Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of novel alternatively spliced isoforms of RTEF-1 within human ocular vascular endothelial cells and murine retina.

PURPOSE Identification of transcription factors that regulate the transcription of the vascular endothelial growth factor (VEGF) gene may facilitate understanding of the etiology and progression of ocular neovascular diseases. The purpose of this study was to determine whether transcriptional enhancer factor 1-related (RTEF-1) was present within ocular vascular endothelial cells and whether it played a role in the control of the transcription of the VEGF gene. METHODS Primary cultures of human retinal vascular endothelial cells (RVECs) were maintained under normoxic or hypoxic conditions before isolation of mRNA. RT-PCR was performed to detect RTEF-1 transcripts. Amplified products were cloned into an expression plasmid. Human VEGF promoter and deletion constructs were cloned into a pSEAP reporter vector. Various RTEF-1 isoforms and VEGF promoter constructs were coelectroporated into human cells, and reporter expression levels were determined. Retinal tissue from a mouse model of retinopathy of prematurity (ROP) was analyzed by RT-PCR for the presence of RTEF-1 transcripts. RESULTS Full-length 1305-bp and novel 936-bp RTEF-1 transcripts were identified in cultured human RVECs under normoxic conditions. A novel 447-bp isoform was present in cells maintained in a hypoxic environment. Four of the 11 translated exons predicted to code for the 1305-bp product were spliced out of the 936-bp transcript. The 1305-bp product enhanced expression from the VEGF promoter 4-fold greater than background, whereas the 936-bp and the 447-bp isoforms enhanced expression 3x and 12x, respectively. Analysis with deletion promoter constructs determined that all isoforms required the presence of Sp1 elements for efficient activation and that the hypoxia response element (HRE) was not essential for enhancement. Transcripts for novel RTEF-1 isoforms were also identified in neural retinal tissue of mice. Different murine-specific isoforms were present at different stages of postnatal development. CONCLUSIONS Novel RTEF-1 transcripts are present within human ocular vascular endothelial cells and mouse neural retina during normal and ROP development, and alternatively spliced products are produced under hyperoxic and hypoxic conditions. Alternative spliced variants of human RTEF-1 transcripts are able to potentiate expression from the VEGF 5' proximal promoter region.
Canonical Correlation Analysis for Analyzing Sequences of Medical Billing Codes

We propose using canonical correlation analysis (CCA) to generate features from sequences of medical billing codes. Applying this novel use of CCA to a database of medical billing codes for patients with diverticulitis, we first demonstrate that the CCA embeddings capture meaningful relationships among the codes. We then generate features from these embeddings and establish their usefulness in predicting future elective surgery for diverticulitis, an important marker in efforts for reducing costs in healthcare.
Learning spatial-semantic representations from natural language descriptions and scene classifications

We describe a semantic mapping algorithm that learns human-centric environment models by interpreting natural language utterances. Underlying the approach is a coupled metric, topological, and semantic representation of the environment that enables the method to fuse information from natural language descriptions with low-level metric and appearance data. We extend earlier work with a novel formulation that incorporates spatial layout into a topological representation of the environment. We also describe a factor graph formulation of the semantic properties that encodes human-centric concepts such as type and colloquial name for each mapped region. The algorithm infers these properties by combining the user's natural language descriptions with image- and laser-based scene classification. We also propose a mechanism to more effectively ground natural language descriptions of distant regions using semantic cues from other modalities. We describe how the algorithm employs this learned semantic information to propose valid topological hypotheses, leading to more accurate topological and metric maps. We demonstrate that integrating language with other sensor data increases the accuracy of the achieved spatial-semantic representation of the environment.
High-quality polygon edging

Applications combining wireframe and shaded primitives often produce unwanted artifacts and thus poor-quality polygon edging. We have developed an algorithm that uses an edging plane to generate clean, high-quality polygon edges when using separately drawn vectors to highlight polygon borders. The algorithm maintains the subpixel adjustments necessary for accurate polygonal rendering. The edging plane is simple to incorporate into existing software and hardware scan convertors. In this article, we describe the problem of edging a single polygon, then extend the discussion to multipolygon surfaces and multiple component assemblies. We introduce our algorithm and compare it to existing methods for improving polygon edges. >
Fire Resistance of High-Strength Concretes for Offshore Concrete Platforms

This paper presents the results of the two test programs involving hydrocarbon fires and high-strength concretes. Both lightweight aggregate concrete and modified normal density concrete (blends of normal density and lightweight aggregate coarse aggregates) were evaluated. Small beams of lightweight concrete, using different lightweight aggregate types, were evaluated for spalling resistance. Polypropylene fibers, used in some beams, were successful in greatly reducing spalling. Large wall sections of modified normal-density concrete experienced significant spalling but retained adequate concrete strength behind the reinforcing bars because of the low rates of heat transfer within the large sections.
Records of lead deposition in Lake Michigan sediments since 1800.

The distribution of stable lead has been determined in several Lake Michigan cores that have been dated using the /sup 210/Pb technique. A mathematical model, based on records of national and regional fuel use, is developed that accounts for the effect of aquatic residence time, processes of sedimentation, compaction, postdepositional redistribution of sediment solids, and the effect of finite core sectioning. The model gives an excellent quantitative description of the data, indicating that the lead profiles reflect the history of lead input from the burning of coal and leaded gasoline since about 1830 and 1920, respectively. The model is applied to obtain the sedimentation and lead deposition rates from stable lead distributions in undated sediment cores measured previously by others. The 1972 anthropogenic lead flux into the southern basin of the lake is determined to be 1.3 . mu.g cm/sup -2/ yr/sup -1/ in comparison to the natural (precultural) flux of approximately 0.16 . mu.g cm/sup -2/ yr/sup -1/. The anthropogenic lead deposited in the southern basin in 1972 is estimated to be approximately 240 metric tons as compared with an estimate of approximately 230 metric tons from air pollution fallout originating in the Chicago-Gary urban-industrial area. The measurement of both leadmore » and lead-210 fluxes in the same core may allow contributions of atmospheric lead to be distinguished from terrigenous pollution inputs. (auth)« less
Candidate Biomarkers for Systemic Inflammatory Response Syndrome and Inflammation: A Pathway for Novel Translational Therapeutics

Objective: Systemic inflammatory response syndrome (SIRS) causes 200,000 deaths/year in the USA and has central nervous system (CNS) and peripheral components. Our aim was to identify candidate biomakers for SIRS and inflammation by studying the molecular pathways implicated in the CNS and the periphery, in order to facilitate translation into conceptually novel treatments. Methods: We used systemic administration of lipopolysaccharide (LPS) of Gram-negative bacteria to cause SIRS in rodents. We compared the transcriptional pattern of gene expression observed in the brain and heart of rodents after intraperitoneal LPS. Results: Only 10 out of 30 transcripts were commonly activated in the brain and the heart, which could be explained by variability of response, dilution effect in the CNS and lack of representation in both microarray platforms. Distinct temporal patterns of transcriptional expression suggest the presence of a tissue-specific inflammatory cascade during SIRS. We found that in the heart there were 240 upregulated transcripts, the majority of which was upregulated at 24 h (n = 154). There were also differences between the total number of transcripts that were upregulated in each ventricle: 209 in the right ventricle (RV) and 114 in the left ventricle; the RV was a site of delayed exacerbated inflammatory response. Conclusions: Given the striking cellular and tissue differences between the mouse brain and the rat heart, the 10 transcripts with shared regulation may be potential candidate biomarkers for SIRS, as they withstand intertissue and interspecies expression variability. We identified two types of temporal transcriptional patterns: (1) transitory activation with a peak around 6 or 24 h and (2) sustained activation. Detailed understanding of specific spatial-temporal patterns in various sites will lead to the identification of candidate biomarkers that can guide future translational efforts towards novel therapeutic strategies for SIRS and related conditions.
The Finite Element Analysis and the Optimum Geometric Design of Linear Motor

Linear motor has been considered to be the most suitable electric machine for linear control with high speed and high precision. Thrust of linear motor is one of the important factors to specify motor performance. Maximum thrust can be obtained by increasing the magnitude of current in conductor and is relative to the sizes of conductor and magnet. However, the magnitude of current and the size of conductor have an effect on temperature of linear motor. Therefore, it is practically important to find optimum design that can effectively maximize thrust of linear motor within limited range of temperature. Finite element analysis was applied to calculate thrust and numerical solutions were compared with experiments. The temperature of the conductor was calculated from the experimentally determined thermal resistance. The ADPL of ANSYS was used for the optimum design process, which is commercial finite element analysis software. Design variables and constraints were chosen based on manufacturing feasibility and existing products. As a result, it is shown that temperature of linear motor plays an important role in determining optimum design.
Multi-strategy Query Expansion Method Based on Semantics

Query expansion adds related words to a user query in order to improve retrieval results. It’s an important step in information retrieval. Most of current query expansion methods pay attention to specific expansion strategies or algorithms, while neglecting the query itself. In reaction to the phenomenon, a multistrategy query expansion method based on semantics was proposed. This method started by analyzing the semantic structure of user query, and adopted corresponding strategy to select expansion terms. The expansion words are derived from three parts: WordNet, massive web page set and search engine performance evaluation data, which were merged semantically in each expansion algorithm later. The experiment showed this method can improve retrieval results to some extent. Subject Categories and Descriptors H.3. 3 [Information Search and Retrieval]; Query Formulation: I.2. 7 [Natural Language Processing] General Terms: Information Retrieval, Query Expansion
Appears in Ecml-98 as a Research Note a Longer Version Is Available as Ece Tr 98-3, Purdue University Pruning Decision Trees with Misclassiication Costs 1 Pruning Decision Trees

We describe an experimental study of pruning methods for decision tree classiiers when the goal is minimizing loss rather than error. In addition to two common methods for error minimization, CART's cost-complexity pruning and C4.5's error-based pruning, we study the extension of cost-complexity pruning to loss and one pruning variant based on the Laplace correction. We perform an empirical comparison of these methods and evaluate them with respect to loss. We found that applying the Laplace correction to estimate the probability distributions at the leaves was beneecial to all pruning methods. Unlike in error minimization , and somewhat surprisingly, performing no pruning led to results that were on par with other methods in terms of the evaluation criteria. The main advantage of pruning was in the reduction of the decision tree size, sometimes by a factor of ten. While no method dominated others on all datasets, even for the same domain diierent pruning mechanisms are better for diierent loss matrices. Decision trees are a widely used symbolic modeling technique for classiication tasks in machine learning. The most common approach to constructing decision tree classiiers is to grow a full tree and prune it back. Pruning is desirable because the tree that is grown may overrt the data by inferring more structure than is justiied by the training set. Speciically, if there are no connicting instances, the training set error of a fully built tree is zero, while the true error is likely to be larger. To combat this overrtting problem, the tree is pruned back with the goal of identifying the tree with the lowest error rate on previously unobserved instances, breaking ties in favor of smaller trees (Breiman, Friedman, Olshen & Stone 1984, Quinlan 1993). Several pruning methods have been introduced in the literature, including cost-complexity pruning, reduced error pruning, pessimistic pruning, error-based pruning, penalty pruning, and MDL pruning. Historically,
Capturing and supporting the analysis process

Visual analytics tools provide powerful visual representations in order to support the sense-making process. In this process, analysts typically iterate through sequences of steps many times, varying parameters each time. Few visual analytics tools support this process well, nor do they provide support for visualizing and understanding the analysis process itself. To help analysts understand, explore, reference, and reuse their analysis process, we present a visual analytics system named CzSaw (See-Saw) that provides an editable and re-playable history navigation channel in addition to multiple visual representations of document collections and the entities within them (in a manner inspired by Jigsaw [24]). Conventional history navigation tools range from basic undo and redo to branching timelines of user actions. In CzSaw's approach to this, first, user interactions are translated into a script language that drives the underlying scripting-driven propagation system. The latter allows analysts to edit analysis steps, and ultimately to program them. Second, on this base, we build both a history view showing progress and alternative paths, and a dependency graph showing the underlying logic of the analysis and dependency relations among the results of each step. These tools result in a visual model of the sense-making process, providing a way for analysts to visualize their analysis process, to reinterpret the problem, explore alternative paths, extract analysis patterns from existing history, and reuse them with other related analyses.
Predicting the self-assembled morphology and mechanical properties of mixtures of diblocks and rod-like nanoparticles

We couple a morphological study of a mixture of diblock copolymers and rod-like, solid nanoparticles with a micromechanical simulation to determine how the spatial distribution and aspect ratio of the particles affects the mechanical behavior of the composite. The morphological studies are conducted through the SCF/DFT technique, which couples the self-consist field theory (SCFT) for the diblocks and a density functional theory (DFT) for parallelepiped particles. Through the SCF/DFT calculations, we obtain the equilibrium morphology of the diblock/particle mixtures. We find that the distribution of particles within the polymers is dependent not only on the relative interaction energies between the particles and the different blocks, but also on the aspect ratio of the rod-like solids. The output of the SCF/DFT model serves as the input to the Lattice Spring Model (LSM), which consists of a three-dimensional network of springs. In particular, the location of the different phases is mapped onto the LSM lattice and the appropriate force constants are assigned to the LSM bonds. A stress is applied to the LSM lattice, and we calculate the local stress and strain fields and overall elastic response of the material. We find that high aspect ratio rods can dramatically increase the Young's modulus of the material. By integrating the morphological and mechanical models, we can isolate how modifications in physical characteristics of the particles and diblocks affect both the structure of the mixture and the macroscopic behavior of the composite. Thus, we can establish how choices made in the components affect the ultimate performance of the material.
Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR

Antimicrobial resistance in Staphylococcus aureus is a major public health threat, compounded by emergence of strains with resistance to vancomycin and daptomycin, both last line antimicrobials. Here we have performed high throughput DNA sequencing and comparative genomics for five clinical pairs of vancomycin-susceptible (VSSA) and vancomycin-intermediate ST239 S. aureus (VISA); each pair isolated before and after vancomycin treatment failure. These comparisons revealed a frequent pattern of mutation among the VISA strains within the essential walKR two-component regulatory locus involved in control of cell wall metabolism. We then conducted bi-directional allelic exchange experiments in our clinical VSSA and VISA strains and showed that single nucleotide substitutions within either walK or walR lead to co-resistance to vancomycin and daptomycin, and caused the typical cell wall thickening observed in resistant clinical isolates. Ion Torrent genome sequencing confirmed no additional regulatory mutations had been introduced into either the walR or walK VISA mutants during the allelic exchange process. However, two potential compensatory mutations were detected within putative transport genes for the walK mutant. The minimal genetic changes in either walK or walR also attenuated virulence, reduced biofilm formation, and led to consistent transcriptional changes that suggest an important role for this regulator in control of central metabolism. This study highlights the dramatic impacts of single mutations that arise during persistent S. aureus infections and demonstrates the role played by walKR to increase drug resistance, control metabolism and alter the virulence potential of this pathogen.
Viscoelastic Free Surface Jets and Filaments

In this paper we examine the necessary versus self-consistent consequences of a slender aspect ratio on viscoelastic free surface jet flows. As in Schultz & Davis (1982), the equations of the 3-D free surface jet problem are nondimensionalized with presumed disparate length scales in the transverse and axial directions, and a perturbation theory for the slender jet is obtained by positing an expansion in the slenderness parameter (i.e. the ratio ε of these scales). A different perturbation problem ensues for each regime of free jet behavior. We exhibit three regimes, one in which the slenderness scaling of the 3-D free surface jet problem forces a separation-of-variables (s-o-v) structure of the solution (that is, the radial coordinate explicitly factors out at each order in ε), another in which the s-o-v structure is not forced but is a solution, and a third in which the s-o-v structure is not a solution. These three regimes are prototypes for general filament behavior: of the many possible regimes, many are of the first type (the separation of variables structure is unique), many more are of the second type (the separation of variables solution exists but cannot be shown to be unique), and the rest are of the third type (if a slender solution exists it does not have a s-o-v structure).
Eye Metrics as an Objective Assessment of Surgical Skill

Objective:Currently, surgical skills assessment relies almost exclusively on subjective measures, which are susceptible to multiple biases. We investigate the use of eye metrics as an objective tool for assessment of surgical skill. Summary Background Data:Eye tracking has helped elucidate relationships between eye movements, visual attention, and insight, all of which are employed during complex task performance (Kowler and Martins, Science. 1982;215:997–999; Tanenhaus et al, Science. 1995;268:1632–1634; Thomas and Lleras, Psychon Bull Rev. 2007;14:663–668; Thomas and Lleras, Cognition. 2009;111:168–174; Schriver et al, Hum Factors. 2008;50:864–878; Kahneman, Attention and Effort. 1973). Discovery of associations between characteristic eye movements and degree of cognitive effort have also enhanced our appreciation of the learning process. Methods:Using linear discriminate analysis (LDA) and nonlinear neural network analyses (NNA) to classify surgeons into expert and nonexpert cohorts, we examine the relationship between complex eye and pupillary movements, collectively referred to as eye metrics, and surgical skill level. Results:Twenty-one surgeons participated in the simulated and live surgical environments. In the simulated surgical setting, LDA and NNA were able to correctly classify surgeons as expert or nonexpert with 91.9% and 92.9% accuracy, respectively. In the live operating room setting, LDA and NNA were able to correctly classify surgeons as expert or nonexpert with 81.0% and 90.7% accuracy, respectively. Conclusions:We demonstrate, in simulated and live-operating environments, that eye metrics can reliably distinguish nonexpert from expert surgeons. As current medical educators rely on subjective measures of surgical skill, eye metrics may serve as the basis for objective assessment in surgical education and credentialing in the future. Further development of this potential educational tool is warranted to assess its ability to both reliably classify larger groups of surgeons and follow progression of surgical skill during postgraduate training.
A System-Wide Investigation of the Dynamics of Wnt Signaling Reveals Novel Phases of Transcriptional Regulation

Aberrant Wnt signaling has been implicated in a wide variety of cancers and many components of the Wnt signaling network have now been identified. Much less is known, however, about how these proteins are coordinately regulated. Here, a broad, quantitative, and dynamic study of Wnt3a-mediated stimulation of HEK 293 cells revealed two phases of transcriptional regulation: an early phase in which signaling antagonists were downregulated, providing positive feedback, and a later phase in which many of these same antagonists were upregulated, attenuating signaling. The dynamic expression profiles of several response genes, including MYC and CTBP1, correlated significantly with proliferation and migration (P<0.05). Additionally, their levels tracked with the tumorigenicity of colon cancer cell lines and they were significantly overexpressed in colorectal adenocarcinomas (P<0.05). Our data highlight CtBP1 as a transcription factor that contributes to positive feedback during the early phases of Wnt signaling and serves as a novel marker for colorectal cancer progression.