PBURC: a patterns-based,unsupervised requirements clustering framework for distributed agile software development

Agile software development methodologies are increasingly adopted by organizations because they focus on the client’s needs, thus safeguarding business value for the final product. At the same time, as the economy and society move toward globalization, more organizations shift to distributed development of software projects. From this perspective, while adopting agile techniques seems beneficial, there are still a number of challenges that need to be addressed; among these notable is the effective cooperation between the stakeholders and the geographically distributed development team. In addition, data collection and validation for requirements engineering demands efficient processing techniques in order to handle the volume of data as well as to manage different inconsistencies, when the data are collected using online tools. In this paper, we present “PBURC,” a patterns-based, unsupervised requirements clustering framework, which makes use of machine-learning methods for requirements validation, being able to overcome data inconsistencies and effectively determine appropriate requirements clusters for optimal definition of software development sprints.     

High prevalence of subclinical hypothyroidism and nodular thyroid disease in patients on hemodialysis

Chronic kidney disease has been known to affect thyroid hormone metabolism. Low serum levels of T3 and T4 are the most remarkable laboratorial findings. A high incidence of goiter and nodules on thyroid ultrasonography has been reported in patients with end‐stage renal disease (ESRD). Our objective is to evaluate the prevalence of laboratorial and morphologic alterations in the thyroid gland in a cohort of patients with ESRD on hemodialysis (HD). Sixty‐one patients with ESRD on HD were selected and compared with 43 healthy subjects matched by age, gender, and weight. Patients were submitted to thyroid ultrasonography. T3, free T4 (FT4), thyroid‐stimulating hormone, antithyroglobulin, and antithyroperoxidase antibodies were measured. The mean age of patients with ESRD was 47.4 ± 12.3 and 61% were women. ESRD was mainly caused by hypertensive nephrosclerosis and diabetic nephropathy. Mean thyroid volume, as determined by ultrasonography, was similar in both groups. Patients with ESRD had more hypoechoic nodules when compared with the control group (24.1% vs. 7.9%, P = 0.056). Mean serum FT4 and T3 levels were significantly lower in patients with ESRD, and subclinical hypothyroidism was more prevalent in patients with ESRD (21.82% vs. 7.14% control group, P = 0.04). Titers of antithyroid antibodies were similar in both groups. ESRD was associated with a higher prevalence of subclinical hypothyroidism and lower levels of T3 and FT4. Almost a quarter of patients showed thyroid nodules >10 mm. Periodic ultrasound evaluation and assessment of thyroid function are recommended in patients with ESRD on HD.     

ST-Audit: guideline-based automatic auditing of electronic patient records

This work presents the ST-Audit system that audits a patient record for conformance to a particular clinical guideline. The system uses ST-Guide which models a guideline as a set of states and transitions. The audit system tries to find a path in the state/transition diagram that corresponds to the actions taken by the physician, taking into consideration issues such as the unavailability of all the data needed to evaluate the transitions. The system was used to audit an outpatient clinic regarding their procedure for hypertension treatment (using the VI JNC guideline for hypertension), and the results of the number of non-compliant actions were presented and discussed. A follow up auditing showed a small but statistically significant reduction on the number of non-compliant actions for patients treated after the first audit.     

Peptide-nanoparticle hybrid SERS probes for optical detection of protease activity

Real-time in situ detection of active proteases is crucial for early-stage cancer screening and cell signaling pathway study; however, it is difficult to achieve using fluorescence or radioactive probes at volumes below 1 nL. Here we demonstrated a hybrid optical probe by incorporating nanocrescent particle and peptides with artificial tag molecules. We performed a proof-of-concept study using prostate specific antigen (PSA), one of the most prominent prostate cancer markers, and a serine protease present in patients' seminal fluid and serum. The Raman spectral signal from the tag molecules is enhanced by the nanocrescent and the signal is monitored as the indicator for peptide cleavage in a femtoliter reaction volume, at levels close to a single proteolytically active PSA molecule. The high reaction specificity of the peptides on individual nanoparticles minimizes the false detection of other serine proteases and background Raman signal, which results in a high-fidelity and high-signal-to-noise-ratio cancer nanoprobe that can be easily incorporated into nano/microfluidic devices.     

Improving student performance in a first-year geography course: Examining the importance of computer-assisted formative assessment

The main objective of this paper is to examine the effectiveness of computer-assisted formative assessment in a large, first-year undergraduate geography course. In particular, the paper evaluates the impact of computer-assisted multiple-choice practice tests on student performance in the course as well as student opinions of this type of formative assessment in two academic years (2008 and 2009). The multiple-choice questions included in the formative assessment vary in their level of difficulty and range from those that focus on knowledge and comprehension to those that focus on application and analysis. While the use of the computer-assisted practice tests is completely voluntary over 50 percent of students used them. Feedback questionnaires from both academic years reveals that students are overwhelmingly positive with over 95 percent indicating that the computer-assisted practice tests assist them in identifying their strengths and weaknesses and help them prepare for in-class midterms and final exams. Statistical analysis of in-class performance on midterms shows that students who use the computer-assisted practice quizzes earn significantly higher grades (i.e., equivalent to three letter grades) than those students who do not. The results of the research demonstrate that computer-assisted formative assessment (in this case practice tests) has a positive impact on student performance.     

Physical and mechanical characterisation of 3D-printed porous titanium for biomedical applications

The elastic modulus of metallic orthopaedic implants is typically 6–12 times greater than cortical bone, causing stress shielding: over time, bone atrophies through decreased mechanical strain, which can lead to fracture at the implantation site. Introducing pores into an implant will lower the modulus significantly. Three dimensional printing (3DP) is capable of producing parts with dual porosity features: micropores by process (residual pores from binder burnout) and macropores by design via a computer aided design model. Titanium was chosen due to its excellent biocompatibility, superior corrosion resistance, durability, osteointegration capability, relatively low elastic modulus, and high strength to weight ratio. The mechanical and physical properties of 3DP titanium were studied and compared to the properties of bone. The mechanical and physical properties were tailored by varying the binder (polyvinyl alcohol) content and the sintering temperature of the titanium samples. The fabricated titanium samples had a porosity of 32.2–53.4 % and a compressive modulus of 0.86–2.48 GPa, within the range of cancellous bone modulus. Other physical and mechanical properties were investigated including fracture strength, density, fracture toughness, hardness and surface roughness. The correlation between the porous 3DP titanium-bulk modulus ratio and porosity was also quantified.     

Towards Controlling the Glycoform: A Model Framework Linking Extracellular Metabolites to Antibody Glycosylation

Glycoproteins represent the largest group of the growing number of biologically-derived medicines. The associated glycan structures and their distribution are known to have a large impact on pharmacokinetics. A modelling framework was developed to provide a link from the extracellular environment and its effect on intracellular metabolites to the distribution of glycans on the constant region of an antibody product. The main focus of this work is the mechanistic in silico reconstruction of the nucleotide sugar donor (NSD) metabolic network by means of 34 species mass balances and the saturation kinetics rates of the 60 metabolic reactions involved. NSDs are the co-substrates of the glycosylation process in the Golgi apparatus and their simulated dynamic intracellular concentration profiles were linked to an existing model describing the distribution of N-linked glycan structures of the antibody constant region. The modelling framework also describes the growth dynamics of the cell population by means of modified Monod kinetics. Simulation results match well to experimental data from a murine hybridoma cell line. The result is a modelling platform which is able to describe the product glycoform based on extracellular conditions. It represents a first step towards the in silico prediction of the glycoform of a biotherapeutic and provides a platform for the optimisation of bioprocess conditions with respect to product quality.     

Direct introduction of phosphonate by the surface modification of polymers enhances biocompatibility

A novel chemical method for the modification of polystyrene and nylon polymers by the reaction of diaryl carbenes permits the direct and efficient introduction of phosphonate residues upon the polymer surface. The method is simple to execute, involving solution coating to adsorb the reactive coating agent, followed by drying and thermolysis at temperatures not greater than 150 °C. This material can be further modified to the calcium phosphonate derivative, by treatment with aqueous calcium hydroxide. The modified polymers show enhanced biocompatibility of the modified polymer, as evidenced by the improved growth of MG63 human osteosarcoma cell line on the surface. This method is of significance since it offers a simple chemical protocol for the tailoring of the surface properties of materials, it avoids the need to construct ab initio new polymers for a given application, it provides an alternative to existing surface modification protocols, and it extends the range of polymers suitable as biocompatible materials .     

Quantitative meanings of verbal probability expressions.

The meanings of 18 verbal probability expressions were studied in 3 ways: (a) frequency distributions of what single number best represented each expression; (b) word-to-number acceptability functions from what range of numbers from 0% to 100% best represented each expression; and (c) number-to-word acceptability functions from which expressions were appropriate for multiples of 5% from 5% to 95%. These results agreed highly with others and were highly consistent across methods. Expressions incorporating the stem probable were quantitatively synonymous with expressions incorporating the stem likely. Except for expressions using the word chance, positive expressions (e.g., likely) were closer to 50% in meaning than corresponding negative expressions (e.g., unlikely). This method proved very useful in deriving fuzzy-set membership functions for probability words, encouraging us in our ongoing codification effort. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

TNFα and Immune Checkpoint Inhibition: Friend or Foe for Lung Cancer?

Tumor necrosis factor-alpha (TNFα) can bind two distinct receptors (TNFR1/2). The transmembrane form (tmTNFα) preferentially binds to TNFR2. Upon tmTNFα cleavage by the TNF-alpha-converting enzyme (TACE), its soluble (sTNFα) form is released with higher affinity for TNFR1. This assortment empowers TNFα with a plethora of opposing roles in the processes of tumor cell survival (and apoptosis) and anti-tumor immune stimulation (and suppression), in addition to angiogenesis and metastases. Its functions and biomarker potential to predict cancer progression and response to immunotherapy are reviewed here, with a focus on lung cancer. By mining existing sequencing data, we further demonstrate that the expression levels of TNF and TACE are significantly decreased in lung adenocarcinoma patients, while the TNFR1/TNFR2 balance are increased. We conclude that the biomarker potential of TNFα alone will most likely not provide conclusive findings, but that TACE could have a key role along with the delicate balance of sTNFα/tmTNFα as well as TNFR1/TNFR2, hence stressing the importance of more research into the potential of rationalized treatments that combine TNFα pathway modulators with immunotherapy for lung cancer patients.