Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptosporidium species, a protean protozoan

Cryptosporidium species is now considered to be an important enteric protozoan pathogen, but recognition of this role evolved slowly in the 80 years since its discovery. Initially described by Tyzzer as an obscure protozoan isolated from the gastric mucosa of asymptomatic mice in 1907 (78), Cryptosporidium species received little attention until it was suspected of causing diarrhea in turkeys in 1955 (72). More widespread disease in animals, particularly calves and lambs, was documented with the use of improved diagnostic techniques (67, 79). The first reported human cases in 1976 were associated with exposure to farm animals (59, 64), and subsequent cases confirmed the classification of cryptosporidiosis as a zoonotic infection (15, 24). In the early 1980s, most reported infections were in patients with the acquired immunodeficiency syndrome (AIDS) (34, 53, 63, 66, 75). Those individuals had protracted, often severe, watery diarrhea and wasting, and Cryptosporidium species was considered to be primarily an opportunistic pathogen. A larger role for Cryptosporidium species in human disease has emerged with an increased awareness of the organism and readily available simplified methods of stool diagnosis (33, 37, 53). Cryptosporidium species is now commonly identified in cases of acute, self-limited diarrheal illness in immunocompetent hosts in both developed (36, 40, 94) and developing (10, 56, 71; N. K. Hojlyng, K. Molbak, and S. Jepsen, Letter, Lancet i:734, 1984) nations. Travelers abroad have become infected (45, 52), and outbreaks have occurred among children in day-care centers (1, 18, 77). Fecal-oral spread among humans and animals and ingestion of contaminated water (26) appear to be the principal modes of transmission. Thus, from incidental finding, veterinary disease, zoonosis, and opportunistic infection, Cryptosporidium species is now acknowledged as a cause of human diarrheal disease worldwide (30). The intriguing discoveries of the epidemiology, pathogenesis, immunology, clinical features, and microbiology of this protozoal pathogen provide an exciting story and constitute the basis of this review.
Drosophila MCRS2 Associates with RNA Polymerase II Complexes To Regulate Transcription

ABSTRACT Drosophila MCRS2 (dMCRS2; MCRS2/MSP58 and its splice variant MCRS1/p78 in humans) belongs to a family of forkhead-associated (FHA) domain proteins. Whereas human MCRS2 proteins have been associated with a variety of cellular processes, including RNA polymerase I transcription and cell cycle progression, dMCRS2 has been largely uncharacterized. Recent data show that MCRS2 is purified as part of a complex containing the histone acetyltransferase MOF (males absent on first) in both humans and flies. MOF mediates H4K16 acetylation and regulates the expression of a large number of genes, suggesting that MCRS2 could also have a function in transcription regulation. Here, we show that dMCRS2 copurifies with RNA polymerase II (RNAP II) complexes and localizes to the 5′ ends of genes. Moreover, dMCRS2 is required for optimal recruitment of RNAP II to the promoter regions of cyclin genes. In agreement with this, dMCRS2 is required for normal levels of cyclin gene expression. We propose a model whereby dMCRS2 promotes gene transcription by facilitating the recruitment of RNAP II preinitiation complexes (PICs) to the promoter regions of target genes.
Hematopoietic Cells Are a Source of Nidogen-1 and Nidogen-2 during Mouse Liver Development

Nidogen-1 and −2 are key components of basement membranes (BMs). Despite the presence of nidogen molecules in the parenchyma of the developing liver, no BMs are formed therein. This suggests that, in the liver, nidogens may also have functions other than BM formation. As a first step toward the elucidation of the possible cell biological functions of nidogens in the developing liver, we aimed to study their cellular origin. We localized expression of nidogen-1 and nidogen-2 on prenatal days 12, 14, and 16 in the developing mouse liver using in situ hybridization at the light and electron microscopic level and light microscopic immunohistochemistry. Our results show that nidogens are produced both in portal anlagen and in the parenchyma during liver development. In the parenchyma, transcripts can be found in hepatocytes, precursors of stellate cells, endothelial cells and, most interestingly, hematopoietic cells. Using real-time PCR, we found that the gene expression for both proteins shows a decrease from day 14 to day 16 concomitant with a decrease in the hepatic hematopoiesis. We suggest that nidogens may, to some extent, take part in the regulation of hepatic hematopoiesis. (J Histochem Cytochem 54:593-604, 2006)
Reconfigurable multi-band quadrature ΣΔ modulators

A new design methodology for reconfigurable quadrature band-pass ΣΔ modulator is proposed. The methodology uses architectures, which locks various range of IF frequencies to the sampling frequency for lower order quadrature modulators. A gereralized integrator based architecture is developed from the delay architectures. The method is presented with derivation of the base circuitry and with this base circuitry stringent performance can be satisfied by extending the work to cascading lower order quadrature modulators with possible image reduction techniques.
Constraint Propagation for Linear Recursive Rules

There are many ways in which the query answering process for deductive databases may be optimised. Many of these methods rely on applying constraints as soon as possible, to avoid the production and later rejection of facts which are not relevant to the query. This propagation of constraints is much simpler for left-linear programs than for many others. In this paper we show how to transform right-linear and mixed-linear programs into a left-linear form, to make constraint propagation more eeective. Our technique generalises the magic set transformation for linear programs; the magic set transformation can only propagate constraints of the form X = a, whereas our technique can handle arbitrary goals as constraints.
An accurate indoor ranging system based on FMCW radar

This paper presents an innovative accurate ranging system based on FMCW (Frequency Modulated Continuous Wave) Radar. Thanks to a combination of nontrivial solutions a centimetre precision is guaranteed even in tough environments, such as warehouses packed with metallic objects or extremely dusty sites, where conventional RF, laser, ultrasonic or video technology may present severe limitations. The proposed solution is currently being applied in Automatic Guided Vehicle for warehouses. The architecture of the system and the obtained results are presented in details.
Predictors of an Appropriate Admission to an ICU after a Major Pulmonary Resection

Background: There are no recommendations about admission to an ICU after a major lung resection and there are considerable differences among institutions in this respect. Objectives: To audit the practice of admission to an ICU after a major lung resection and evaluate factors predicting the need for intensive care. Methods: Clinicalrecords of all patients who underwent major pulmonary resections in a 14-month period were reviewed retrospectively. The criteria for postoperative admission to the ICU were: (1) standard pneumonectomy if comorbidity index (CI) >0 and/or ASA score >1, and/or abnormal spirometry or arterial gas analysis; (2) extended pneumonectomy; (3) lobectomy if CI ≧4 and/or ASA ≧3; (4) lobectomy if FEV1 <60% of predicted; (5) lobectomy if FEV1 is between 60 and 80% and hypercapnia. Results: Among the 49 patients postoperatively admitted to the surgical ward, only 1 needed late intensive care. Among the 55 patients admitted to the ICU, 25 did not require specific intensive care and were discharged 24 h postoperatively, whereas the remaining 30 patients required specific intensive care. Multivariate analysis identified ASA score, predictive postoperative DLCO, and predictive postoperative product (PPP) as independent predictors of a need for admission to an ICU. Conclusion: This empirical protocol was useful in identifying patients not likely to need admission to the ICU. ASA score, predictive postoperative DLCO, and PPP are independent predictors of a need for admission to an ICU.
Electronic Structure and Half-Metallic Properties of Cubic Perovskite BaRu1-XTixO3 System

The electronic structures of the titanium-doped cubic perovskite ruthenates BaRu1-xTixO3 with x=0.125, 0.25, 0.375, 0.5, 0.625, 0.75, and 0.875 are investigated using the spin-polarized density functional theory within the pseudopotential plane wave method. It is found that a half-metallic phase appears in the 0.75- and 0.875-doped systems, and the origin of half-metallic property is the decrease of t2g bandwidth of Ru 4d states with the increase in x. In addition, the energy gap of BaRu0.25Ti0.75O3 is as large as 1.7 eV at the Fermi level in the up-spin density of states, which suggests a stable half-metallic phase can be obtained in the present systems.
3D seismic data denoising using two-dimensional sparse coding scheme

Seismic data denoising is vital to geophysical applications and the transform-based function method is one of the most widely used techniques. However, it is challenging to design a suit- able sparse representation to express a transform-based func- tion group due to the complexity of seismic data. In this paper, we apply a seismic data denoising method based on learning- type overcomplete dictionaries which uses two-dimensional sparse coding (2DSC). First, we model the input seismic data and dictionaries as third-order tensors and introduce tensor- linear combinations for data approximation. Second, we ap- ply learning-type overcomplete dictionary, i.e., optimal sparse data representation is achieved through learning and training. Third, we exploit the alternating minimization algorithm to solve the optimization problem of seismic denoising. Finally we evaluate its denoising performance on synthetic seismic data and land data survey. Experiment results show that the two-dimensional sparse coding scheme reduces computational costs and enhances the signal-to-noise ratio.
Neuronal encoding models of complex receptive fields: A comparison of nonparametric and parametric approaches

Parametric models have been widely used to estimate conditional intensity functions of neuronal spike train point processes and are efficient to construct from experimental data. Furthermore, parametric models are easy to interpret. However, neurons that have more complex receptive fields may not be sufficiently characterized through parametric modeling since it imposes strict structure on the encoding fields. In this paper, we consider a pyramidal neuron recorded from the rat hippocampus, called a “place” cell, that has a diverse apparently multimodal receptive field that encodes information about the spatial position while the rat freely-forages in a circular environment. We construct encoding models for this place cell using two nonparametric modeling approaches, our recently developed band-limited maximum likelihood (BLML) estimator and a kernel density estimator (KDE); and compare them to models constructed using two parametric approaches that have been previously applied to these neurons. We found that the BLML and KDE better capture the complex receptive field of the studied cell as measured by the KS-statistic and log-likelihood.
Towards context-aware face recognition

In this paper, we focus on the use of context-aware, collaborative filtering, machine-learning techniques that leverage automatically sensed and inferred contextual metadata together with computer vision analysis of image content to make accurate predictions about the human subjects depicted in cameraphone photos. We apply Sparse-Factor Analysis (SFA) to both the contextual metadata gathered in the MMM2 system and the results of PCA (Principal Components Analysis) of the photo content to achieve a 60% face recognition accuracy of people depicted in our cameraphone photos, which is 40% better than media analysis alone. In short, we use context-aware media analysis to solve the face recognition problem for cameraphone photos.
The CCR5 Receptor-Based Mechanism of Action of 873140, a Potent Allosteric Noncompetitive HIV Entry Inhibitor

4-{[4-({(3R)-1-Butyl-3-[(R)-cyclohexyl(hydroxy)methyl]-2,5dioxo-1,4,9-triazaspiro[5.5]undec-9-yl}methyl)phenyl]oxy}benzoic acid hydrochloride (873140) is a potent noncompetitive allosteric antagonist of the CCR5 receptor (pKB = 8.6 ± 0.07; 95% CI, 8.5 to 8.8) with concomitantly potent antiviral effects for HIV-1. In this article, the receptor-based mechanism of action of 873140 is compared with four other noncompetitive allosteric antagonists of CCR5. Although (Z)-(4-bromophenyl){1′-[(2,4-dimethyl-1-oxido-3-pyridinyl)carbonyl]-4′-methyl-1,4′-bipiperidin-4-yl}methanone O-ethyloxime (Sch-C; SCH 351125), 4,6-dimethyl-5-{[4-methyl-4-((3S)-3-methyl-4-{(1R)-2-(methyloxy)-1-[4-(trifluoromethyl)phenyl]ethyl}-1-piperazinyl)-1-piperidinyl]carbonyl}pyrimidine (Sch-D; SCH 417,690), 4,4-difluoro-N-((1S)-3-{(3-endo)-3-[3-methyl-5-(1-methylethyl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2. 1]oct-8-yl}-1-phenyl-propyl)cyclohexanecarboxamide (UK-427,857), and N,N-dimethyl-N-[4-[[[2-(4-methylphenyl)-6,7-dihydro-5H-benzocyclo-hepten-8-yl]carbonyl]amino]benzyl]tetrahydro-2H-pyran-4-aminium chloride (TAK779) blocked the binding of both chemokines 125I-MIP-1α (also known as 125I-CCL3, 125I-LD78) and 125I-RANTES (125I-CCL5), 873140 was an ineffectual antagonist of 125I-RANTES (regulated on activation normal T cell expressed and secreted) binding (but did block binding of 125I-MIP-1α). Furthermore, 873140 blocked the calcium response effects of CCR5 activation by CCL5 (RANTES) (as did the other antagonists), indicating a unique divergence of blockade of function and binding with this antagonist. The antagonism of CCR5 by 873140 is saturable and probe-dependent, consistent with an allosteric mechanism of action. The blockade of CCR5 by 873140 was extremely persistent with a rate constant for reversal of <0.004 h- 1 (t1/2 > 136 h). Coadministration studies of 873140 with the four other allosteric antagonists yielded data that are consistent with the notion that all five of these antagonists bind to a common allosteric site on the CCR5 receptor. Although these ligands may have a common binding site, they do not exert the same allosteric effect on the receptor, as indicated by their differential effects on the binding of 125I-RANTES. This idea is discussed in terms of using these drugs sequentially to overcome HIV viral resistance in the clinic.
Moment-based power estimation in very deep submicron technologies

The significant power optimization possibilities in the early stages of the design flow advice the use of energy evaluation techniques at high levels of abstraction. With this aim, the present work addresses the estimation of the energy consumption in very deep submicron technologies. Using the characterization of the probability density function with a projection in an orthogonal polynomial base, and a symbolic propagation mechanism, a technique is presented to estimate the dynamic and static power consumption in digital systems. The proposed approach has been validated with circuits and excitations from realistic applications. Comparisons with reference transistor and bit level simulations are reported in order to asses the the accuracy of the technique.
Gamification of Learning Deactivates the Default Mode Network

We hypothesized that embedding educational learning in a game would improve learning outcomes, with increased engagement and recruitment of cognitive resources evidenced by increased activation of working memory network (WMN) and deactivation of default mode network (DMN) regions. In an fMRI study, we compared activity during periods of learning in three conditions that were increasingly game-like: Study-only (when periods of learning were followed by an exemplar question together with its correct answer), Self-quizzing (when periods of learning were followed by a multiple choice question in return for a fixed number of points) and Game-based (when, following each period of learning, participants competed with a peer to answer the question for escalating, uncertain rewards). DMN hubs deactivated as conditions became more game-like, alongside greater self-reported engagement and, in the Game-based condition, higher learning scores. These changes did not occur with any detectable increase in WMN activity. Additionally, ventral striatal activation was associated with responding to questions and receiving positive question feedback. Results support the significance of DMN deactivation for educational learning, and are aligned with recent evidence suggesting DMN and WMN activity may not always be anti-correlated.
Co-Clustering WSDL Documents to Bootstrap Service Discovery

With the increasing popularity of web service, it is indispensable to efficiently locate the desired service. Utilizing WSDL documents to cluster web services into functionally similar service groups is becoming mainstream in recent years. However, most existing algorithms cluster WSDL documents solely and ignore the distribution of words rather than cluster them simultaneously. Different from the traditional clustering algorithms that are on one-way clustering, this paper proposes a novel approach named WCCluster to simultaneously cluster WSDL documents and the words extracted from them to improve the accuracy of clustering. WCCluster poses co-clustering as a bipartite graph partitioning problem, and uses a spectral graph algorithm in which proper singular vectors are utilized as a real relaxation to the NP-complete graph partitioning problem. To evaluate the proposed approach, we design comprehensive experiments based on a real-world data set, and the results demonstrate the effectiveness of WCCluster.
Parental refusal of varicella vaccination and the associated risk of varicella infection in children.

OBJECTIVE To quantify both the individual-level and attributable risk of varicella infection requiring medical care in children whose parents refuse varicella immunizations. DESIGN Matched case-control study with conditional logistic regression analysis. SETTING Kaiser Permanente of Colorado (KPCO) health plan between 1998 and 2008. PARTICIPANTS Each pediatric physician-diagnosed case of varicella (n = 133) was matched to 4 randomly selected controls (n = 493). Cases were matched by age, sex, and length of enrollment in KPCO. Main Exposures Varicella vaccine refusal. OUTCOME MEASURES Varicella infection. RESULTS There were 7 varicella vaccine refusers (5%) among the cases and 3 (0.6%) among the controls. Children of parents who refused varicella immunizations were at a greatly increased risk of varicella infection requiring medical care (odds ratio, 8.6; 95% confidence interval, 2.2-33.3) compared with children of parents who accepted vaccinations (P = .004). In the entire KPCO pediatric population, 5% of varicella cases were attributed to parental vaccine refusal. CONCLUSIONS Children of parents who refuse varicella immunizations are at high risk of varicella infection relative to vaccinated children. These results will be helpful to health care providers and parents when making decisions about immunizing children.
Development and Characterization of a GaAs nipi Superlattice Solar Cell

Kate Gleason College of Engineering Rochester Institute of Technology Degree: Doctorate of Philosophy Program: Microsystems Engineering Author’s Name: Michael A. Slocum Advisor’s Name: Dr. Seth M. Hubbard Dissertation Title: Development and Characterization of a GaAs nipi Superlattice Solar Cell Doping superlattices have been explored theoretically and some historic work has used these superlattices to form nipi solar cells with alternating n-type, intrinsic, p-type, intrinsic layers. Multiple purposes exist for evaluating nipi solar cells, which include radiation hardness, an electronically adjustable absorption edge, use with nanostructures, and the possibility of an intermediate band solar cell (IBSC). The primary motivation for this work is to develop the nipi solar cell for evaluation as an IBSC, while also evaluating the radiation tolerance of the design for potential use in space applications. This has been completed through a theoretical and experimental analysis of nipi superlattice layers, and an extensive evaluation of the fabrication and growth processes required to achieve a high efficiency solar cell. As a part of this evaluation an improved model for nipi diodes and solar cells has been developed. Also a novel process for fabricating nipi solar cells through epitaxial regrowth and diffused junctions has been developed, where record efficiencies for nipi solar cells have been measured for devices fabricated via epitaxial regrowth at 12.5%. An understanding of the effect of adding quantum dots (QD) into a nipi superlattice has been obtained. Finally a greater understanding of the intrinsic radiation hardness of the nipi design has been achieved and possible methods to improve it have been evaluated. The techniques and processes developed here have the possibility to be used to further the understanding of nipi devices, and lead to the potential development of an IBSC with a QD-nipi design.
The Stellar Cusp around the Supermassive Black Hole in the Galactic Center

We analyze deep near-IR adaptive optics imaging (taken with NAOS/CONICA on the Very Large Telescope at the European Southern Observatory, Chile), as well as new proper-motion data of the nuclear star cluster of the Milky Way. The surface density distribution of faint (H ≤ 20, Ks ≤ 19) stars peaks within 0. ″2 of the black hole candidate Sgr A*. The radial density distribution of this stellar "cusp" follows a power law of exponent α ~ 1.3-1.4. The K-band luminosity function of the overall nuclear stellar cluster (within 9′′ of Sgr A*) resembles that of the large-scale Galactic bulge but shows an excess of stars at Ks≤ 14. It fits population synthesis models of an old, metal-rich stellar population with a contribution from young, early, and late-type stars at the bright end. In contrast, the cusp within ≤1. ″5 of Sgr A* appears to have a featureless luminosity function, suggesting that old, low-mass, horizontal-branch/red-clump stars are lacking. Likewise, there appear to be fewer late-type giants. The innermost cusp also contains a group of moderately bright, early-type stars that are tightly bound to the black hole. We interpret these results as evidence that the stellar properties change significantly from the outer cluster (≥a few arcseconds) to the dense innermost region around the black hole. We find that most of the massive early-type stars at distances of 1''-10'' from Sgr A* are located in two rotating and geometrically thin disks. These disks are inclined at large angles and counterrotate with respect to each other. Their stellar content is essentially the same, indicating that they formed at the same time. We conclude that of the possible formation scenarios for these massive stars the most probable one is that 5-8 million years ago two clouds fell into the center, collided, were shock compressed, and then formed two rotating (accretion) disks orbiting the central black hole. For the OB stars in the central arcsecond, on the other hand, a stellar merger model is the most appealing explanation. These stars may thus be "super-blue stragglers," formed and "rejuvenated" through mergers of lower mass stars in the very dense (≥108 M☉ pc-3) environment of the cusp. The "collider model" also accounts for the lack of giants within the central few arcseconds. The star closest to Sgr A* in 2002, S2, exhibits a 3.8 μm excess. We propose that the mid-IR emission comes either from the accretion flow around the black hole itself or from dust in the accretion flow that is heated by the ultraviolet emission of S2.