Logic programming and artificial neural networks in breast cancer detection

About 90% of breast cancers do not cause or are capable of producing death if detected at an early stage and treated properly. Indeed, it is still not known a specific cause for the illness. It may be not only a beginning, but also a set of associations that will determine the onset of the disease. Undeniably, there are some factors that seem to be associated with the boosted risk of the malady. Pondering the present study, different breast cancer risk assessment models where considered. It is our intention to develop a hybrid decision support system under a formal framework based on Logic Programming for knowledge representation and reasoning, complemented with an approach to computing centered on Artificial Neural Networks, to evaluate the risk of developing breast cancer and the respective Degree-of-Confidence that one has on such a happening.

PTX3-based genetic testing for risk of aspergillosis after lung transplant

PTX3-based genetic testing for risk of aspergillosis after lung transplant

Towards the design and implementation of aspect-oriented programming for spreadsheets

A spreadsheet usually starts as a simple and singleuser software artifact, but, as frequent as in other software systems, quickly evolves into a complex system developed by many actors. Often, different users work on different aspects of the same spreadsheet: while a secretary may be only involved in adding plain data to the spreadsheet, an accountant may define new business rules, while an engineer may need to adapt the spreadsheet content so it can be used by other software systems.Unfortunately,spreadsheetsystemsdonotoffermodular mechanisms, and as a consequence, some of the previous tasks may be defined by adding intrusive “code” to the spreadsheet. In this paper we go through the design and implementation of an aspect-oriented language for spreadsheets so that users can work on different aspects of a spreadsheet in a modular way. For example, aspects can be defined in order to introduce new business rules to an existing spreadsheet, or to manipulate the spreadsheet data to be ported to another system. Aspects are defined as aspect-oriented program specifications that are dynamically woven into the underlying spreadsheet by an aspect weaver. In this aspect-oriented style of spreadsheet development, differentusers develop,orreuse,aspects withoutaddingintrusive code to the original spreadsheet. Such code is added/executed by the spreadsheet weaving mechanism proposed in this paper.

Metaphorisms in programming

This paper introduces the metaphorism pattern of relational specification and addresses how specification following this pattern can be refined into recursive programs. Metaphorisms express input-output relationships which preserve relevant information while at the same time some intended optimization takes place. Text processing, sorting, representation changers, etc., are examples of metaphorisms. The kind of metaphorism refinement proposed in this paper is a strategy known as change of virtual data structure. It gives sufficient conditions for such implementations to be calculated using relation algebra and illustrates the strategy with the derivation of quicksort as example.

A genetic perspective on African prehistory

The various genetic systems (mitochondrial DNA, the Y-chromosome and the genome-wide autosomes) indicate that Africa is the most genetically diverse continent in the world and the most likely place of origin for anatomically modern humans. However, where in Africa modern humans arose and how the current genetic makeup within the continent was shaped is still open to debate. Here, we summarize the debate and focus especially on the maternally inherited mitochondrial DNA (mtDNA) and a recently revised chronology for the African mtDNA tree. We discuss the possible origin of modern humans in southern, eastern or Central Africa; the possibility of a migration from southern to eastern Africa more than 100 ka, carrying lineages within mtDNA haplogroup L0; the evidence for a climate-change-mediated population expansion in eastern Africa involving mtDNA haplogroup L3, leading to the “out-of-Africa” migration around 70–60 ka; the re-population of North Africa from the Near East around 40–30 ka suggested by mtDNA haplogroups U6 and M1; the evidence for population expansions and dispersals across the continent at the onset of the Holocene ; and the impact of the Bantu dispersals in Central, eastern and southern Africa within the last few millennia.

Echocardiographic assessment of the different left ventricular geometric patterns in hypertensive patients

OBJECTIVE: To identiy left ventricular geometric patterns in hypertensive patients on echocardiography, and to correlate those patterns with casual blood pressure measurements and with the parameters obtained on a 24-hour ambulatory blood pressure monitoring. METHODS: We studied sixty hypertensive patients, grouped according to the Joint National Committee stages of hypertension.. Using the single- and two-dimensional Doppler Echocardiography, we analyzed the left ventricular mass and the geometric patterns through the correlation of left ventricular mass index and relative wall thickness. On ambulatory blood pressure monitoring we assessed the means and pressure loads in the different geometric patterns detected on echocardiography RESULTS: We identified three left ventricular geometric patterns: 1) concentric hypertrophy, in 25% of the patients; 2) concentric remodeling, in 25%; and 3) normal geometry, in 50%. Casual systolic blood pressure was higher in the group with concentric hypertrophy than in the other groups (p=0.001). Mean systolic pressure in the 24h, daytime and nighttime periods was also higher in patients with concentric hypertrophy, as compared to the other groups (p=0.003, p=0.004 and p=0.007). Daytime systolic load and nighttime diastolic load were higher in patients with concentric hypertrophy ( p=0.004 and p=0.01, respectively). CONCLUSIONS: Left ventricular geometric patterns show significant correlation with casual systolic blood pressure, and with means and pressure loads on ambulatory blood pressure monitoring.

Genetic regulatory mechanisms by means of extended interactive Petri nets

In our work we have chosen to integrate formalism for knowledge representation with formalism for process representation as a way to specify and regulate the overall activity of a multi-cellular agent. The result of this approach is XP,N, another formalism, wherein a distributed system can be modeled as a collection of interrelated sub-nets sharing a common explicit control structure. Each sub-net represents a system of asynchronous concurrent threads modeled by a set of transitions. XP,N combines local state and control with interaction and hierarchy to achieve a high-level abstraction and to model the complex relationships between all the components of a distributed system. Viewed as a tool XP,N provides a carefully devised conflict resolution strategy that intentionally mimics the genetic regulatory mechanism used in an organic cell to select the next genes to process.

Distribution of cardiac geometric patterns on echocardiography in essential hypertension. Impact of two criteria of stratification

PURPOSE: To evaluate 2 left ventricular mass index (LVMI) normality criteria for the prevalence of left ventricular geometric patterns in a hypertensive population ( HT ) . METHODS: 544 essential hypertensive patients, were evaluated by echocardiography, and different left ventricular hypertrophy criteria were applied: 1 - classic : men - 134 g/m² and women - 110 g/m² ; 2- obtained from the 95th percentil of LVMI from a normotensive population (NT). RESULTS: The prevalence of 4 left ventricular geometric patterns, respectively for criteria 1 and 2, were: normal geometry - 47.7% and 39.3%; concentric remodelying - 25.4% and 14.3%; concentric hypertrophy - 18.4% and 27.7% and excentric hypertrophy - 8.8% and 16.7%, which confered abnormal geometry to 52.6% and 60.7% of hypertensive. The comparative analysis between NT and normal geometry hypertensive group according to criteria 1, detected significative stuctural differences,"( *p < 0.05):LVMI- 78.4 ± 1.50 vs 85.9 ±0.95 g/m² *; posterior wall thickness -8.5 ± 0.1 vs 8.9 ± 0.05 mm*; left atrium - 33.3 ± 0.41 vs 34.7 ± 0.30 mm *. With criteria 2, significative structural differences between the 2 groups were not observed. CONCLUSION: The use of a reference population based criteria, increased the abnormal left ventricular geometry prevalence in hypertensive patients and seemed more appropriate for left ventricular hypertrophy detection and risk stratification.

Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.

Risk factors, biochemical markers, and genetic polymorphisms in early coronary artery disease

OBJECTIVE: To assess the risk factors, lipid and apolipoprotein profile, hemostasis variables, and polymorphisms of the apolipoprotein AI-CIII gene in early coronary artery disease (CAD). METHODS: Case-control study with 112 patients in each group controlled by sex and age. After clinical evaluation and nutritional instruction, blood samples were collected for biochemical assays and genetic study. RESULTS: Familial history of early CAD (64 vs 39%), arterial hypertension (69 vs 36%), diabetes mellitus (25 vs 3%), and previous smoking (71 vs 46%) were more prevalent in the case group (p<0.001). Hypertension and diabetes were independent risk factors. Early CAD was characterized by higher serum levels of total cholesterol (235 ± 6 vs 209 ± 4 mg/dL), of LDL-c (154 ± 5 vs 135 ± 4 mg/dL), triglycerides (205 ± 12 vs 143 ± 9 mg/dL), and apolipoprotein B (129 ± 3 vs 105 ± 3 mg/dL), and lower serum levels of HDL-c (40 ± 1 vs 46 ± 1 mg/dL) and apolipoprotein AI (134 ± 2 vs 146 ± 2mg/dL) [p<0.01], in addition to an elevation in fibrinogen and D-dimer (p<0.02). The simultaneous presence of the rare alleles of the APO AI-CIII genes in early CAD are associated with hypertriglyceridemia (p=0.03). CONCLUSION: Of the classical risk factors, hypertension and diabetes mellitus were independently associated with early CAD. In addition to an unfavorable lipid profile, an increase in the thrombotic risk was identified in this population. An additive effect of the APO AI-CIII genes was observed in triglyceride levels.

Genetic diversity and population structure in Vicia faba L. landraces and wild related species assessed by nuclear SSRs

Research Article

Preservación de la información génica en bacterias; mecanismos y modulación molecular. Preservation of the genetic information in bacteria; mechanisms and molecular modulation.

El objetivo general del presente proyecto es contribuir a la caracterización genética y bioquímica molecular de mecanismos involucrados en el mantenimiento de la información génica, a través del estudio de sistemas fisiológicos involucrados en la prevención, reparación y tolerancia de mutaciones. Dichos sistemas se encuentran evolutivamente conservados y ampliamente distribuidos en los seres vivos. La importancia de los mismos se refleja en el hecho que su deficiencia genera en humanos, enfermedades genéticas, apoptosis y cáncer; y en especies procariotas, células denominadas "hipermutadoras". En los últimos años el estudio de la hipermutabilidad en bacterias ha cobrado gran interés ya que se le atribuye importancia en procesos infectivos y en aspectos básicos relacionados a evolución. Nuestro modelo de estudio son las bacterias Pseudomonas aeruginosa y Escherichia coli, siendo esta última especie no solo modelo de estudio sino también especie de referencia. P. aeruginosa es una bacteria ambiental gram negativa, e importante patógeno oportunista de humanos. Específicamente nos proponemos estudiar en P. aeruginosa algunos aspectos particulares del Sistema de Reparación de Bases Apareadas Incorrectamente (Mismatch Repair System, MRS), del Sistema de Prevención/Reparación de Lesiones Oxidativas generadas a través de 8-oxo-7,8-dihidroguanina (8-oxo-dG ó GO) y el papel de las ADN Polimerasas de baja fidelidad en la modulación de la tasa de mutación. Asimismo estamos interesados en estudiar en cepas de E. coli deficientes en el sistema Dam, la existencia de subpoblaciones de alta estabilidad genética debido a la eliminación de posibles mutantes por incremento de la expresión de los otros componentes del MRS. Metodológicamente la caracterización bioquímica de factores proteicos se llevará a cabo utilizando proteínas recombinantes purificadas, análisis de interacción proteína-proteína y proteína-ADN mediante electroforesis en geles y resonancia plasmónica de superficie (Biacore), mutagenésis dirigida in vitro, y estudios de complementación en cepas mutantes específicas. Aspectos fenotípicos y de regulación génica en cultivos de biofilm y células en suspensión serán estudiados mediante la construcción de cepas mutantes, fusiones transcripcionales, PCR en tiempo real, western blot y microscopia de fluorescencia confocal.