Miracle-dz/UniFAR-FTUs huggingface dataset:
Cbr Textuality

Current textual CBR research focuses on generating knowledge-rich representations for working with document-cases. However, there are many \weakly-textual" contexts in which textual information plays an important , but ancillary role in case composition and reasoning. For retrieving weakly-textual \semi-structured" cases that contain one or more textual features, it is desirable to measure the similarity of the textual components in a simple manner that is easily integrated with standard, non-textual similarity metrics, such as nearest-neighbor methods. This paper describes an investigation of the issues involved in weakly-textual CBR, which has been motivated by work on the DRAMA system for aerospace design support. It describes a characterization of textual CBR along a continuum of textual importance in case composition and reasoning, that places weakly-textual CBR in relation to current practice and motivates a focus on weakly-textual methods. The paper goes on to discuss methods, which are currently being incorporated into DRAMA, that integrate simple information retrieval techniques into standard CBR similarity metrics for weakly-textual contexts, and it concludes with a discussion of related work and future directions.
CLASS-GUIDED BUILDING EXTRACTION FROM IKONOS IMAGERY

ofstereoIkonosimagery showsthat5-to10-mcontour linescan Recent high-resolution satellite images provide a valuable new bederivedwith thehighesttopographicstandard(Toutin etal., data source for geospatial information acquisition. This paper 2001). As forgeospatial feature extraction for topographicmapaddresses building extraction from Ikonos images in urban ping, Baltsaviaset al.(2001a) andFraser etal. (2001;2002) presareas. The proposed approach uses the classification results ent results on building extraction from Ikonos stereo images. A of Ikonos multispectral images to provide approximate loca- comparative study withthe results obtained fromaerial phototion and shape for candidate building objects. Their fine graphs concludes that about 15 percent of the building areas, as extraction is then carried out in the corresponding panchro- measured in aerial images, cannot be modeled using Ikonos matic image through segmentation and squaring. The ECHO images. An assessment based on 19 GPS surveyed check points classifier is used for supervised classification while the ISODATA atroofcorners suggeststhattheIkonos-derivedbuilding model algorithm is used for unsupervised classification and subse- can reach an accuracy of better than 1 meter both in planimetry quent image segmentation. The classification performance is and elevation (Baltsavias et al., 2001a). Sohn and Dowman evaluated using the classification confusion matrix, while the (2001) used a local Fourier transformation to analyze the domifinal building extraction results are assessed based on the nantorientation angleina buildingcluster andextractrectilinmanually delineated results. A building squaring approach ear building outlines from Ikonos imagery based on a binarybased on the Hough transformation is developed that detects space partitioning tree. Dial et al. (2001) present an investigaand forms the rectilinear building boundaries. A number of tion on automated road extraction in wide suburban roads. sample results are presented to illustrate the approach and Regarding the fundamental methodology in geospatial feademonstrate its efficiency. It is shown that about 64.4 percent ture extraction from aerial and space images, abundant experiof the buildings can be detected, extracted, and accurately ence hasbeen gainedin thepast few years.A collectionof stateformed through this process. Remaining difficulties are high of-the-art articles can be found in the periodical proceedings
Using real-time alerts for clinical trials

Summary Background: Clinical trials are widely accepted as a necessary step in evaluating the safety and efficacy of new pharmaceutical products. In order for a sufficiently powered study, a clinical trial depends on the effective and unbiased recruitment of eligible patients. Trials involving seasonal diseases like influenza pose additional challenges. Objective: This is a feasibility study of a mobile real-time alerting system to systematically identify potential study subjects for a randomized controlled trial evaluating the safety and efficacy of early intervention with interferon alfacon-1 for patients hospitalized for influenza virus infection. Methods: The alerting system was setup in a 471-bed acute care teaching hospital, enabled with computerized physician order entry (CPOE) and a rules-based alerting system. Patients were identified from the entire hospital using two alerts types: pharmacy prescription records for antiviral drugs, and positive influenza laboratory results. Email alerts were generated and sent to BlackBerry® devices carried by the study personnel for a 6 month period. The alerts were archived automatically on a secure server and were exported for analysis in Microsoft Access. Results: Over a period of 21 weeks, 779 total alerts were received. The study team was alerted to 241 patients, of whom 85 were potential study subjects. The alert system identified all but one of the patients independently identified by infection control. Conclusions: Real-time identification of potential study subjects is possible with the integration of computerized physician order entry and BlackBerry® technology. It is a viable method for the systematic identification of patients throughout a hospital, particularly for trials investigating time-sensitive disease progression.
Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome

LINE-1 elements (L1s) are a family of highly successful retrotransposons comprising ∼17% of the human genome, the majority of which have inserted through an endonuclease-dependent mechanism termed target-primed reverse transcription. Recent in vitro analyses suggest that in the absence of non-homologous end joining proteins, L1 elements may utilize an alternative, endonuclease-independent pathway for insertion. However, it remains unknown whether this pathway operates in vivo or in cell lines where all DNA repair mechanisms are functional. Here, we have analyzed the human genome to demonstrate that this alternative pathway for L1 insertion has been active in recent human evolution and characterized 21 loci where L1 elements have integrated without signs of endonuclease-related activity. The structural features of these loci suggest a role for this process in DNA double-strand break repair. We show that endonuclease-independent L1 insertions are structurally distinguishable from classical L1 insertion loci, and that they are associated with inter-chromosomal translocations and deletions of target genomic DNA.
Effect of one-minute and five-minute step-ups on performance of simple addition.

Abstract Twenty-six subjects who were accustomed to step-ups were randomly assigned to three treatments: rest, 1-min. step-ups, and 5-min. step-ups. The same procedure was followed with 32 subjects who had not been performing bench-stepping regularly. Each subject took a 5-min. test of simple addition followed by an alternate form of the same test 7 min. later. During the 7 min. between tests the rest groups lay quietly on mats, the 1-min. group rested for 6 min. and stepped up 30 times in 1 min. on a 20-in. bench, and the 5-min. groups rested for 2 min. and stepped up for 5 min. at 30 steps per minute. Among the subjects accustomed to step-ups the 1-min. group performed significantly worse than the 5-min. and rest groups on speed of addition. No other significant differences between groups were found. However, was a tendency for the conditioned subjects to improve in accuracy of addition as a result of 5-min. step-ups whereas the unconditioned subjects tended to do more poorly following a 5-min. bout of .
Poly(ε-caprolactone) Scaffolds Fabricated by Melt Electrospinning for Bone Tissue Engineering

Melt electrospinning is a promising approach to manufacture biocompatible scaffolds for tissue engineering. In this study, melt electrospinning of poly(ε-caprolactone) onto structured, metallic collectors resulted in scaffolds with an average pore size of 250–300 μm and an average fibre diameter of 15 μm. Scaffolds were seeded with ovine osteoblasts in vitro. Cell proliferation and deposition of mineralised extracellular matrix was assessed using PicoGreen® (Thermo Fisher Scientific, Scoresby, Australia) and WAKO® HR II (WAKO, Osaka, Japan) calcium assays. Biocompatibility, cell infiltration and the growth pattern of osteoblasts on scaffolds was investigated using confocal microscopy and scanning electron microscopy. Osteoblasts proliferated on the scaffolds over an entire 40-day culture period, with excellent survival rates and deposited mineralized extracellular matrix. In general, the 3D environment of the structured melt electrospun scaffold was favourable for osteoblast cultures.
Reformulating the Dual Graphs of CSPs to Improve the Performance of Relational Neighborhood Inverse Consistency

Freuder and Elfe (1996) introduced Neighborhood Inverse Consistency (NIC) as a new local consistency property for binary Constraint Satisfaction Problems (CSPs). Two advantages of the algorithm for enforcing NIC is that it automatically adapts its filtering power to the local connectivity of the network and has insignificant space overhead. However, studies on binary CSPs have shown that enforcing NIC is not effective on sparse graphs and too costly on dense graphs. In (Woodward et al. 2011), we introduced an algorithm for enforcing Relational Neighborhood Inverse Consistency (RNIC), which is an extension of NIC to non-binary CSPs. In this paper, we discuss how we enhance the propagation effectiveness of our algorithm and reduce its computational cost by reformulating the dual graph of the CSP. For that purpose, we describe two reformulation techniques that modify the topology of the dual graph without affecting the solution set of the problem. We present the two reformulations and their combinations, and discuss their effects on the consistency property enforced by the algorithm. We also describe a selection policy that nicely ties together the various components of our approach in a consistent, adaptive framework. Finally, we show that our automated selection policy outperforms all approaches in a statistically significant manner.
Interleukin-21 Is Required for the Development of Type 1 Diabetes in NOD Mice

OBJECTIVE Interleukin (IL)-21 is a type 1 cytokine that has been implicated in the pathogenesis of type 1 diabetes via the unique biology of the nonobese diabetic (NOD) mouse strain. The aim of this study was to investigate a causal role for IL-21 in type 1 diabetes. RESEARCH DESIGN AND METHODS We generated IL-21R–deficient NOD mice and C57Bl/6 mice expressing IL-21 in pancreatic β-cells, allowing the determination of the role of insufficient and excessive IL-21 signaling in type 1 diabetes. RESULTS Deficiency in IL-21R expression renders NOD mice resistant to insulitis, production of insulin autoantibodies, and onset of type 1 diabetes. The lymphoid compartment in IL-21R−/− NOD is normal and does not contain an increased regulatory T-cell fraction or diminished effector cytokine responses. However, we observed a clear defect in autoreactive effector T-cells in IL-21R−/− NOD by transfer experiments. Conversely, overexpression of IL-21 in pancreatic β-cells induced inflammatory cytokine and chemokines, including IL-17A, IL17F, IFN-γ, monocyte chemoattractant protein (MCP)-1, MCP-2, and interferon-inducible protein-10 in the pancreas. The ensuing leukocytic infiltration in the islets resulted in destruction of β-cells and spontaneous type 1 diabetes in the normally diabetes-resistant C57Bl/6 and NOD × C57Bl/6 backgrounds. CONCLUSIONS This work provides demonstration of the essential prodiabetogenic activities of IL-21 on diverse genetic backgrounds (NOD and C57BL/6) and indicates that IL-21 blockade could be a promising strategy for interventions in human type 1 diabetes.
Principal graphs and piecewise linear subspace constrained mean-shift

Principal curves have been defined as self-consistent smooth curves that pass through the middle of data. One of the important problems with most existing principal curve algorithms is that they are seeking for a smooth curve. In reality, data may take complicated shapes, which may include loops, self-intersections, and and bifurcation points; hence, a smooth curve passing through the data may not be a good representor of the data. Generally, there is, in fact, a principal graph, a collection of smooth curves that represents the dataset. We propose a nonparametric principal graph algorithm, and apply it to optical character recognition, where handling the above mentioned irregularities like loops and self-intersections is a serious problem that appear in many characters.
Induction of experimental mammary carcinogenesis in rats with 7,12-dimethylbenz(a)anthracene.

PURPOSE To test an experimental model of chemical mammary carcinogenesis induction in rats. METHODS Twenty young virgin Sprague-Dawley female rats, aged 47 days, received 20 mg of 7,12-dimethylbenz(a)anthracene (DMBA) intragastrically by gavage. Afterwards, at 8 and 13 weeks, their mammary glands were examined. At the end of the experiment, the animals were sacrificed, and the mammary tumors were measured and weighed. Tumor fragments were analyzed using light microscopy. RESULTS Eight weeks after DMBA injection, 16 rats presented at least 1 breast tumor (80%). After 13 weeks, all of them (100%) developed breast carcinomas that were confirmed by histopathological analysis. CONCLUSION This experimental animal model of chemical mammary induced carcinogenesis is feasible and can be used in further experiments on the role of tumorigenic biomodulator substances.
mRNA and DNA selection via protein multimerization: YB-1 as a case study

Translation is tightly regulated in cells for keeping adequate protein levels, this task being notably accomplished by dedicated mRNA-binding proteins recognizing a specific set of mRNAs to repress or facilitate their translation. To select specific mRNAs, mRNA-binding proteins can strongly bind to specific mRNA sequences/structures. However, many mRNA-binding proteins rather display a weak specificity to short and redundant sequences. Here we examined an alternative mechanism by which mRNA-binding proteins could inhibit the translation of specific mRNAs, using YB-1, a major translation regulator, as a case study. Based on a cooperative binding, YB-1 forms stable homo-multimers on some mRNAs while avoiding other mRNAs. Via such inhomogeneous distribution, YB-1 can selectively inhibit translation of mRNAs on which it has formed stable multimers. This novel mechanistic view on mRNA selection may be shared by other proteins considering the elevated occurrence of multimerization among mRNA-binding proteins. Interestingly, we also demonstrate how, by using the same mechanism, YB-1 can form multimers on specific DNA structures, which could provide novel insights into YB-1 nuclear functions in DNA repair and multi-drug resistance.
Study on the Optimum Cutting Parameters of an Aluminum Mold for Effective Bonding Strength of a PDMS Microfluidic Device

Master mold fabricated using micro milling is an easy way to develop the polydimethylsiloxane (PDMS) based microfluidic device. Achieving high-quality micro-milled surface is important for excellent bonding strength between PDMS and glass slide. The aim of our experiment is to study the optimal cutting parameters for micro milling an aluminum mold insert for the production of a fine resolution microstructure with the minimum surface roughness using conventional computer numerical control (CNC) machine systems; we also aim to measure the bonding strength of PDMS with different surface roughnesses. Response surface methodology was employed to optimize the cutting parameters in order to obtain high surface smoothness. The cutting parameters were demonstrated with the following combinations: 20,000 rpm spindle speed, 50 mm/min feed rate, depth of cut 5 µm with tool size 200 µm or less; this gives a fine resolution microstructure with the minimum surface roughness and strong bonding strength between PDMS–PDMS and PDMS–glass.
Amplification and overexpression of HER2/neu gene and HER2/neu protein in salivary duct carcinoma of the parotid gland.

OBJECTIVES To detect amplification of the HER2/neu gene by means of fluorescence in situ hybridization (FISH) in a series of 13 salivary duct carcinomas (SDCs) and to compare the results with immunohistochemical (IHC) assessment of HER2/neu protein expression. DESIGN Retrospective analysis. SETTING Department of Pathology, University of Brescia. PATIENTS We studied 13 cases of SDC diagnosed between January 1, 1997, and June 30, 2004, all arising from the parotid gland. Twelve patients were treated with surgery and radiotherapy, and 1 patient received only palliative radiotherapy. Seven patients died of disease, 3 patients were alive with disease, and 3 were free of disease. MAIN OUTCOME MEASURES HER2/neu protein expression and HER2/neu gene amplification detected by means of IHC assessment and FISH, respectively. RESULTS With IHC assessment, 10 cases showed overexpression (grade 3+) of HER2/neu protein, whereas 3 cases were negative for this protein (grade 0/1+). Using FISH, amplification of the HER2/neu gene was found in 8 of the 10 grade 3+ cases, whereas none of the cases negative for the protein according to IHC assessment had amplification of the gene. Because of the small number of patients, it was not possible to statistically correlate HER2/neu protein expression or HER2/neu gene amplification and survival. CONCLUSION Our data demonstrate that HER2/neu protein is frequently overexpressed in SDC, and in contrast to previous reports, overexpression of the protein is associated in most cases with HER2/neu gene amplification.
Structure of cortical microtubule arrays in plant cells

Serial sectioning was used to track the position and measure the lengths of cortical microtubules in glutaraldehyde-osmium tetroxide- fixed root tip cells. Microtubules lying against the longitudinal walls during interphase, those overlying developing xylem thickenings, and those in pre-prophase bands are oriented circumferentially but on average are only about one-eighth of the cell circumference in length, i.e., 2-4 micrometer. The arrays consist of overlapping component microtubules, interconnected by cross bridges where they are grouped and also connected to the plasma membrane. Microtubule lengths vary greatly in any given array, but the probability that any pass right around the cell is extremely low. The majority of the microtubule terminations lie in statistically random positions in the arrays, but nonrandomness in the form of groups of terminations and terminations in short lines parallel to the axis of cell elongation has been observed. Low temperature induces microtubule shortening and increases the frequency of C-shaped terminations over the 1.7% found under normal conditions; colchicine and high pressures produce abnormally large proportions of very short microtubules amongst those that survive the treatments. Deuterium oxide (D2O) treatment probably induces the formation of additional microtubules as distinct from increasing the length of those already present. The distribution of C-shaped terminations provides evidence for at least local polarity in the arrays. The validity of the findings is discussed, along with implications for the development, maintenance, and orientation of the arrays and their possible relationship to the orientation of cellulose deposition.
An assessment of bacterial small RNA target prediction programs

Most bacterial regulatory RNAs exert their function through base-pairing with target RNAs. Computational prediction of targets is a busy research field that offers biologists a variety of web sites and software. However, it is difficult for a non-expert to evaluate how reliable those programs are. Here, we provide a simple benchmark for bacterial sRNA target prediction based on trusted E. coli sRNA/target pairs. We use this benchmark to assess the most recent RNA target predictors as well as earlier programs for RNA-RNA hybrid prediction. Moreover, we consider how the definition of mRNA boundaries can impact overall predictions. Recent algorithms that exploit both conservation of targets and accessibility information offer improved accuracy over previous software. However, even with the best predictors, the number of true biological targets with low scores and non-targets with high scores remains puzzling.
Early Impact and Performance Characteristics of an Established Anal Dysplasia Screening Program: Program Evaluation Considerations

Background: Screening for invasive anal cancer and its precursors is being increasingly advocated as a response to increasing incidence among HIV-infected persons. We implemented a comprehensive screening program in 2001 and report our early experience to inform monitoring and evaluation of such programs. Our research aims were: (1) to estimate incidence of and mortality from invasive anal cancer (IAC) before (1995-2000) and after (2001-2005) screening program implementation and (2) to examine potential screening program quality indicators. Methods: The study cohort included all patients under care for HIV infection at UCSD Owen Clinic between 1995-2005. Person-time incidence rates (IR) and case survival of IAC were estimated for the pre-screening (1995-2000) and post-screening (2001-2005) periods. High resolution anoscopy (HRA) operator accuracy was estimated by kappa agreement between cyto-histologic comparisons. Program quality indicators included: (1) screening coverage; (2) percent technically unsatisfactory cytology smears; (3) time between 1st abnormal cytology and 1st HRA; and (4) time between last clinic visit and last cytology. Results: 28 cases of IAC and 13,411 person-years were observed between 1995-2005. IRs (95% CI) pre-screening and post-screening were 199 and 216 per 100,000 person-years, respectively. There was no routine treatment of high grade squamous intraepithelial lesions (HSIL) during the study period. The percent of patients with IAC requiring chemoradiation decreased from 90.9% to 70.6% (p=0.36). There was a significant improvement in cyto-histologic agreement at HRA with increasing operator experience (r=0.92, p=0.025). Screening coverage was 73% of the target population. Among 14 providers, the percent unsatisfactory cytology smears averaged 27% but varied from 0 – 62%. The median time from 1st abnormal cytology to 1st HRA was 258 days. The median interval between the last cytology and the last clinic visit was 207 days. Conclusion: (1) The overall IR of IAC did not decline in the screening era and was higher than previous estimates for HIV cohorts; (2) stage shift to IAC of more favorable prognosis is a reasonable screening goal; (3) HRA accuracy varied by provider experience; (4) because of delay in access to HRA, digital rectal exam should be combined with cytology screening to detect palpable disease.