Aspect oriented implementation of design patterns using metadata

Computer programming paradigms aim to provide better separation of concerns. Aspect oriented programming extends object oriented programming by managing crosscutting concerns using aspects. Two of the most important critics of aspect oriented programming are the “tyranny of the dominant signature” and lack of visibility of program's flow. Metadata, in form of Java annotations, is a solution to both problems. Design patterns are assumed as the general solutions for Object-Oriented matters. They assist in software complexity management and serve as a bridge among software designers as well. These properties have led the patterns to be introduced as a choice in order to prove new technologies. Successful implementations share a generic solution: the usage of annotation to configure and mark the participants, while the pattern's code is encapsulated in aspects. This loses the coupling between aspects and type signatures and between the code base and a specific AOP framework. Also, it increases the developer's awareness of the program's flow. In the present article, aspect oriented programming and design patterns are introduced and also taking the benefit of annotation equipment in java language is proposed as a solution to reduce tight coupling and increase program flow observation rate for aspect oriented programming. Keywords: aspect oriented programming, design patterns, object oriented programming, metadata

Plasmon-Mediated Drilling in Thin Metallic Nanostructures

Tetrahedral nanopyramids made of silver and gold over ITO/glass surfaces are fabricated. Our protocol is based on nanosphere lithography (NSL) with the deposition of thicker metal layers. After removing the microspheres used in the NSL process, an array of metallic tetrahedral nanostructures of ~350-400 nm height is formed. The reported procedure avoids the use of any stabilizing surfactant molecules that are generally necessary to segregate the individual particles onto surfaces. We focus here on the optical and the physical properties of these plasmonic surfaces using near-field spectroscopy in conjunction with finite difference time domain (FDTD) modeling of the electric field. Remarkably, FDTD shows that the localized surface plasmon resonance is confined in the plane formed by the edges of two facing pyramids that is parallel to the polarization of the impinging excitation laser. The variable gap between the edges of two adjacent pyramids shows a broader localized surface plasmon and larger specific surface as opposed to the usual nanotriangle array. Localized enhancement of the electric field is experimentally investigated by coating the plasmonic surface with a thin film of photosensitive azopolymer onto the surface of the nanopyramids. The reported deformation upon radiation of the surface topography is visualized by atomic force microscopy and suggests the potentiality of these 3D nanopyramids for near-field enhancement. This last feature is clearly confirmed by surface-enhanced Raman scattering measurement with 4-nitrothiophenol molecules deposited on the pyramid platforms. The potentiality of such 3D nanostructures in plasmonics and surface spectroscopy is thus clearly demonstrated

Evaluation of Gasoline Samples from Several Erbil Petrol Stations

Gasoline is one of the main petroleum products used in transportation sectors in the Kurdistan region. The amount of gasoline provided from official refineries present in the region, which cover only a small portion of the total gasoline demand. The second source, which is the main one, is provided from outside of the region by private companies and includes three grades of gasoline (regular, premium, and super). The third source is blended gasoline, prepared locally in the region. Accordingly, to evaluate the available gasoline in the region, more than 100 samples of the three grades of gasoline were collected from different oil stations in Erbil City. Physical and chemical specifications were carried out, including sulfur content, octane number (RON and MON), density, vapour pressure, distillation curve, aromatic content, and olefin content using ASTM methods. The obtained results were compared with regional standards, Iraqi standards and worldwide standards. The results revealed that the majority of the gasoline samples had greater sulfur content, greater vapour pressure, low Initial Boiling Point (IBP), low distillation temperature at 10% and regular 50% and final boiling points (FBP). In addition, the majority of samples failed to meet all specifications in tests conducted following international, Kurdistan and Iraqi standards. The low quality of gasoline leads to an increase the environmental pollution, increase fire hazards of cars, and destroyed engine cars

Clinicopathologic predictors of finding additional inguinal lymph node metastases in penile cancer patients following positive dynamic sentinel node biopsy:a European multicentre evaluation

OBJECTIVES: Following tumour positive sentinel lymph node biopsy (+DSNB), completion inguinal lymph node dissection (ILND) is negative in 84-89% of basins. Thus, ILND after +DSNB may be considered overtreatment resulting in substantial morbidity. This study aimed to develop a predictive model for additional inguinal lymph node metastases (LNM) at ILND following +DSNB using DSNB characteristics to identify a patient group in which ILND might be omitted. PATIENTS AND METHODS: A retrospective study of 407 inguinal basins with a +DSNB of penile cancer patients who underwent subsequent ILND from seven European centres. From the histopathology reports, the number of positive and negative lymph nodes, extranodal extension and size of the metastasis were recorded. Using bootstrapped logistic regression, variables were selected for the clinical prediction model based on the optimisation of Akaike's information criterion. The area under the curve (AUC) of the receiver operating characteristic (ROC) curve was calculated for the resulting model. Decision curve analysis (DCA) was used to evaluate the clinical utility of the model. RESULTS: 64 (16%) of +DSNB harboured additional LNM at ILND. The number of positive nodes at +DSNB (odds ratio (OR) 2.19; 95% confidence interval (CI) 1.17-4.00; p=0.01) and the largest metastasis size in mm (OR 1.06; 95%CI 1.03-1.10; p=0.001) were selected for the clinical prediction model. The AUC was 0.67 (95%CI 0.60-0.74). The DCA showed no clinical benefit of using the clinical prediction model. CONCLUSION: A small but clinically important group of basins harbour additional LNM at completion ILND following +DSNB. While DSNB characteristics were associated with additional LNM, they did not improve the selection of basins in which ILND could be omitted. Thus, completion ILND remains necessary in all basins with a +DSNB

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the “ortholog conjecture”, or standard model of phylogenomics, protein function changes rapidly after duplication, leading to paralogs with different functions, while orthologs retain the ancestral function. We report here that a comparison of experimentally supported functional annotations among homologs from 13 genomes mostly supports this model. We show that to analyze GO annotation effectively, several confounding factors need to be controlled: authorship bias, variation of GO term frequency among species, variation of background similarity among species pairs, and propagated annotation bias. After controlling for these biases, we observe that orthologs have generally more similar functional annotations than paralogs. This is especially strong for sub-cellular localization. We observe only a weak decrease in functional similarity with increasing sequence divergence. These findings hold over a large diversity of species; notably orthologs from model organisms such as E. coli, yeast or mouse have conserved function with human proteins

An evaluation of urinary microRNA reveals a high sensitivity for bladder cancer

Background: Urinary biomarkers are needed to improve the care and reduce the cost of managing bladder cancer. Current biomarkers struggle to identify both high and low-grade cancers due to differing molecular pathways. Changes in microRNA (miR) expression are seen in urothelial carcinogenesis in a phenotype-specific manner. We hypothesised that urinary miRs reflecting low- and high-grade pathways could detect bladder cancers and overcome differences in genetic events seen within the disease. Methods: We investigated urinary samples (n ¼ 121) from patients with bladder cancer (n ¼ 68) and age-matched controls (n ¼ 53). Fifteen miRs were quantified using real-time PCR. Results: We found that miR is stable within urinary cells despite adverse handling and detected differential expression of 10 miRs from patients with cancer and controls (miRs 15a/15b/24-1/27b/100/135b/203/212/328/1224, ANOVA Po0.05). Individually, miR-1224-3p had the best individual performance with specificity, positive and negative predictive values and concordance of 83%, 83%, 75% and 77%, respectively. The combination of miRs-135b/15b/1224-3p detected bladder cancer with a high sensitivity (94.1%), sufficient specificity (51%) and was correct in 86% of patients (concordance). Conclusion: The use of this panel in patients with haematuria would have found 94% of urothelial cell carcinoma, while reducing cystoscopy rates by 26%. However, two invasive cancers (3%) would have been missed

Quantitative sequence-function relationships in proteins based on gene ontology

<p>Abstract</p> <p>Background</p> <p>The relationship between divergence of amino-acid sequence and divergence of function among homologous proteins is complex. The assumption that homologs share function – the basis of transfer of annotations in databases – must therefore be regarded with caution. Here, we present a quantitative study of sequence and function divergence, based on the Gene Ontology classification of function. We determined the relationship between sequence divergence and function divergence in 6828 protein families from the PFAM database. Within families there is a broad range of sequence similarity from very closely related proteins – for instance, orthologs in different mammals – to very distantly-related proteins at the limit of reliable recognition of homology.</p> <p>Results</p> <p>We correlated the divergence in sequences determined from pairwise alignments, and the divergence in function determined by path lengths in the Gene Ontology graph, taking into account the fact that many proteins have multiple functions. Our results show that, among homologous proteins, the proportion of divergent functions decreases dramatically above a threshold of sequence similarity at about 50% residue identity. For proteins with more than 50% residue identity, transfer of annotation between homologs will lead to an erroneous attribution with a totally dissimilar function in fewer than 6% of cases. This means that for very similar proteins (about 50 % identical residues) the chance of completely incorrect annotation is low; however, because of the phenomenon of recruitment, it is still non-zero.</p> <p>Conclusion</p> <p>Our results describe general features of the evolution of protein function, and serve as a guide to the reliability of annotation transfer, based on the closeness of the relationship between a new protein and its nearest annotated relative.</p

Self-assessment framework for promoting racial equity in educational psychology services. Division of Educational and Child Psychology 2023

Following a global pandemic and the worldwide resurgence of the Black Lives Matter (BLM) movement for racial justice (as a result of the brutal public murder of a black man in the United States of America), in 2021, a Division of Educational and Child Psychology (DECP) working group was formed. The purpose of the group was to address racial equity regarding the profession of Educational Psychology, including its practice and application of psychology. This group comprised of practising psychologists, including Main Grade, Senior and Principal Educational Psychologists, University Lecturers and Programme Directors, Tutors on Programmes for the Initial Training of Educational Psychologists, Educational Psychologists in Private Practice, and representatives from interest groups: Black and Ethnic Minority Educational Psychology (BEEP), Trainee EPs’ Initiative for Cultural Change (TEPICC), Educational Psychologists’ Race and Culture Forum (EPRCF), the Association of Educational Psychologists (AEP) and the National Association of Principal Psychologists (NAPEP). In short, the group has been working together to update and further develop a number of tools, training events and resources to support the profession, education providers and the communities they serve. This preface concerns the updating of the ‘Self-Assessment Framework for Promoting Racial Equality in Educational Psychology Services’

Is DRE essential for the follow up of prostate cancer patients? A prospective audit of 194 patients

BACKGROUND: Prostate cancer follow up forms a substantial part of the urology outpatient workload. Nurse led prostate cancer follow up clinics are becoming more common. Routine follow-up may involve performing DRE, which may require training. OBJECTIVES: The aim of this audit was to assess the factors that influenced the change in the management of prostate cancer patients during follow up. This would allow us to pave the way towards a protocol driven follow up clinic led by nurse specialists without formal training in DRE. RESULTS: 194 prostate cancer patients were seen over a period of two months and all the patients had DRE performed on at least one occasion. The management was changed in 47 patients. The most common factor influencing this change was PSA trend. A change in DRE findings influenced advancement of the clinic visit in 2 patients. CONCLUSIONS: PSA is the most common factor influencing change in the management of these patients. Nurse specialists can run prostate cancer follow-up clinics in parallel to existing consultant clinics and reserve DRE only for those patients who have a PSA change or have onset of new symptoms. However larger studies are required involving all the subgroups of patients to identify the subgroups of patients who will require DRE routinely