Miracle-dz/UniFAR-FTUs huggingface dataset:
The ReqWiki Approach for Collaborative Software Requirements Engineering with Integrated Text Analysis Support

The requirements engineering phase within a software project is a heavily knowledge-driven, collaborative process that typically involves the analysis and creation of a large number of textual artifacts. We know that requirements engineering has a large impact on the success of a project, yet sophisticated tool support, especially for small to mid-size enterprises, is still lacking. We present Reqwiki, a novel open source web-based approach based on a semantic wiki that includes natural language processing (NLP) assistants, which work collaboratively with humans on the requirements specification documents. We evaluated Reqwiki with a number of software engineers to investigate the impact of our novel semantic support on software requirements engineering. Our user studies prove that (i) software engineers unfamiliar with NLP can easily leverage these assistants and (ii) semantic assistants can help to significantly improve the quality of requirements specifications.
Inferring a probability distribution function for the pose of a sensor network using a mobile robot

In this paper we present an approach for localizing a sensor network augmented with a mobile robot which is capable of providing inter-sensor pose estimates through its odometry measurements. We present a stochastic algorithm that samples efficiently from the probability distribution for the pose of the sensor network by employing Rao-Blackwellization and a proposal scheme which exploits the sequential nature of odometry measurements. Our algorithm automatically tunes itself to the problem instance and includes a principled stopping mechanism based on convergence analysis. We demonstrate the favourable performance of our approach compared to that of established methods via simulations and experiments on hardware.
Cell heterogeneity in clear cell renal cell carcinoma

The aim of this study was to define the histological spectrum, frequency and significance of nonconventional tumour cells in clear cell renal cell carcinomas (CCRCC). Fifty‐one totally sampled CCRCC were studied histologically to evaluate the spectrum of cell morphology variability, its frequency and significance, and their correlation with tumour grade and stage, and other histological parameters of aggressive behaviour like necrosis. Aside from conventional clear/eosinophilic granular cells, three additional cellular types were identified and considered in this study: small clear cells, syncytial cells and rhabdoid cells. Small clear cells were detected in 11 cases (21.5%), syncytial cells in 8 (15.6%) and rhabdoid cells in 5 (9.8%). The presence of syncytial and rhabdoid cells statistically correlated with grade (p = 0.003 and p = 0.006) and stage (p = 0.049 and p = 0.05) in CCRCC. Necrosis correlated with stage (p = 0.018) and grade (p = 0.004), but not with syncytial, rhabdoid or small clear cells. The presence of syncytial and rhabdoid cells in CCRCC is a relatively frequent event that significantly correlates with high‐grade tumours and high stage status.
SoQueT: Query-Based Documentation of Crosscutting Concerns

Understanding crosscutting concerns is difficult because their underlying relations remain hidden in a class-based decomposition of a system. Based on an extensive investigation of crosscutting concerns in existing systems and literature, we identified a number of typical implementation idioms and relations that allow us to group such concerns around so- called "sorts". In this paper, we present SoQueT, a tool that uses sorts to support the consistent description and documentation of crosscutting relations using pre-defined, sort- specific query templates.
Genome‐wide scans between two honeybee populations reveal putative signatures of human‐mediated selection

Summary Human‐mediated selection has left signatures in the genomes of many domesticated animals, including the European dark honeybee, Apis mellifera mellifera, which has been selected by apiculturists for centuries. Using whole‐genome sequence information, we investigated selection signatures in spatially separated honeybee subpopulations (Switzerland, n = 39 and France, n = 17). Three different test statistics were calculated in windows of 2 kb (fixation index, cross‐population extended haplotype homozygosity and cross‐population composite likelihood ratio) and combined into a recently developed composite selection score. Applying a stringent false discovery rate of 0.01, we identified six significant selective sweeps distributed across five chromosomes covering eight genes. These genes are associated with multiple molecular and biological functions, including regulation of transcription, receptor binding and signal transduction. Of particular interest is a selection signature on chromosome 1, which corresponds to the WNT4 gene, the family of which is conserved across the animal kingdom with a variety of functions. In Drosophila melanogaster, WNT4 alleles have been associated with differential wing, cross vein and abdominal phenotypes. Defining phenotypic characteristics of different Apis mellifera ssp. , which are typically used as selection criteria, include colour and wing venation pattern. This signal is therefore likely to be a good candidate for human mediated‐selection arising from different applied breeding practices in the two managed populations.
Induction of adipose-derived stem cells into Schwann-like cells and observation of Schwann-like cell proliferation

The peripheral nervous system has the potential for full regeneration following injury and recovery, predominantly controlled by Schwann cells (SCs). Therefore, obtaining a sufficient number of SCs in a short duration is crucial. In the present study, rat adipose-derived stem cells (ADSCs) were isolated and cultured, following which characterization of the ADSCs was performed using flow cytometry. The results showed that the cells were positive for the CD29 and CD44 markers, and negative for the CD31, CD45, CD49 and CD106 markers. The multilineage differentiation potential of the ADSCs was assayed by determining the ability of the cells to differentiate into osteoblasts and adipocytes. Following this, the ADSCs were treated with a specific medium and differentiated into Schwann-like cells. Immunofluorescence, western blot and reverse transcription-quantitative polymerase chain reaction analyses showed that ~95% of the differentiated cells expressed glial fibrillary acidic protein, S100 and p75. In addition, the present study found that a substantial number of SCs can be produced in a short duration via the mitotic feature of Schwann-like cells. These data indicated that Schwann-like cells derived from ADSCs can undergo mitotic proliferation, which may be beneficial for the treatment of peripheral nerve injury in the future.
AMP-Activated Protein Kinase Activates p38 Mitogen-Activated Protein Kinase by Increasing Recruitment of p38 MAPK to TAB1 in the Ischemic Heart

AMP-activated protein kinase (AMPK) promotes glucose transport, maintains ATP stores, and prevents injury and apoptosis during ischemia. AMPK has several direct molecular targets in the heart but also may interact with other stress-signaling pathways. This study examined the role of AMPK in the activation of the p38 mitogen-activated protein kinase (MAPK). In isolated heart muscles, the AMPK activator 5-aminoimidazole-4-carboxy-amide-1-β-d-ribofuranoside (AICAR) increased p38 MAPK activation. In AMPK-deficient mouse hearts, expressing a kinase-dead (KD) α2 catalytic subunit, p38 MAPK activation was markedly reduced during low-flow ischemia (2.3- versus 7-fold in wild-type hearts, P<0.01) and was similarly reduced during severe no-flow ischemia in KD hearts (P<0.01 versus ischemic wild type). Knockout of the p38 MAPK upstream kinase, MAPK kinase 3 (MKK3), did not affect ischemic activation of either AMPK or p38 MAPK in transgenic mkk3−/− mouse hearts. Ischemia increased p38 MAPK recruitment to transforming growth factor-β-activated protein kinase 1–binding protein 1 (TAB1), a scaffold protein that promotes p38 MAPK autophosphorylation. Moreover, TAB1 was associated with the α2 catalytic subunit of AMPK. p38 MAPK recruitment to TAB1/AMPK complexes required AMPK activation and was reduced in ischemic AMPK-deficient transgenic mouse hearts. The potential role of p38 MAPK in mediating the downstream action of AMPK to promote glucose transport was also assessed. The p38 MAPK inhibitor SB203580 partially inhibited both AICAR- and hypoxia-stimulated glucose uptake and GLUT4 translocation. Activation of p38 MAPK by anisomycin also increased glucose transport in heart muscles. Thus, AMPK has an important role in promoting p38 MAPK activation in the ischemic heart by inducing p38 MAPK autophosphorylation through interaction with the scaffold protein TAB1.
Synthesis, Singlet Oxygen Photogeneration and DNA Photocleavage of Porphyrins with Nitrogen Heterocycle Tails

Eight novel compounds were prepared by reaction of 5-(bromo- propoxyphenyl)-10,15,20-triphenylporphyrin with oxazole thiols, 1,3,4-oxadiazole thiols and 1,3,4-thiadiazole thiols, and their structures confirmed by UV-vis, IR, 1H-NMR, MS and elemental analysis. The assessment of indirectly measured 1O2 production rates against 5,10,15,20-tetraphenyl porphyrin (H2TPP) were described and the relative singlet oxygen production yields were: porphyrin 5 > porphyrins 1, 3, 4, 6-8, H2TPP > porphyrin 2. Porphyrin 4 and porphyrin 7 showed substantial photocleavage activities toward DNA, with over 75% cleavage observed at 40 µM. It suggested that these those porphyrins with nitrogen heterocycle tails are potential photosensitive agents.
Porous Media: Fluid Transport and Pore Structure

Pore Structure. Capillarity in Porous Media. Single-Phase Transport Phenomena in Porous Media. Selected Operations Involving Transport of a Single Fluid Phase through a Porous Medium. Multiphase Flow of Immiscible Fluids in Porous Media. Miscible Displacement and Dispersion. Index.
Standards for talking and thinking about validity.

Standards for talking and thinking about validity have been promulgated in North America for decades. In 1954 two foundational standards were announced: (a) Thou shalt not refer to "the validity of the test" and (b) thou shalt use validity modifier labels, such as "content validity" or "predictive validity. " Subsequently, in 1985, the latter became, thou shalt not use validity modifier labels. These standards for talking about validity have repeatedly been disregarded over the years. Possible reasons include intentional misuse, while upholding standards for thinking about validity; lack of awareness or misunderstanding of standards for thinking about validity; and genuine divergence from standards for thinking about validity. A historical analysis of disregard for these standards provides a basis for reappraising the concept of validity. We amassed a new body of evidence with which to challenge the frequently asserted claim that a general consensus exists over the meaning of validity. Indeed, the historical analysis provides reason to believe that prospects for achieving consensus over the meaning of validity are low. We recommend that the concept of validity be abandoned in favor of the more general, all-encompassing concept of quality, to be judged in relation to measurement aims, decision making aims, and broader policy aims, respectively.
Spicy: a unified deep packet inspection framework for safely dissecting all your data

Deep packet inspection systems (DPI) process wire format network data from untrusted sources, collecting semantic information from a variety of protocols and file formats as they work their way upwards through the network stack. However, implementing corresponding dissectors for the potpourri of formats that today's networks carry, remains time-consuming and cumbersome, and also poses fundamental security challenges. We introduce a novel framework, Spicy, for dissecting wire format data that consists of (i) a format specification language that tightly integrates syntax and semantics; (ii) a compiler toolchain that generates efficient and robust native dissector code from these specifications just-in-time; and (iii) an extensive API for DPI applications to drive the process and leverage results. Furthermore, Spicy can reverse the process as well, assembling wire format from the high-level specifications. We pursue a number of case studies that show-case dissectors for network protocols and file formats---individually, as well as chained into a dynamic stack that processes raw packets up to application-layer content. We also demonstrate a number of example host applications, from a generic driver program to integration into Wireshark and Bro. Overall, this work provides a new capability for developing powerful, robust, and reusable dissectors for DPI applications. We publish Spicy as open-source under BSD license.
Targeting of hematopoietic progenitor cells with MR contrast agents.

PURPOSE To label human hematopoietic progenitor cells with various magnetic resonance (MR) imaging contrast agents and to obtain 1.5-T MR images of them. MATERIALS AND METHODS Hematopoietic progenitor cells, labeled with ferumoxides, ferumoxtran, magnetic polysaccharide nanoparticles-transferrin, P7228 liposomes, and gadopentetate dimeglumine liposomes underwent MR imaging with T1- and T2-weighted spin-echo and fast field-echo sequences. Data were analyzed by measuring MR signal intensities and R1 and R2* relaxation rates of labeled cells and nonlabeled control cells. Mean quantitative data for the various contrast agent groups were assessed for significant differences compared with control cells by means of the Scheffe test. As a standard of reference, MR imaging data were compared with electron microscopic and spectrometric data. RESULTS For all contrast agents, intracellular cytoplasm uptake was demonstrated with electron microscopy and was quantified with spectrometry. When compared with nonlabeled control cells, progenitor cells labeled with iron oxides showed significantly (P <.05) increased R2*. Cells labeled with gadopentetate dimeglumine liposomes showed significantly increased R1. Detection thresholds were 5 x 10(5) cells for gadopentetate dimeglumine liposomes and ferumoxtran, 2.5 x 10(5) cells for ferumoxides and P7228 liposomes, and 1 x 10(5) cells for magnetic polysaccharide nanoparticles-transferrin. CONCLUSION Hematopoietic progenitor cells can be labeled with MR contrast agents and can be depicted with a standard 1.5-T MR imager.
The Vireo Team at MediaEval 2013: Violent Scenes Detection by Mid-level Concepts Learnt from Youtube

The Violent Scenes Detection task continues to pose challenge in detecting violent scenes in Hollywood movies. In this working notes paper, we present the framework of our system and briefly discuss the performance results obtained in both objective and subjective subtasks. Besides using the low-level features for training the SVM classifiers for violent scenes detection, we show the feasibility in using the concept detectors to infer the occurrence of violent scenes. External Youtube data is exploited in our implementation to provide more diverse definition to violent scene concepts. Furthermore, we explore the feasibility of using Conditional Random Fields (CRF) to refine the concept detection of movie shots holistically, given the relationships extracted from ConceptNet and the co-occurrence information defined by normalized Google distance (NGD). We demonstrate solid improvements in performance by using mid-level concept based detectors and CRF refinement in both objective and subjective subtasks.
Genetric Programming to Learn an Agent''s Monitoring Strategy

Return-Path: weston@cs.umass. EDU Date: Wed, 31 Mar 93 09:10 EST From: Peggy Weston 31-Mar-1993 0910 Subject: Abstract 93-26 To: sutherla@freya.cs.umass.edu Message-Id: X-Envelope-To: sutherla@freya.cs.umass.edu X-Vms-To: sutherland@cs.umass. EDU Received: from freya.cs.umass.edu by cs.umass. EDU; Wed, 31 Mar 93 09:09 EST Received: by freya.cs.umass.edu (5.57/Ultrix3.0-C) id AA02541; Wed, 31 Mar 93 09:10:35 -0500 Date: Wed, 31 Mar 93 09:16:25 -0500 From: Peggy Weston Subject: Abstract 93-26 To: sutherland@cs.umass. EDU Message-id: Content-Type: TEXT/plain; charset=US-ASCII TR 93-26 -- Marc Atkin and Paul R. Cohen Many tasks require an agent to monitor its environment, but little is known about appropriate monitoring strategies to use in particular situations. Our approach is to learn good monitoring strategies with a genetic programming algorithm. To this end, we have developed a simple agent programming language in which we represent monitoring strategies as programs that control a simulated robot, and a simulator in which the programs can be evaluated. The effects of different environments and tasks is determined experimentally; changing features of the environment will change which strategies are learned. The correspondence can then be analyzed. We present the simulated robot with the task of getting as close to an obstacle as possible without touching it. We know of two strategies that might be used to solve this problem: periodic monitoring, and proportional reduction, in which the robot moves a fixed fraction of the remaining distance to the obstacle between monitoring events. Our hypotheses concerned the environmental conditions in which each strategy might be learned. An experiment confirmed some of our hypotheses and left the status of others ambiguous. At the same time, the experiment revealed new monitoring stragegies and set the stage for the further exploration of this field.
SystemC Modeling of a Dynamic Power Management Architecture

The present invention relates to an ingestible aggregate comprising a pre-swelled substantially anhydrous hydrocolloid and a substrate. More particularly this invention relates to an aggregate having as a substrate a dietary fiber and/or drug wherein the composition can be administered in a therapeutically effective amount. Hydrocolloids useful include natural and modified gums, celluloses, modified celluloses, pectins, mucillages, modified starches, noncellulose polysaccharides, algal polysaccharides and mixtures thereof. The aggregate should be in the size range of about 4 to about 70 U.S. mesh. The unpleasant taste and mouthfeel of the fiber and/or drug is effectively masked and substantial hydration is delayed until the compositions reaches the stomach. The compositions are substantially more palatable, devoid of grainless, bitterness or fibrous texture. The pleasant taste of the composition encourages patient compliance with their fiber or drug therapy.
Using Knowledge Tracing in a Noisy Environment to Measure Student Reading Proficiencies

Constructing a student model for language tutors is a challenging task. This paper describes using knowledge tracing to construct a student model of reading proficiency and validates the model. We use speech recognition to assess a student's reading proficiency at a subword level, even though the speech recognizer output is at the level of words and is statistically noisy. Specifically, we estimate the student's knowledge of 80 letter to sound mappings, such as ch making the sound /K/ in "chemistry. " At a coarse level, the student model did a better job at estimating reading proficiency for 47.2% of the students than did a standardized test designed for the task. Although not quite as strong as the standardized test, our assessment method can provide a report on the student at any time during the year and requires no break from reading to administer. Our model's estimate of the student's knowledge on individual letter to sound mappings is a significant predictor of whether he will ask for help on a particular word. Thus, our student model is able to describe student performance both at a coarse- and at a fine-grain size.
Hierarchical Recovery in Compressive Sensing

A combinatorial approach to compressive sensing based on a deterministic column replacement technique is proposed. Informally, it takes as input a pattern matrix and ingredient measurement matrices, and results in a larger measurement matrix by replacing elements of the pattern matrix with columns from the ingredient matrices. This hierarchical technique yields great flexibility in sparse signal recovery. Specifically, recovery for the resulting measurement matrix does not depend on any fixed algorithm but rather on the recovery scheme of each ingredient matrix. In this paper, we investigate certain trade-offs for signal recovery, considering the computational investment required. Coping with noise in signal recovery requires additional conditions, both on the pattern matrix and on the ingredient measurement matrices.
Searching ... in a Web

Search engines—"web dragons"—are the portals through which we access society's treasure trove of information. They do not publish the algorithms they use to sort and filter information, yet what they do and how they do it are amongst the most important questions of our time. They deal not just with information per se, but evaluate it in order to prioritize it for the user. To do this they assess the prestige of each web page in terms of who links to it. This article explains in non-technical terms what is known about how web search engines work. We describe the dominant way of measuring prestige, relating it to the experience of a surfer condemned to click randomly around the web forever—and also to standard techniques of bibliometric evaluation. We review alternatives: some strive to identify subcommunities of the web; others learn based on implicit user feedback. We also takes a critical look at how people use search engines, and identify issues of bias, privacy, and personalization that crucially affect our world of information today.
Reactive Oxygen Species and the Regulation of Hyperproliferation in a Colonial Hydroid

Colonies of Podocoryna carnea circulate gastrovascular fluid among polyps via tubelike stolons. At polyp-stolon junctions, mitochondrion-rich cells in part regulate this gastrovascular flow. During competition, colonies hyperproliferate nematocytes and stolons; nematocysts are discharged until one colony is killed. Hyperproliferation then ceases, and normal growth resumes. Here, competing colonies were treated with azide, which inhibits respiration and upregulates reactive oxygen species (ROS). After the cessation of competition, azide-treated colonies continued to hyperproliferate. In azide-treated competing colonies, however, mitochondrion-rich cells were found to produce similar amounts of ROS as those in untreated competing colonies. Subsequent experiments showed that both azide treatment and competition diminished the lumen widths at polyp-stolon junctions, where mitochondrion-rich cells are found. In competing colonies, these diminished widths may also diminish the metabolic demand on these cells, causing mitochondria to enter the resting state and emit more ROS. Indeed, results with two fluorescent probes show that mitochondrion-rich cells in competing colonies produce more ROS than those in noncompeting colonies. In sum, these results suggest that competition perturbs the usual activity of mitochondrion-rich cells, altering their redox state and increasing ROS formation. Via uncharacterized pathways, these ROS may contribute to hyperproliferation.
Comparing operating systems using robustness benchmarks

When creating mission-critical distributed systems using off-the-shelf components, it is important to assess the dependability of not only the hardware, but the software as well. This paper proposes a way to test operating system dependability. The concept of response regions is presented as a way to visualize erroneous system behavior and gain insight into failure mechanisms. A 5-point "CRASH" (catastrophic, restart, abort, silent, hindering) scale is defined for grading the severity of robustness vulnerabilities encountered. Test results from five operating systems are analyzed for robustness vulnerabilities, and exhibit a range of dependability. Robustness benchmarking comparisons of this type may provide important information to both users and designers of off-the-shelf software for dependable systems.