. We illustrate how both the diversity of GRB time profiles and some important average statistical properties can be reproduced in this way using a simple toy model for a stochastic pulse avalanche, which behaves as a chain reaction in a near-critical regime. We suggest that one possibility for the underlying physical process for generating GRBs could be a “chain detonation” in which reconnecting magnetic turbulent features trigger each other.
The prevalence of glaucoma in Chinese residents of Singapore: a cross-sectional population survey of the Tanjong Pagar district.

BACKGROUND Data on prevalence of glaucoma in East Asia are scarce. OBJECTIVE To determine the prevalence and clinical characteristics of glaucoma in adult Chinese Singaporeans. METHODS A group of 2000 Chinese people, aged 40 to 79 years, were selected from the electoral register of Tanjong Pagar district in Singapore using a disproportionate, stratified, clustered, random-sampling procedure. Glaucoma was diagnosed in people with an excavated optic neuropathy and a reproducible visual field defect or on the basis of severe structural disc abnormality alone, if reliable field results could not be obtained. The diagnosis was also made in blind subjects with raised intraocular pressure or previous glaucoma surgery. RESULTS Of 1717 eligible subjects, 1232 were examined, with a response rate of 71.8%. There were 45 cases of glaucoma: 27 were men and 18 were women. The main diagnoses were primary open-angle glaucoma (n = 22 [49%]), primary angle-closure glaucoma (n = 14 [31%]), and secondary glaucoma (n = 7 [16%]). It was not possible to determine the mechanism in 2 (4%). CONCLUSIONS The age-standardized prevalence of glaucoma was 3.2% (95% confidence interval, 2.3-4.1) in the population 40 years and older. Glaucoma was the leading cause of blindness. Primary angle-closure glaucoma and secondary glaucoma were the most visually destructive forms of the disease. Our findings suggest current projections of glaucoma prevalence among ethnic Chinese are a substantial underestimate. Arch Ophthalmol. 2000;118:1105-1111
Folate Intake along with Genetic Polymorphisms in Methylenetetrahydrofolate Reductase and Thymidylate Synthase in Patients with Advanced Gastric Cancer

Background: A relationship between dietary folate intake and efficacy of fluorouracil (FU) is supported by preclinical data. Furthermore, there are several reports that evaluated genetic polymorphisms of MTHFR (methylenetetrahydrofolate reductase) or TYMS (thymidylate synthase) and efficacy of FU. However, to our knowledge, there are no reports that evaluate simultaneously the effects of folate intake and genetic polymorphisms on clinical outcome of gastric cancer patients. Methods: We retrospectively analyzed the survival impact of estimated folate intake by a food frequency questionnaire and MTHFR and TYMS polymorphisms in 132 patients with advanced gastric cancer who were treated with first-line FU-based chemotherapy. Results: Median overall survival was 11.3 months (95% confidence interval, 9.4-13.4 mo) and median progression-free survival was 5.2 months (95% confidence interval, 4.1-6.3 mo). Patients with folate intake of >260 μg/day (n = 88) showed longer overall survival compared with low folate intake (n = 44; overall survival, 12.2 versus 8.4 mo). In a multivariate Cox model, patients who had folate intake of >260 μg/day, MTHFR 677 TT polymorphism, and TYMS-3′ untranslated region 6-bp insertion were associated with better survival. Similar tendency was observed in progression-free survival. No interaction was observed between folate intake and favorable genotypes. Conclusion: Folate intake and genetic polymorphisms of MTHFR and TYMS were associated with better clinical outcome by FU-based chemotherapy in advanced gastric cancer. Impact: Our results suggested folate intake and folate-related genetic polymorphisms may play an important role in efficacy of FU-based chemotherapy in advanced gastric cancer. Cancer Epidemiol Biomarkers Prev; 19(5); 1311–9. ©2010 AACR.
Reduced Hyperpolarization-Activated Current Contributes to Enhanced Intrinsic Excitability in Cultured Hippocampal Neurons from PrP−/− Mice

Genetic ablation of cellular prion protein (PrPC) has been linked to increased neuronal excitability and synaptic activity in the hippocampus. We have previously shown that synaptic activity in hippocampi of PrP-null mice is increased due to enhanced N-methyl-D-aspartate receptor (NMDAR) function. Here, we focused on the effect of PRNP gene knock-out (KO) on intrinsic neuronal excitability, and in particular, the underlying ionic mechanism in hippocampal neurons cultured from P0 mouse pups. We found that the absence of PrPC profoundly affected the firing properties of cultured hippocampal neurons in the presence of synaptic blockers. The membrane impedance was greater in PrP-null neurons, and this difference was abolished by the hyperpolarization-activated cyclic nucleotide-gated (HCN) channel blocker ZD7288 (100 μM). HCN channel activity appeared to be functionally regulated by PrPC. The amplitude of voltage sag, a characteristic of activating HCN channel current (Ih), was decreased in null mice. Moreover, Ih peak current was reduced, along with a hyperpolarizing shift in activation gating and slower kinetics. However, neither HCN1 nor HCN2 formed a biochemical complex with PrPC. These results suggest that the absence of PrP downregulates the activity of HCN channels through activation of a cell signaling pathway rather than through direct interactions. This in turn contributes to an increase in membrane impedance to potentiate neuronal excitability.
Letting the puss in boots sweat: detecting fake access points using dependency of clock skews on temperature

The only available IEEE 802.11 network identifiers (i.e., the network name and the MAC address) can be easily spoofed. Consequently, an attacker is able to fake a real hotspot and attract its traffic. By this means, the attacker can intercept, collect, or change users' traffic (often even if it is encrypted). In this paper, we describe an efficient method for detecting the replacement of access points (APs) by passive remote physical device fingerprinting. The main feature of our fingerprinting approach is the clock skew - an unavoidable phenomenon that causes clocks to run at minuscule yet remotely observable different speeds - which is extracted from information contained in beacon frames. We are the first to achieve a high discriminability of devices by completely eliminating the fingerprinters' influence and considering the clock skew's dependency on temperature. Finally, we develop a method for reliable detection of the presence of AP impostors that works without explicit temperature information. Compared to the best state-of-the-art approach, our method improves detection accuracy from about 30% to 90% without generating any traffic and requires less than one minute to collect a sufficient number of observations. Our approach yields a strong feature for passive remote physical device fingerprinting in wireless networks.
In vivo synaptic transmission and morphology in mouse models of Tuberous sclerosis, Fragile X syndrome, Neurofibromatosis type 1, and Costello syndrome

Defects in the rat sarcoma viral oncogene homolog (Ras)/extracellular-signal-regulated kinase and the phosphatidylinositol 3-kinase-mammalian target of rapamycin (mTOR) signaling pathways are responsible for several neurodevelopmental disorders. These disorders are an important cause for intellectual disability; additional manifestations include autism spectrum disorder, seizures, and brain malformations. Changes in synaptic function are thought to underlie the neurological conditions associated with these syndromes. We therefore studied morphology and in vivo synaptic transmission of the calyx of Held synapse, a relay synapse in the medial nucleus of the trapezoid body (MNTB) of the auditory brainstem, in mouse models of tuberous sclerosis complex (TSC), Fragile X syndrome (FXS), Neurofibromatosis type 1 (NF1), and Costello syndrome. Calyces from both Tsc1+/- and from Fmr1 knock-out (KO) mice showed increased volume and surface area compared to wild-type (WT) controls. In addition, in Fmr1 KO animals a larger fraction of calyces showed complex morphology. In MNTB principal neurons of Nf1+/- mice the average delay between EPSPs and APs was slightly smaller compared to WT controls, which could indicate an increased excitability. Otherwise, no obvious changes in synaptic transmission, or short-term plasticity were observed during juxtacellular recordings in any of the four lines. Our results in these four mutants thus indicate that abnormalities of mTOR or Ras signaling do not necessarily result in changes in in vivo synaptic transmission.
Convergence of posterior distribution in the mixture of regressions

Mixture models provide a method of modelling a complex probability distribution in terms of simpler structures. In particular, the method of mixture of regressions has received considerable attention due to its modelling flexibility and availability of convenient computational algorithms. This paper aims to contribute to theoretical justification for the mixtures of regression model from the Bayesian perspective. In particular, we establish consistency of posterior distribution and determine how fast posterior distribution converges to the true value of the parameter in the context of mixture of binary, Poisson, and Gaussian regressions.