Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental changes of cone opsin expression but not retinal morphology in the hypothyroid Pax8 knockout mouse.

PURPOSE The effects of postnatal hypothyroidism on retinal development and spatial patterning of cone opsin expression were studied in Pax8-deficient mice. Pax8(-/-) mice are incapable of synthesizing thyroxine and serve as a model for congenital hypothyroidism. METHODS Pax8(-/-), Pax8(+/-), and Pax8(+/+) littermates were studied. Serum thyroid hormone levels, body weight, and eye size were measured. Retinal cell-type-specific antibodies were used on frozen sections to examine the postnatal development of the major retinal cell classes and of retinal structure. The expression of short-wavelength-sensitive (S) and middle-to-long-wavelength-sensitive (M) cone opsins was assessed with opsin antibodies on retinal sections and whole retinas. The pattern of S opsin mRNA was assessed by in situ hybridization. RESULTS In Pax8(-/-) mice, S opsin was upregulated in all cones, whereas M opsin was downregulated throughout the retina, the wild-type dorsoventral gradients of S and M opsin expression were absent. Otherwise, Pax8(-/-) mice showed no overt mutant phenotype in eye size, gross retinal anatomy, and the time-course of structural differentiation of retinal photoreceptors, horizontal cells, bipolars, amacrines, ganglion cells, and Müller glia cells. CONCLUSIONS Pax8(-/-) mice show a pattern of cone opsin expression that differs substantially from the wild-type pattern, but exhibit no apparent alterations in general retinal development. The finding that a postnatal decrease in serum thyroid hormone yields changes in postnatal cone opsin expression is consistent with a ligand-dependent role of thyroid hormone receptor beta2 in S opsin repression and M opsin activation.
Scientific Misconduct and the Myth of Self-Correction in Science

The recent Stapel fraud case came as a shattering blow to the scientific community of psychologists and damaged both their image in the media and their collective self-esteem. The field responded with suggestions of how fraud could be prevented. However, the Stapel fraud is only one among many cases. Before basing recommendations on one case, it would be informative to study other cases to assess how these frauds were discovered. The authors analyze a convenience sample of fraud cases to see whether (social) psychology is more susceptible to fraud than other disciplines. They also evaluate whether the peer review process and replications work well in practice to detect fraud. There is no evidence that psychology is more vulnerable to fraud than the biomedical sciences, and most frauds are detected through information from whistleblowers with inside information. On the basis of this analysis, the authors suggest a number of strategies that might reduce the risk of scientific fraud.
Institutionalization after stroke

Background and purpose: There are widespread regional variations in the institutionalization rate after stroke. This study sought to identify the factors that predict institutionalization after a primary diagnosis of stroke and determine whether institutionalization rate could be used to assess the quality of hospital care. Methods: A retrospective case note audit of 2778 consecutive admissions with stroke, between 1 September and 31 October 2000 from a randomly selected sample of 79 hospitals in England, Wales and Northern Ireland. Data were collected on demographics, case-mix, clinical outcome, organization of discharge, and place of residence at discharge and at three and six months. The figures from this audit were validated using data from the 1998 National Sentinel Audit of Stroke. Results: Overall 14% of patients previously living at home were discharged to nursing or residential homes. Using logistic regression, Barthel Index score at discharge accounted for 40% of variation. Two-thirds of patients with a discharge Barthel score of B=5 were institutionalized. Age alone explained 14% and when taken together with discharge Barthel and length of stay it accounted for 54% of variation. On admission 22% of the variation in institutionalization rate could be accounted for by total Glasgow Coma Score (15, B=15), age and ability to walk unaided. Regional variations in institutionalization rates are evident and may in part be explained by differences in ease of access to the institutions. Conclusions: Discharge disability and older age were the dominant factors determining admission to nursing and residential homes. It is not possible to predict sufficiently reliably for an individual patient the likelihood of institutionalization at admission or at 72 h after admission, to justify early resource allocation decisions.
Trade-Offs in HW/SW Codesign

HW/SW codesign is becoming an increasingly more interesting research field because most practical systems consist of both HW and SW. In this paper we explore a bottom up HW/SW codesign strategy to investigate trade-offs in time behavior and area. A comparison of hardw are and software implementations of low level modules is given. A first prototype implementation extracts time and area criteria analyzing the softw are code generated.
A new video text extraction approach

Video text provides precise and meaningful information about video content. Video text extraction is a crucial step to retrieve video text characters. Most of papers perform video text extraction in a whole text row. Compared with whole text row extraction, single character extraction can achieve higher accuracy because the background of single character is relatively simple. However, character segmentation is difficult because of the low resolution of the characters in video. Therefore, we propose a character segmentation method, which can accurately locate the character boundary in the text row. In the text extraction, we perform k-means clustering in single character and define a method to quickly select one of the images as the final binary image. Experimental results on TV news video show the encouraging performance of the proposed algorithm.
Automatic Target Recognition (ATR) System using Recurrent Neural Network (RNN) for Pulse Radar

The most fundamental problem in radar is the detection of an object or a physical phenomenon. This requires proper discrimination between signal and noise content at the receiver even after the echo containing target information is surrounded by clutter. Traditionally, a series of signal processing operations are carried out to perform this discrimination with varying levels of success. These series of signal processing operations can be supplemented by an Artificial Neural Network (ANN), which is a non-parametric prediction tool with the ability to retain the learning acquired from the surroundings. The Recurrent Neural Network (RNN) is a dynamic ANN which can track time variations in the input patterns. The RNN captures time-varying contextual information and use this knowledge subsequently to make discrimination between adjacent patterns. As viewed from the time domain, the target waveform can also be regarded as a time sequence such that it can be classified using RNN which is suitable for time sequence processing. This work describes the processing steps of signals from pulse radars so that these can be used to train a RNN for use to discriminate between target and false echoes. The experimental results show that the proposed system works effectively while dealing with target echoes surrounded by thermal noise and ground clutter at varying distances [1].
Surface attachment of Salmonella typhimurium to intestinal epithelia imprints the subepithelial matrix with gradients chemotactic for neutrophils

During intestinal disease induced by Salmonella typhimurium transepithelial migration of neutrophils (PMN) rapidly follows attachment of the bacteria to the epithelial apical membrane. Among the events stimulated by these interactions is the release of chemotaxins that guide PMN through the subepithelial matrix and subsequently through the epithelium itself (McCormick, B.A., S.P. Colgan, C. Delp- Archer, S.I. Miller, and J.L. Madara. 1993. J. Cell Biol. 123:895-907). Given the substantial volume flow that normally characterizes matrix compartments underlying transporting epithelia, it is unclear how such transmatrix signaling is sustained. Here we show that when underlying matrices are isolated from biophysically confluent polarized monolayers of the human intestinal epithelial cell line T84, they fail to support substantial transmatrix migration of PMN unless an exogenous chemotactic gradient is imposed. In contrast, such matrices isolated from confluent monolayers apically colonized with S. typhimurium support spontaneous transmatrix migration of PMN. Such chemotactic imprinting of underlying matrices is resistant to volume wash and is paralleled by secretion of the known matrix-binding chemokine IL-8. Chemotactic imprinting of the matrix underlying S. typhimurium- colonized monolayers is dependent on epithelial protein synthesis, is directional implying the existence of a gradient, and is neutralized by antibodies either to IL-8 or to the IL-8 receptor on PMN. An avirulent S. typhimurium strain, PhoPc, which attaches to epithelial cells as efficiently as wild-type S. typhimurium, fails to induce basolateral secretion of IL-8 and likewise fails to imprint matrices. Together, these observations show that the epithelial surface can respond to the presence of a luminal pathogen and subsequently imprint the subepithelial matrix with retained IL-8 gradients sufficient to resist washout effects of the volume flow that normally traverses this compartment. Such data further support the notion that the primary role for basolateral secretion of IL-8 by the intestinal and likely other epithelia is recruitment of PMN through the matrix to the subepithelial space, rather than directing the final movement of PMN across the epithelium.
Nontrivial spacetime topology, CPT violation, and photons

A physical mechanism for CPT violation is reviewed, which relies on chiral fermions, gauge interactions, and nontrivial spacetime topology. The nontrivial topology can occur at the very largest scale (e.g., at the "edge" of the universe) or at the very smallest scale (e.g., from a hypothetical spacetime foam). The anomalous effective gauge field action includes, most likely, a CPT-odd Chern-Simons-like term. Two phenomenological photon models with Abelian Chern-Simons-like terms are discussed.
A Novel Technique for Detection of Time Delay Switch Attack on Load Frequency Control

In this paper, we focus on the estimation of time delays caused by adversaries in the sensing loop (SL). Based on the literature review, time delay switch (TDS) attacks could make any control system, in particular a power control system, unstable. Therefore, future smart grids will have to use advanced methods to provide better situational awareness of power grid states keeping smart grids reliable and safe from TDS attacks. Here, we introduce a simple method for preventing time delay switch attack on networked control systems. The method relies on an estimator that will estimate and track time delays introduced by an adversary. Knowing the maximum tolerable time delay of the plant’s optimal controller for which the plant remains stable, a time-delay detector issues an alarm signal when the estimated time delay is larger than the minimum one and directs the system to alarm state. In an alarm state, the plant operates under the control of an emergency controller that is local to the plant and remains in this mode until the networked control system state is restored. This method is an inexpensive and simple way to guarantee that an industrial control system remains stable and secure.
Capabilities for External Uniqueness

Unique object references have many important applications in object-oriented programming. For instance, with sufficient encapsulation properties they enable safe and efficient transfer of message objects between concurrent processes. However, it is a long-standing challenge to integrate unique references into practical object-oriented programming languages. This paper introduces a new approach to external uniqueness. The idea is to use capabilities for enforcing both aliasing constraints that guarantee external uniqueness, and linear consumption of unique references. We formalize our approach as a type system, and prove a type preservation theorem. Type safety rests on an alias invariant that builds on a novel formalization of external uniqueness. We show how a capability-based type system can be used to integrate external uniqueness into widely available object- oriented programming languages. Practical experience suggests that our system allows adding uniqueness information to common collection classes in a simple and concise way.
Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes

MOTIVATION The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative concept space (ACS) has been developed for the representation of information extracted from biomedical literature. The ACS is a Euclidean space in which thesaurus concepts are positioned and the distances between concepts indicates their relatedness. The ACS uses co-occurrence of concepts as a source of information. In this paper we evaluate how well the system can retrieve functionally related genes and we compare its performance with a simple gene co-occurrence method. RESULTS To assess the performance of the ACS we composed a test set of five groups of functionally related genes. With the ACS good scores were obtained for four of the five groups. When compared to the gene co-occurrence method, the ACS is capable of revealing more functional biological relations and can achieve results with less literature available per gene. Hierarchical clustering was performed on the ACS output, as a potential aid to users, and was found to provide useful clusters. Our results suggest that the algorithm can be of value for researchers studying large numbers of genes. AVAILABILITY The ACS program is available upon request from the authors.
Equitable coloring of random graphs

An equitable coloring of a graph is a proper vertex coloring such that the sizes of any two color classes differ by at most one. The least positive integer k for which there exists an equitable coloring of a graph G with k colors is said to be the equitable chromatic number of G and is denoted by χ=(G). The least positive integer k such that for any k′ ≥ k there exists an equitable coloring of a graph G with k′ colors is said to be the equitable chromatic threshold of G and is denoted by χ=*(G). In this paper, we investigate the asymptotic behavior of these coloring parameters in the probability space G(n,p) of random graphs. We prove that if n−1/5+ϵ < p < 0.99 for some 0 < ϵ, then almost surely χ(G(n,p)) ≤ χ=(G(n,p)) = (1 + o(1))χ(G(n,p)) holds (where χ(G(n,p)) is the ordinary chromatic number of G(n,p)). We also show that there exists a constant C such that if C/n < p < 0.99, then almost surely χ(G(n,p)) ≤ χ=(G(n,p)) ≤ (2 + o(1))χ(G(n,p)). Concerning the equitable chromatic threshold, we prove that if n−(1−ϵ) < p < 0.99 for some 0 < ϵ, then almost surely χ(G(n,p)) ≤ χ=* (G(n,p)) ≤ (2 + o(1))χ(G(n,p)) holds, and if ${{\log^{1+\epsilon}n}\over {n}}$ < p < 0.99 for some 0 < ϵ, then almost surely we have χ(G(n,p)) ≤ χ=*(G(n,p)) = Oϵ(χ(G(n,p))). © 2009 Wiley Periodicals, Inc. Random Struct. Alg. , 2009
C-reactive protein levels in patients with aggressive periodontitis.

BACKGROUND Sera from patients with periodontal infections contain elevated levels of C-reactive protein (CRP) compared to periodontally healthy individuals. Most studies to date have included patients with chronic periodontitis, and few investigators have studied CRP levels in subjects with aggressive periodontitis (AgP). The purpose of this study was to determine the relative levels of serum CRP in AgP patients and periodontally healthy subjects and to examine patients' characteristics that might account for intergroup differences. METHODS Serum samples were collected from 93 patients with generalized AgP (GAgP), from 97 patients with localized AgP (LAgP), and from 91 healthy controls (non-periodontitis [NP]). Periodontal examination consisted of plaque index, gingival index, probing depth, bleeding index, and attachment loss measurements. Current smoking was assessed by determination of serum cotinine levels by enzyme-linked immunosorbent assay (ELISA), and serum CRP levels were determined using a high-sensitivity ELISA assay. RESULTS The three groups were significantly different from one another (P <0.0001). The 95% confidence interval for serum CRP concentrations were as follows: NP, 0.65919 (0.4901 to 0.8869); LAgP, 1.10138 (0.8265 to 1.468); and GAgP, 2.05318 (1.5313 to 2.7538) mg/l. CRP levels in both LAgP and GAgP subjects were significantly greater than those in NP subjects, and levels in GAgP were significantly greater than those in LAgP. Following adjustment of the data for periodontal and demographic variables and current smoking, both mean probing depth and periodontal diagnosis remained correlated with CRP levels. CONCLUSIONS Patients with AgP have statistically significant elevations in serum CRP levels compared to subjects without periodontitis. Elevated CRP in these subjects might represent a contribution of periodontal infections to systemic inflammation in relatively young individuals.
Structures and developmental alterations of N- glycans of zebrafish embryos

Zebrafish is a model organism suitable for studying vertebrate development. We analyzed the N-glycan structures of zebrafish embryos and their alterations during zebrafish embryogenesis to obtain basic data for studying the roles of N-glycosylation. Multiple modes of high-performance liquid chromatography and multistage mass spectrometry were used for structural analysis of N-glycans. The N-glycans from deyolked embryos at 36 hours postfertilization, a mid-pharyngula stage, contained relatively higher amounts of complex- and hybrid-type glycans with LacNAc (Galβ1-4GlcNAc) and/or sialyl LacNAc without additional β1,4-Gal, which are commonly found in mammalian tissues, as well as abundant oligomannose-type glycans. Some of the complex- and hybrid-type glycans possessed various extended LacNAc structures, such as Galβ1-4LacNAc, LacNAc-repeat or unique (+/- dHex)-GalNAcα1-GlcNAcβ1-LacNAc. In contrast, the yolk of the embryo contains predominant oligomannose-type glycans and complex-type glycans with Galβ1-4(Siaα2-3)Galβ1-4(Fucα1-3)GlcNAc antennae. N-Glycan profiles obtained from deyolked embryos at different stages showed stage-dependent variation of complex- and hybrid-type glycans. At gastrula and early segmentation stages, complex- and hybrid-type glycans were minor components, and their antenna structures were mainly sialyl LacdiNAc (Siaα2-6GalNAcβ1-4GlcNAc). From the mid-segmentation to pharyngula stages, those with LacNAc and/or α2,6-sialyl LacNAc antenna structures increased remarkably, and those with α2,3-sialyl LacNAc antenna, core α1,6-Fuc and bisecting GlcNAc modifications increased gradually. These results suggest the presence of mechanisms for regulating the antenna structures of complex/hybrid N-glycan biosynthesis in the phylotypic stage of vertebrate development.
Estimating Second Order Probability Beliefs from Subjective Survival Data

Based on subjective survival probability questions in the Health and Retirement Study (HRS), we use an econometric model to estimate the determinants of individual-level uncertainty about personal longevity. This model is built around the modal response hypothesis (MRH), a mathematical expression of the idea that survey responses of 0%, 50%, or 100% to probability questions indicate a high level of uncertainty about the relevant probability. We show that subjective survival expectations in 2002 line up very well with realized mortality of the HRS respondents between 2002 and 2010. We show that the MRH model performs better than typically used models in the literature of subjective probabilities. Our model gives more accurate estimates of low probability events and it is able to predict the unusually high fraction of focal 0%, 50%, and 100% answers observed in many data sets on subjective probabilities. We show that subjects place too much weight on parents' age at death when forming expectations about their own longevity, whereas other covariates such as demographics, cognition, personality, subjective health, and health behavior are under weighted. We also find that less educated people, smokers, and women have less certain beliefs, and recent health shocks increase uncertainty about survival, too.
Mathematical Systems Theory Complexity Classes and Theories of Finite Models

Let LC_Y. * be accepted in t imef(n) by a nondeterministic Turing machine. Then there is a monadic existential second-order sentence o in the language of + such that for every x E Y . * , x E L if and only if a certain structure 9~ of cardinality f(lx]) satisfies o. It follows that if L is accepted in nondeterministic time n a, d a natural number, then there is a sentence whose relational symbols are d-ary or less, whose finite spectrum is L.
Cluster Analysis for Acid Rain Data in Norway

Cluster Analysis for Acid Rain Data in Norway by Ali Ghafourian, Master of Science Utah State University, 1983 Major Professor: Dr. Robert Gunderson Department: Mathematics vi This paper gives a description of three well known clustering methods, and discusses the advantages and disadvantages of each. Then, the results of these three clustering methods are compared through examining them on a specific set of data.
Diagnosis and management of community-acquired pneumonia in childhood – South African Thoracic Society guidelines

Background: Community-acquired pneumonia (CAP) is a major cause of morbidity and mortality in South African children. The incidence, severity and spectrum of childhood pneumonia have changed owing to the HIV epidemic. Increasing emergence of antimicrobial resistance necessitates a rational approach to the use of antibiotics in pneumonia management.Objective: To develop guidelines for the diagnosis, management and prevention of CAP in South African children.Methods: The Paediatric Assembly of the South African Thoracic Society established fve expert subgroups to address: (i) epidemiology and aetiology; (ii) diagnosis; (iii) antibiotic treatment; (iv) supportive therapy; and (v) prevention of CAP. Each subgroup developed a position paper based on the available published evidence; in the absence of evidence, expert opinion was accepted. After peer review and revision, the position papers were synthesised into an overall guideline which was further reviewed and revised.Recommendations: Recommendations based o.
An investigation of two interventions for micrographia in individuals with Parkinson’s disease

Objective: This pilot study was designed to compare a change in micrographia between using grid lines and parallel horizontal lines as visual cues in individuals with Parkinson’s disease. Design: Single group pre- and post-test. Setting: Research lab. Participants: Eleven males with Parkinson’s disease. Interventions: Practice writing words with parallel and grid lines. The sequence of practising was randomized. Main outcome measures: Length of words. Results: The length of the words after practising with parallel lines was longer than in the initial free writing condition (17.83 ± 3.93 cm vs. 23.36 ± 5.82 cm, P =0.008). The length of the words after practising with grid lines was also longer than during free writing (17.83 ± 3.93 cm vs. 22.65 ± 4.04 cm, P =0.003). The length of the words after practising with parallel lines was not different from that after practising with grid lines. Conclusion: Improvements in letter size after practising with horizontal parallel lines and grid lines were not different. The addition of vertical lines to form a grid did not appear to improve the writing more than horizontal lines alone in persons with Parkinson’s disease who experienced micrographia.