Miracle-dz/UniFAR-FTUs huggingface dataset:
High Pneumococcal DNA Loads Are Associated With Mortality in Malawian Children With Invasive Pneumococcal Disease

Background: In bacteremia owing to Streptococcus pneumoniae, high bacterial counts at presentation have been shown to be predictive of the development of serious invasive disease. Using real-time PCR, we aimed to determine pneumococcal DNA loads in blood and CSF, and their relationship to cytokine concentrations, clinical presentation and outcome. Methods: Children with confirmed meningitis (n = 82) or pneumonia (n = 13) were prospectively recruited, and blood and CSF samples taken for pneumococcal bacterial DNA loads and cytokine determination. Results: At the time of admission, the median bacterial load in blood was 1.6 × 103 DNA copies/mL (range 0.00–1.54 × 106) and in CSF it was 5.77 × 107 DNA copies/mL (range 4.42 × 102 to 6.15 × 108). Median blood and CSF bacterial loads (log DNA copies/mL) were significantly higher in nonsurvivors than in survivors; blood (3.80 vs. 2.97, P = 0.003), CSF (8.17 vs. 7.50, P = 0.03). In HIV-infected children (n = 59), blood and CSF loads and plasma tumor necrosis factor-α, interleukin-1β (IL-1β), IL-6 and IL-10 were all significantly higher in nonsurvivors than in survivors, but in HIV-uninfected children (n = 36) this difference was not significant. Blood bacterial loads and plasma cytokine concentrations were significantly associated, and were all significantly higher in children with meningitis than in those with pneumonia. In children with meningitis, median CSF cytokine concentrations were significantly higher than median plasma cytokine concentrations (P < 0.001) and CSF bacterial loads were significantly associated with CSF IL-1β (P = 0.002) and IL-10 (P = 0.001) concentrations. Conclusions: Pneumococcal DNA loads are associated with plasma cytokine concentrations, and are higher in meningitis than in pneumonia. High blood and CSF pneumococcal DNA loads are associated with a fatal outcome.
Development of surgical simulator based on FEM and deformable volume-rendering

An apparatus for classifying a plurality of poultry eggs includes means for detecting the opacities of the eggs, means for detecting the temperatures of the eggs, and means for classifying the eggs using the opacities and the temperatures of the eggs. A method for classifying poultry eggs includes measuring the opacities of the eggs, measuring the temperatures of the eggs, and classifying the eggs as a function of the opacities and the temperatures of the eggs.
System representation of stochastic models of flrst-order chemical reactions

A tunable, coaxial-vacuum magnetron is shown having a cathode surrounded by an anode within a surrounding evacuated anode cavity. Located between the cathode-anode interaction space and an output from the anode cavity is a tuning mechanism which includes a single symmetrical ceramic tuning rod that is adjusted along its axis into and out of the anode cavity. The adjustment mechanism includes a tuning nut rotatably mounted in a tuning housing which turns to move a threaded shaft along the axis thereof. Separating the threaded shaft from the anode cavity is a bellows attached to the tuning housing and to which is attached the symmetrical tuning rod for sealing the vacuum cavity.
Essays on multiple selves and temporal framing

There exist numerous documented behavioral deviations from standard discounted utility maximizing behavior. These include time inconsistency, violations of the axiom of independence of irrelevant alternatives, preferences for commitment, and preferences over the timing of information. I develop two novel models which provide new insights into, and plausible explanations for, several of these deviations. In the first model, Multiself Bargaining, I propose a dual-self model in which two selves have conflicting preferences over the action to be taken by an agent. The selves have identical payoff utility, and only differ in their time preference factor. The default action of the agent is modeled as the outcome of a Tullock contest among the selves, where the self who wins chooses their preferred action. Viewing the outcome of this contest as the point of disagreement, the selves are allowed to negotiate to a mutually preferred outcome, and this negotiation is modeled as a Nash bargaining problem. I show that many of the deviations of interest are generated by this model, including time inconsistent behavior, such as diminishing impatience, as well as violations of independence of irrelevant alternatives in choice problems. Notably the preference reversals from time inconsistency are “smooth”, as opposed to the singular reversal in quasi-hyperbolic discounting, the standard model used in the literature. In the second model, Temporal Reference Points, I develop an alternate form of prospect evaluation in which agents form a set of subjectively important points in time in the life of a prospect, termed “temporal reference points. ” When determining the present value of a prospect, agents discount based on the time between each of these temporal reference points, as opposed to based on the entire time between the present and the payout of the prospect. Under restrictions on the formation of temporal reference points, diminishing impatience in an agent is shown to be equivalent to a preference for informational updates occurring at the same time. Finally, the model is shown to allow the novel resolution of an apparent conflict in the experimental evidence on diminishing impatience. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Economics First Advisor David Dillenberger Second Advisor Mallesh Pai
Effect of Average Happiness for Twitter on the Dow Jones Industrial Average Return Volatility

The stock market is well known for its volatility and many models are proposed to capture the volatility. Volatility is naturally unobservable and the absolute values of the returns work as the realized volatility. The Dow Jones Industrial Average is the study object and the models used are generalized autoregressive conditional heteroskedasticity (GARCH) models with different extensions. The unique extension in this study is to add happiness data into the model and check whether it helps to better capture the volatility and improve the forecasting accuracy. The happiness data is extracted from Twitter and it is an index to show people’s happiness level based on their online expressions. The one day lagged happiness data is also used as one extension to the models. The leverage effects and the heavy tails problems are also addressed in this study, EGARCH models and GJR-GARCH models with other error distributions such as student’s T distribution are used to deal with these specific problems. The forecasting performance of these models is checked and we find out that the happiness data does help to better capture the volatility. However, the forecasting accuracy of the models with happiness data is not statistically different compared to the models without happiness data. This illustrates that the happiness data does not help to improve the forecasting performance.
FrameNet’s Using relation as a source of concept-based paraphrases

Characterizing paraphrases formally has proven to be a challenging task. Hasegawa et al. (2011) pointed out the usefulness of FrameNet for paraphrase research, focusing on paraphrases which are backed by underlying classical linguistic relationships such as synonymy or voice alternations. This article proposes that other frame-to-frame-relations, notably Using, can serve as a source for concept-based paraphrases – that is, paraphrases that are backed by common sense knowledge, as in he called him a hero – he praised him for being a hero. While the predicates in these sentences are not synonymous, we would argue that the sentences are paraphrases – albeit of a kind that involves world knowledge about the relationship between different event classes. In this article, we propose a shallow taxonomy for the frame pairs which instantiate Using, that is motivated by their ability to form concept-based paraphrases. Second, we analyze the subclass of Using instances which supports concept-based paraphrasing, and provide a formalization of some prominent types of side conditions that are necessary to produce felicitous paraphrases.
Generation of variability in shape, aspect and time of 3D Fruits and Vegetables

With the growth of organic Fruits and Vegetables (FaVs) markets, there is now a trend in marketing research toward studies of non-standardized fruits and vegetables in stores. Yet, because of the decaying nature of FaVs, it is difficult to conduct such studies. A solution is to conduct them within a Virtual Environment (VE) (with virtual FaVs). Therefore, it is of interest to develop an approach to generate a large variety and variability of FaVs, so one can later use them in a VE. In this paper we introduce a pipeline to generate a large variability of FaVs, focusing both on their shape and on their external appearance. Regarding the shape, we use a semi-automated approach. A parametric Skeletal Structure and Generalized Cylinders (GCs) generates their overall shape and metaball-based techniques give them an organic aspect. Regarding their external appearance, we use a particle system approach to simulate their modifications over time. This particle system-based approach decomposes FaVs appearance changes into distinct visual characteristics producing different texture maps that can be combined.
Transfection of Mouse Cochlear Explants by Electroporation

The sensory epithelium of the mammalian inner ear, also referred to as the organ of Corti, is a remarkable structure comprised of highly ordered rows of mechanosensory hair cells and non‐sensory supporting cells located within the coiled cochlea. This unit describes an in vitro explant culture technique that can be coupled with gene transfer via electroporation to study the effects of altering gene expression during development of the organ of Corti. While the protocol is largely focused on embryonic cochlea, the same basic protocol can be used on cochleae from mice as old as P5. Curr. Protoc. Neurosci. 51:4.34. 1‐4.34. 10. © 2010 by John Wiley & Sons, Inc.
Clustering NMF basis functions using Shifted NMF for monaural sound source separation

Non-negative Matrix Factorization (NMF) has found use in single channel separation of audio signals, as it gives a parts-based decomposition of audio spectrograms where the parts typically correspond to individual notes or chords. However, a notable shortcoming of NMF is the need to cluster the basis functions to their sources after decomposition. Despite recent improvements in algorithms for clustering the basis functions to sources, much work still remains to further improve these algorithms. To this end we present a novel clustering algorithm which overcomes some of the limitations of previous clustering methods. This involves the use of Shifted Nonnegative Matrix Factorization (SNMF) as a means of clustering the frequency basis functions obtained from NMF. Results show that this gives improved clustering of pitched basis functions over previous methods.
Deliberative versus nondeliberative evaluation of a minority group after viewing an entertainment portrayal

This study tests whether entertainment portrayals of international medical graduate physicians may influence attitudes toward such physicians among television viewers. Given the growing importance of international physicians in U.S. health care delivery, such effects would have the potential to impact significant numbers of patient–physician interactions. From a theoretical and methodological standpoint, this examination extends existing work on entertainment portrayals of often-stigmatized minorities and its impact on minorities for whom stereotypes may be in some respects favorable. An experiment manipulating positive versus negative portrayals of the communicative and professional competence of an Asian Indian female physician on the program ER found that exposure had no effect on conventional, deliberative measures of attitude toward such physicians. However, use of attitude-accessibility measurement suggested that viewers (to the extent that they identified with the narrative character, an Asian Indian physician) who saw the negative portrayal were slower to respond that they liked other Asian Indian female physicians who were presented in photos in a judgment task afterwards—in other words, the negative portrayal inhibited an approach response to other similar physicians. An implication of this finding is that such television portrayals may have the potential to influence affective responses to medical providers from the same demographic as the character portrayed, in ways viewers are likely to be unaware of. Such responses may well influence patient expectations and interactions with such physicians.
Structure Determination of Feline Calicivirus Virus-Like Particles in the Context of a Pseudo-Octahedral Arrangement

The vesivirus feline calicivirus (FCV) is a positive strand RNA virus encapsidated by an icosahedral T=3 shell formed by the viral VP1 protein. Upon its expression in the insect cell - baculovirus system in the context of vaccine development, two types of virus-like particles (VLPs) were formed, a majority built of 60 subunits (T=1) and a minority probably built of 180 subunits (T=3). The structure of the small particles was determined by x-ray crystallography at 0.8 nm resolution helped by cryo-electron microscopy in order to understand their formation. Cubic crystals belonged to space group P213. Their self-rotation function showed the presence of an octahedral pseudo-symmetry similar to the one described previously by Agerbandje and co-workers for human parvovirus VLPs. The crystal structure could be solved starting from the published VP1 structure in the context of the T=3 viral capsid. In contrast to viral capsids, where the capsomers are interlocked by the exchange of the N-terminal arm (NTA) domain, this domain is disordered in the T=1 capsid of the VLPs. Furthermore it is prone to proteolytic cleavage. The relative orientation of P (protrusion) and S (shell) domains is alerted so as to fit VP1 to the smaller T=1 particle whereas the intermolecular contacts around 2-fold, 3-fold and 5-fold axes are conserved. By consequence the surface of the VLP is very similar compared to the viral capsid and suggests a similar antigenicity. The knowledge of the structure of the VLPs will help to improve their stability, in respect to a use for vaccination.
Neutrophil Elastase Subverts the Immune Response by Cleaving Toll-Like Receptors and Cytokines in Pneumococcal Pneumonia

Excessive activation of neutrophils results in the release of neutrophil elastase (NE), which leads to lung injury in severe pneumonia. Previously, we demonstrated a novel immune subversion mechanism involving microbial exploitation of this NE ability, which eventually promotes disruption of the pulmonary epithelial barrier. In the present study, we investigated the effect of NE on host innate immune response. THP-1-derived macrophages were stimulated with heat-killed Streptococcus pneumoniae or lipopolysaccharide in the presence or absence of NE followed by analysis of toll-like receptor (TLR) and cytokine expression. Additionally, the biological significance of NE was confirmed in an in vivo mouse intratracheal infection model. NE downregulated the gene transcription of multiple cytokines in THP-1-derived macrophages through the cleavage of TLRs and myeloid differentiation factor 2. Additionally, NE cleaved inflammatory cytokines and chemokines. In a mouse model of intratracheal pneumococcal challenge, administration of an NE inhibitor significantly increased proinflammatory cytokine levels in bronchoalveolar lavage fluid, enhanced bacterial clearance, and improved survival rates. Our work indicates that NE subverts the innate immune response and that inhibition of this enzyme may constitute a novel therapeutic option for the treatment of pneumococcal pneumonia.
A subset of Rosai–Dorfman disease cases show increased IgG4‐positive plasma cells: another red herring or a true association with IgG4‐related disease?

that they belong to a basic and shared clone of cells in the tumour. The copy number alterations involving 6q and 9p affected MYB and NFIB with breakpoints in both genes. Skin metastases of salivary gland ACC are rare and may pose significant diagnostic challenges, as in the present case (Table S3). Therefore, adjuvant techniques such as RT-PCR screening for tumour typespecific fusion genes may be helpful in confirming the diagnosis. Our findings clearly demonstrate the clinical utility of the MYB–NFIB gene fusion as a diagnostic biomarker for ACC, as well as for metastatic lesions with an ACC-like morphology, such as basal cell carcinoma. In addition, we have shown that genomic profiling is a useful tool for demonstrating genomic similarities between primary and metastatic ACC lesions. Taken together, these findings strongly indicate that the skin lesions in the current case do indeed represent metastatic deposits of an ACC originally arising in the paranasal sinus.
Two-pore Channels (TPC2s) and Nicotinic Acid Adenine Dinucleotide Phosphate (NAADP) at Lysosomal-Sarcoplasmic Reticular Junctions Contribute to Acute and Chronic β-Adrenoceptor Signaling in the Heart*

Background: The Ca2+-releasing messenger nicotinic acid adenine dinucleotide phosphate (NAADP) acts via lysosomal two-pore channels (TPC2). Results: Tpcn2−/− cardiac myocytes showed reduced acute responses to β-adrenoreceptor stimulation and chronically reduced cardiac hypertrophy and arrhythmogenesis. Conclusion: Acute and chronic effects of cardiac β-adrenoreceptor stimulation depend on NAADP acting via TPC2 in lysosomes. Significance: NAADP/TPC2 signaling pathways offer new strategies for cardiac therapeutics. Ca2+-permeable type 2 two-pore channels (TPC2) are lysosomal proteins required for nicotinic acid adenine dinucleotide phosphate (NAADP)-evoked Ca2+ release in many diverse cell types. Here, we investigate the importance of TPC2 proteins for the physiology and pathophysiology of the heart. NAADP-AM failed to enhance Ca2+ responses in cardiac myocytes from Tpcn2−/− mice, unlike myocytes from wild-type (WT) mice. Ca2+/calmodulin-dependent protein kinase II inhibitors suppressed actions of NAADP in myocytes. Ca2+ transients and contractions accompanying action potentials were increased by isoproterenol in myocytes from WT mice, but these effects of β-adrenoreceptor stimulation were reduced in myocytes from Tpcn2−/− mice. Increases in amplitude of L-type Ca2+ currents evoked by isoproterenol remained unchanged in myocytes from Tpcn2−/− mice showing no loss of β-adrenoceptors or coupling mechanisms. Whole hearts from Tpcn2−/− mice also showed reduced inotropic effects of isoproterenol and a reduced tendency for arrhythmias following acute β-adrenoreceptor stimulation. Hearts from Tpcn2−/− mice chronically exposed to isoproterenol showed less cardiac hypertrophy and increased threshold for arrhythmogenesis compared with WT controls. Electron microscopy showed that lysosomes form close contacts with the sarcoplasmic reticulum (separation ∼25 nm). We propose that Ca2+-signaling nanodomains between lysosomes and sarcoplasmic reticulum dependent on NAADP and TPC2 comprise an important element in β-adrenoreceptor signal transduction in cardiac myocytes. In summary, our observations define a role for NAADP and TPC2 at lysosomal/sarcoplasmic reticulum junctions as unexpected but major contributors in the acute actions of β-adrenergic signaling in the heart and also in stress pathways linking chronic stimulation of β-adrenoceptors to hypertrophy and associated arrhythmias.
Class Specific TF-IDF Boosting for Short-text Classification: Application to Short-texts Generated During Disasters

Proper formulation of features plays an important role in short-text classification tasks as the amount of text available is very little. In literature, Term Frequency - Inverse Document Frequency (TF-IDF) is commonly used to create feature vectors for such tasks. However, TF-IDF formulation does not utilize the class information available in supervised learning. For classification problems, if it is possible to identify terms that can strongly distinguish among classes, then more weight can be given to those terms during feature construction phase. This may result in improved classifier performance with the incorporation of extra class label related information. We propose a supervised feature construction method to classify tweets, based on the actionable information that might be present, posted during different disaster scenarios. Improved classifier performance for such classification tasks can be helpful in the rescue and relief operations. We used three benchmark datasets containing tweets posted during Nepal and Italy earthquakes in 2015 and 2016 respectively. Experimental results show that the proposed method obtains better classification performance on these benchmark datasets.
What's New in Neuroimaging Methods?

The rapid advancement of neuroimaging methodology and its growing availability has transformed neuroscience research. The answers to many questions that we ask about how the brain is organized depend on the quality of data that we are able to obtain about the locations, dynamics, fluctuations, magnitudes, and types of brain activity and structural changes. In this review an attempt is made to take a snapshot of the cutting edge of a small component of the very rapidly evolving field of neuroimaging. For each area covered, a brief context is provided along with a summary of a few of the current developments and issues. Then, several outstanding papers, published in the past year or so, are described, providing an example of the directions in which each area is progressing. The areas covered include functional magnetic resonance imaging (fMRI), voxel‐based morphometry (VBM), diffusion tensor imaging (DTI), electroencephalography (EEG), magnetoencephalography (MEG), optical imaging, and positron emission tomography (PET). More detail is included on fMRI; its subsections include fMRI interpretation, new fMRI contrasts, MRI technology, MRI paradigms and processing, and endogenous oscillations in fMRI.
Modeling of Light-Driven Bending Vibration of a Liquid Crystal Elastomer Beam

In this paper, we study light-driven bending vibration of a liquid crystal elastomer (LCE) beam. Inhomogeneous and time-dependent number fraction of photochromic liquid crystal molecules in cis state in an LCE beam is considered in our model. Using mode superposition method, we obtain semi-analytic form of light-driven bending vibration of the LCE beam. Our results show that periodic vibration or a statically deformed state can be induced by a static light source in the LCE beam, which depends on the light intensity and position of the light source. We also demonstrate that the amplitude of the bending vibration of the LCE beam can be regulated by tuning light intensity, damping factor of the beam, and thermal relaxation time from cis to trans state, while the frequency of the vibration in the beam mainly depends on the thermal relaxation time. The method developed in the paper can be important for designing light-driven motion structures and photomechanical energy conversion systems.