usecasedocs

Reference Studies who have been using the data (in any form) are required to include the following reference: @inproceedings{Liu:2014:AED:2642937.2642969, author = {Liu, Shuang and Sun, Jun and Liu, Yang and Zhang, Yue and Wadhwa, Bimlesh and Dong, Jin Song and Wang, Xinyu}, title = {Automatic Early Defects Detection in Use Case Documents}, booktitle = {Proceedings of the 29th ACM/IEEE International Conference on Automated Software Engineering}, series = {ASE '14}, year = {2014}, isbn = {978-1-4503-3013-8}, location = {Vasteras, Sweden}, pages = {785--790}, numpages = {6}, url = {http://doi.acm.org/10.1145/2642937.2642969}, doi = {10.1145/2642937.2642969}, acmid = {2642969}, publisher = {ACM}, address = {New York, NY, USA}, keywords = {natural language processing, use cases}, } About the Data Overview of Data It has been reported that “More than 60% of the errors in a software product are committed during the design and less than 40% during coding.”[1] and “Finding and fixing a software problem after delivery is often 100 times more expensive than finding and fixing it during the requirements and design phase” [2]. So finding defects in an early stage of software development is of great importance. Use cases are widely used in Model-Driven Development to capture user requirements. Since the majority part of a use case document is written in natural language, it is thus highly desirable to rely on advanced natural language processing techniques to automatic the procedure of defects detection in use case documents. Natural Language Parser Zpar is a statistical muti-language parser. It has the state-of-the-art speed and accuracy for both Chinese and English on standard Penn Treebank data. Zpar provides word segmentation, part-of-speech tagging, dependency parsing and phrase structure parsing functionalities. Use Case Defect Finder (UCDF) We developed a tool (UCDF) to automatically analysis use case documents and find defects. The source code is available here. Input Use Case Documents We tested UCDF on two use case documents (for real systems). One is a stock trading system and the other is a personalized health informatics system for a reference implementation for IEEEP2407-compliant system. The stock trading system is in real use, thus the specifications of the system are confidential. We release the use case document for the personalized health informatics system, the automated guided vehicle system, the emergency monitoring system and the online shopping system. Paper Abstract Use cases, as the primary techniques in the user requirement analysis, have been widely adopted in the requirement engineering practice. As developed early, use cases also serve as the basis for function requirement development, system design and testing. Errors in the use cases could potentially lead to problems in the system design or implementation. It is thus highly desirable to detect errors in use cases. Automatically analyzing use case documents is challenging primarily because they are written in natural languages. In this work, we aim to achieve automatic defect detection in use case documents by leveraging on advanced parsing techniques. In our approach, we first parse the use case document using dependency parsing techniques. The parsing results of each use case are further processed to form an activity diagram. Lastly, we perform defect detection on the activity diagrams. To evaluate our approach, we have conducted experiments on 200+ real-world as well as academic use cases. The results show the effectiveness of our method.</p

The effects of AhR/ARNT on <i>αB-crystallin</i> promoter activity.

<p>A. Structure of the pFLHspB2αBRL dual reporter plasmid used for reporter assays. B. AhR/ARNT up-regulates <i>αB-crystallin</i> but not <i>HspB2</i> promoter activity. 50 ng pcDNA3.1/B6AhR and 50 ng pcDNA/ARNT were co-transfected into HeLa cells with 100 ng pFLHspB2αBRL and 10 ng β-gal control vector. Luciferase activities were determined 48 h later. Data are presented as the ratio of firefly luciferase activity to β-gal activity (<u>R</u>elative <u>L</u>uciferase <u>U</u>nit, RLU) to indicate <i>HspB2</i> promoter activity, or the ratio of <i>Renilla</i> luciferase activity to β-gal activity to indicate <i>αB-crystallin</i> promoter activity. The results are presented as mean values; S.D. values were derived from three independent experiments.</p

AhR binds <i>in vivo</i> to <i>αB-crystallin</i> enhancer containing the XRE-like motif.

<p>αTN4 cells were transfected with pcDNA3.1/B6AhR and pcDNA/ARNT and treated with TCDD (10 nM) for 2 h. Cells were subjected to ChIP assay described under “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017904#s4" target="_blank">Materials and Methods</a>”. A. Schematics of the regions in αB-cystallin enhancer for amplification by ChIP. Arrows indicate the locations of the primers. B. C. The AhR-associated DNA was immunoprecipitated with anti-AhR antibody and amplified by PCR (B) and real time PCR (C). A specific band of 250 bp could be amplified only from which contained the XRE-like site. The samples that were precipitated with IgG did not give any amplified product. The specificity of the commercially obtained antibody has been confirmed by Western immunoblotting elsewhere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017904#pone.0017904-Matsumura1" target="_blank">[40]</a>. (**, p<0.01; ***, p<0.001).</p

Synthesis, Characterization, and Structures of Indium In(DTPA-BA₂) and Yttrium Y(DTPA-BA₂)(CH₃OH) Complexes (BA = Benzylamine): Models for ¹¹¹In- and ⁹⁰Y-Labeled DTPA-Biomolecule Conjugates

To explore structural differences in In3+, Y3+, and Lu3+ chelates, we prepared M(DTPA-BA2) complexes (M = In, Y, and Lu; DTPA-BA2 = N,N‘ ‘-bis(benzylcarbamoylmethyl)diethylenetriamine-N,N‘,N‘ ‘-triacetic acid) by reacting the trisodium salt of DTPA-BA2 with 1 equiv of metal chloride or nitrate. All three complexes have been characterized by elemental analysis, HPLC, IR, ES-MS, and NMR (1H and 13C) methods. ES-MS spectral and elemental analysis data are consistent with the proposed formula for M(DTPA-BA2) (M = In, Y, and Lu) and have been confirmed by the X-ray crystal structures of both In(DTPA-BA2)·2H2O and Y(DTPA-BA2)(CH3OH) complexes. By a reversed-phase HPLC method, it was found that In(DTPA-BA2) is more hydrophilic than M(DTPA-BA2) (M = Y and Lu), most likely due to the dissociation of the two carbonyl oxygen donors in solution. The X-ray crystal structure of In(DTPA-BA2) revealed a rare example of an eight-coordinated In3+ complex with DTPA-BA2 bonding to the In3+ in a distorted square antiprism coordination geometry. Both benzylamine groups are in the trans position relative to the acetate-chelating arm that is attached to the central N atom. The Y3+ in Y(DTPA-BA2)(CH3OH) is nine-coordinated with an octadentate DTPA-BA2 and a methanol oxygen. The coordination geometry is best described as a tricapped trigonal prism. One benzylamine group is trans and the other cis to the acetate-chelating arm that is attached to the central N atom. All three M(DTPA-BA2) complexes (M = In, Y, and Lu) exist as at least three isomers in solution (∼10 mM), as shown by the presence of 6−8 overlapped 1H NMR signals from the methylene hydrogens of the benzylamine groups. The coordinated DTPA-BA2 remains rigid even at temperatures >85 °C. The exchange rate between different isomers in M(DTPA-BA2) (M = In, Y, and Lu) is relatively slow at high concentrations (>1.0 mM), but it is fast due to the partial dissociation and rapid interconversion of different isomers at lower concentrations (∼10 μM). It is not surprising that M(DTPA-BA2) complexes (M = In, Y, and Lu) appear as a single peak in their respective HPLC chromatogram

Competitions between XRE-like motif and XRE-I motif or XRE-II motif for AhR binding.

<p>The XRE-like, XRE-I and XRE-II motif oligonuccleotides were labels with ³²P and incubated with nuclear extracts from pcDNA3.1/B6AhR and pcDNA/ARNT transfected, TCDD (10 nM)-treated HeLa cells. 10-, 25-, and 100-fold molar excess of unlabeled oligonucleotides were pre-incubated with the nuclear extract prior to incubation with the labeled oligonucleotides. The bands indicated by arrows in the gel shift experiments represent the specific complexes of AhR.</p

αB-crystallin is decreased in AhR^−/− mice.

<p>A. Cornea, retina, lens, heart, and skeletal muscle were isolated from adult AhR^−/− and AhR^+/+ mice and tissue proteins extracted. Primary fibroblasts from skeletal muscle were cultured and cell proteins extracted. αB-crystallin was analyzed by Western immunoblotting. β-actin was detected as an internal control. (n = 4, *, p<0.05). B. αB-crystallin mRNA levels were determined by real time-PCR using total RNA extracted from whole eyes, heart and limb skeletal muscle. GAPDH mRNA levels were determined as an internal control (n = 2, **, p<0.01).</p

Synthesis, Characterization, and Structures of Mn(DMHP)₃·12H₂O and Mn(DMHP)₂Cl·0.5H₂O

This report describes the synthesis, characterization, and X-ray crystal structures of two Mn(III) complexes, Mn(DMHP)3·12H2O and Mn(DMHP)2Cl·0.5H2O (DMHP = 1,2-dimethyl-3-hydroxy-4-pyridinone). Mn(DMHP)2Cl was prepared from the reaction of Mn(II) chloride with 2 equiv of DMHP under reflux in the presence of triethylamine. Mn(DMHP)3 was obtained by reacting Mn(II) acetate with 3 equiv of DMHP in the presence of sodium acetate. Mn(DMHP)3 could also be prepared by reacting Mn(OAc)3·2H2O with 3 equiv of DMHP in the presence of triethylamine. Both Mn(III) complexes have been characterized by elemental analysis, infrared spectroscopy, electronic paramagnetic resonance, electrospray ionization spectroscopy, electrochemical method, and X-ray crystallography. The X-ray crystal structure of Mn(DMHP)2Cl·0.5H2O revealed a rare example of five-coordinated Mn(III) complexes with two bidentate ligands and a square pyramidal coordination geometry. Surprisingly, the average Mn−O (hydroxy) bond distance in Mn(DMHP)2Cl·0.5H2O is ∼0.025 Å longer than that of the average Mn−O (carbonyl) bond, suggesting an extensive delocalization of electrons in the two pyridinone rings. The structure of Mn(DMHP)3·12H2O, a rare example of six-coordinate high-spin Mn(III) complexes without Jahn−Teller distortion, is isostructural to M(DMHP)3·12H2O (M = Al, Ga, Fe, and In). The electrochemical data for Mn(DMHP)3 suggests that the Mn(III) oxidation state is highly stabilized by three DMHP ligands. DMHP has the potential as a chelator for the removal of excess intracellular Mn and the treatment of chronic Mn toxicity

Synthesis, Characterization, and Structures of Mn(DMHP)₃·12H₂O and Mn(DMHP)₂Cl·0.5H₂O

This report describes the synthesis, characterization, and X-ray crystal structures of two Mn(III) complexes, Mn(DMHP)3·12H2O and Mn(DMHP)2Cl·0.5H2O (DMHP = 1,2-dimethyl-3-hydroxy-4-pyridinone). Mn(DMHP)2Cl was prepared from the reaction of Mn(II) chloride with 2 equiv of DMHP under reflux in the presence of triethylamine. Mn(DMHP)3 was obtained by reacting Mn(II) acetate with 3 equiv of DMHP in the presence of sodium acetate. Mn(DMHP)3 could also be prepared by reacting Mn(OAc)3·2H2O with 3 equiv of DMHP in the presence of triethylamine. Both Mn(III) complexes have been characterized by elemental analysis, infrared spectroscopy, electronic paramagnetic resonance, electrospray ionization spectroscopy, electrochemical method, and X-ray crystallography. The X-ray crystal structure of Mn(DMHP)2Cl·0.5H2O revealed a rare example of five-coordinated Mn(III) complexes with two bidentate ligands and a square pyramidal coordination geometry. Surprisingly, the average Mn−O (hydroxy) bond distance in Mn(DMHP)2Cl·0.5H2O is ∼0.025 Å longer than that of the average Mn−O (carbonyl) bond, suggesting an extensive delocalization of electrons in the two pyridinone rings. The structure of Mn(DMHP)3·12H2O, a rare example of six-coordinate high-spin Mn(III) complexes without Jahn−Teller distortion, is isostructural to M(DMHP)3·12H2O (M = Al, Ga, Fe, and In). The electrochemical data for Mn(DMHP)3 suggests that the Mn(III) oxidation state is highly stabilized by three DMHP ligands. DMHP has the potential as a chelator for the removal of excess intracellular Mn and the treatment of chronic Mn toxicity

AhR/ARNT up-regulates <i>αB-crystallin</i> promoter activity independently of TCDD.

<p>A. AhR and ARNT dose-dependently up-regulate <i>αB-crystallin</i> promoter activity. Increasing doses of pcDNA3.1/B6AhR and pcDNA/ARNT were co-transfected with fixed amounts of pFLHspB2αBRL and β-gal control vector into HeLa cells. After 24 h the cells were treated for another 24 h with TCDD (10 nM) or DMSO (0.01%) and then assayed for luciferase activities. B. Effects of TCDD on <i>αB-crystallin</i> promotor activity. HeLa cells transfected with pcDNA3.1/B6AhR and pcDNA/ARNT or control vector were treated with progressive concentrations of TCDD as indicated. After 24 h the cells were assayed for luciferase activities. <b>C</b>. Effects of high ligand-affinity AhR (B6/AhR) and low ligand-affinity AhR (D2/AhR) on <i>αB-crystallin</i> promoter activity. HeLa cells were co-transfected with pcDNA3.1/B6AhR or pcDNA3.1/D2AhR with pFLHspB2αBRL and β-gal control vector. After 24 h the cells were treated with TCDD (10 nM) or DMSO (0.01%) for another 24 h and then assayed for luciferase activities. The fold change was recorded by determining luciferase activity in AhR/ARNT transfected and/or TCDD-treated cells relative to that in the pcDNA3.1 transfected and DMSO-treated cells. The means and S.D. values were derived from three independent experiments.</p

Synthesis, Characterization, and Structures of Indium In(DTPA-BA₂) and Yttrium Y(DTPA-BA₂)(CH₃OH) Complexes (BA = Benzylamine): Models for ¹¹¹In- and ⁹⁰Y-Labeled DTPA-Biomolecule Conjugates

To explore structural differences in In3+, Y3+, and Lu3+ chelates, we prepared M(DTPA-BA2) complexes (M = In, Y, and Lu; DTPA-BA2 = N,N‘ ‘-bis(benzylcarbamoylmethyl)diethylenetriamine-N,N‘,N‘ ‘-triacetic acid) by reacting the trisodium salt of DTPA-BA2 with 1 equiv of metal chloride or nitrate. All three complexes have been characterized by elemental analysis, HPLC, IR, ES-MS, and NMR (1H and 13C) methods. ES-MS spectral and elemental analysis data are consistent with the proposed formula for M(DTPA-BA2) (M = In, Y, and Lu) and have been confirmed by the X-ray crystal structures of both In(DTPA-BA2)·2H2O and Y(DTPA-BA2)(CH3OH) complexes. By a reversed-phase HPLC method, it was found that In(DTPA-BA2) is more hydrophilic than M(DTPA-BA2) (M = Y and Lu), most likely due to the dissociation of the two carbonyl oxygen donors in solution. The X-ray crystal structure of In(DTPA-BA2) revealed a rare example of an eight-coordinated In3+ complex with DTPA-BA2 bonding to the In3+ in a distorted square antiprism coordination geometry. Both benzylamine groups are in the trans position relative to the acetate-chelating arm that is attached to the central N atom. The Y3+ in Y(DTPA-BA2)(CH3OH) is nine-coordinated with an octadentate DTPA-BA2 and a methanol oxygen. The coordination geometry is best described as a tricapped trigonal prism. One benzylamine group is trans and the other cis to the acetate-chelating arm that is attached to the central N atom. All three M(DTPA-BA2) complexes (M = In, Y, and Lu) exist as at least three isomers in solution (∼10 mM), as shown by the presence of 6−8 overlapped 1H NMR signals from the methylene hydrogens of the benzylamine groups. The coordinated DTPA-BA2 remains rigid even at temperatures >85 °C. The exchange rate between different isomers in M(DTPA-BA2) (M = In, Y, and Lu) is relatively slow at high concentrations (>1.0 mM), but it is fast due to the partial dissociation and rapid interconversion of different isomers at lower concentrations (∼10 μM). It is not surprising that M(DTPA-BA2) complexes (M = In, Y, and Lu) appear as a single peak in their respective HPLC chromatogram