Mining the pharmacogenomics literature--a survey of the state of the art

This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.     

Structure of the mammillary bodies of the hypothalamus of the bottlenosed dolphin

In the bottlenosed dolphin (Tursiops truncatus) the hypothalamic corpus mammillaris has been studied using interperpendicular, sagittal, frontal and horizontal serial sections, impregnated in silver and stained with cresil-violet. Comparatively small dimentions of the corpora mammillaria in the bottlenosed dolphin are explained by presence of only two nuclei, medial and lateral. The lateral nucleus is nearly three times as large as the medial one. The size of the neurons in the medial nucleus is on the average two times as large as that of neurons in the lateral nucleus. The density of the neural cells distribution is a little greater in the lateral nucleus. The structure of the bottlenosed dolphin corpora mammillaria is compared with similar structures in other animals and the human being.     

Theoretical study of the optimal shape of the front profile of the lens in the eye of the scallop,Pecten

The optimal shape of the front profile of the thick lens in the eye of the scallop,Pecten is theoretically, geometric optically investigated as a function of the refractive index of the lens and the retina, as well as of the geometrical parameters of the eye. The shape of the theoretical front surfaces is compared with that of the real, experimentally determined front face of the lens. The degree of correction of the lens for spherical aberration of the reflecting spherical mirror in thePecten eye is examined. The optimal shape of the front profile of the lens depends strongly on a set of parameters, such that a certain fine tuning is required among them to assure a full correction for spherical aberration. The extreme variability of the eye parameters and the shape of the front face of the lens in the scallop is inconsistent with this fine tuning requirement. The degree of correction of thePecten lens for spherical aberration might not be as good as it could be, a possible biooptical reason for which is discussed.     

The dopaminergic innervation of the intermediate lobe and of the neural lobe of the pituitary gland

The intermediate and the neural lobe of the pituitary gland are innervated by two, virtually independent, groups of dopaminergic neurons which, until recently, were considered as a uniform system and referred to as the "tubero-hypophyseal dopamine system". Some aspects of the separate physiological functions of these neurons in the intermediate and in the neural lobe, of their microanatomy and biochemistry as well as of dopamine release from their terminals are discussed in this review.     

Information value of the indices of the nonspecific resistance of the body

A number of nonspecific resistance characteristics in mice, such as the total number of peritoneal exudate cells, the percentage and absolute number of macrophages, their cytochemical activity in the spontaneous tetrazolium test and cytochemical capacity, have been studied by comparison with the resistance of the animals to tularemia infection induced by Francisella tularensis, Ga?ski?'s vaccinal strain 15. Of these characteristics, the cytochemical capacity of peritoneal exudate macrophages, i.e. the total cytochemical activity of macrophages contained in a unit of volume, has been the most informative as regards the level of nonspecific resistance to this infection. Other characteristics under study cannot serve as criteria for the evaluation of the nonspecific resistance of the body to F. tularensis.     

Effect of reserpine on the differentiation of the external granular layer of the cerebellum in the chick embryo

In this work we analyse the effect produced by reserpine on the development of thickness and cell number in the external granular layer in the cerebellum of chick embryo. A striking 48-hour histogenetic delay is observed in the treated embryos relative to controls, as show by greater thickness and cell density of this layer in the former, as well as by retarded appearance of a typical radial morphological organization of the external granular layer.     

The effect of distension of the left ventricle of the heart on the length of the individual myocardial fibers

Based on the ellipsoid model of the left ventricle and the helicoidal course of the left ventricular myocardial fibers, a theory has been developed for calculating the length of the individual myocardial fibers. Numerical solutions of the final equation show that when the left ventricle is distended, the increase in length of the myocardial fibers is not uniform throughout the thickness of the myocardial wall. It was shown that with increasing dimensions of the left ventricle, the distension of the myocardial fibers becomes smaller as one advances from the endocardium to the middle layer of fibers, whereas it increases as one advances from the middle layer to the epicardial layer. The mechanism by which this effect is brought about as well as its physiological implications are discussed.     

Cytochemical study of the DNA and histone in the tissues of the lily anther in the course of microsporo- and gametogenesis]

The DNA and histone content in the microsporocytes, microspores, generative and vegetative cells of the pollen grain of Lilium candidum L., as well as in the anther wall tissues, was estimated by double wavelength cytophotometry. The lack of histone, as compared with DNA content, was demonstrated in the microsporocytes at the late premeiotic interphase and early meiotic prophase, as well as in the young microspores and anther wall tissues. The analysis of hydrolysis curves suggests the increase of non-condensed chromatin during endothelial cell differentiation.     

Forms of the Word and the Mystery of the Objectified Nature of the Word

The time has come to proceed from forms of givenness of the word to forms of the word as such. They can, if you like, be called external and inner structures. Humboldt, however, preferred to speak of the external and inner forms of the language. Shpet adopted precisely this distinction. Why did this problem interest Shpet? Already in [Appearance and sense], he had set the task of returning to the source of pretheoretical, living science. Shpet wrote that the outer cover of words and logical expressions obscure the objectified meaning and that it was necessary to remove another cover from the objectified sign so as to grasp a certain genuine intimacy, and in it the fullness of being (Shpet, 1914. Pp. 5-6). We shall keep in mind this major undertaking posed by this scientist. The existence of the inner form of words should not come as a surprise. That same year (1914) Ortega y Gasset wrote that material objects have a third dimension. However, we cannot see or touch it: "For just as depth needs a surface beneath which to be concealed, the surface, or outer cover, in order to be so, needs something over which to spread, covering it" (Ortega y Gasset, 2000. Pp. 62-63).     

Features of the morphofunctional state of the endocrine part of the pancreas during the development of experimental diabetes in the presence of regulatory peptides

The multiple 7-day intranasal introduction of PGArg and GPArg peptides at a dose of 1 mg per kg body weight before the injection of the diabetogenic dose of alloxan provided the maintenance of normoglycemia in rats. The similar introduction of PGPArg peptide did not provide any protection against the development of diabetes mellitus. The quantity of pancreatic islets in the animals from this group remained quite comparable to the norm, but the total number of cells per islet was below the norm, as well as in the control group. The GPArg peptide showed the best results as a preventive anti-diabetic agent.     

The revolution of the biology of the genome

Sequence data of entire eukaryotic genomes and their detailed comparison have provided new evidence on genome evolution. The major mechanisms involved in the increase of genome sizes are polyploidization and gene duplication.Subsequent gene silencing or mutations, preferentially in regulatory sequences of genes, modify the genome and permit the development of genes with new properties. Mechanisms such as lateral gene transfer, exon shuffling or the creation of new genes by transposition contribute to the evolution of a genome, but remain of relatively restricted relevance.Mechanisms to decrease genome sizes and, in particular, to remove specific DNA sequences, such as blocks of satellite DNAs, appear to involve the action of RNA interference (RNAi). RNAi mechanisms have been proven to be involved in chromatin packaging related with gene inactivation as well as in DNA excision during the macronucleus development in ciliates.     

Riding the waves of the intercalated disc of the heart

Cardiomyocytes interact with each other at their ends through the specialised membrane complex, the intercalated disck (ID). It is a fascinating structure. It allows cardiomyocytes to interact with several neighbouring cells, thereby allowing the complex structure of the heart to develop. It acts as tension transducer, structural prop, and multi signalling domain as well as a regulator of growth. It achieves its many functions through a number of specialised domains and intercellular junctions associated with its complex folded membrane. This review outlines the results of some 20 years of fascination with the ups and downs of the ID. These include locating the spectrin-associated membrane cytoskeleton in the ID and investigating the role of Protein 4.1R in calcium signalling; structural studies of the relationship of the ID to myofibrils, sarcoplasmic reticulum and mitochondria and, finally, consideration of the role of the ID in cardiomyocyte growth and heart disease.     

Effect of the state of the lipid phase of the membrane on the effectiveness of photochemical modification of erythrocyte acetylcholinesterase

Modification of the lipid phase structure of the erythrocyte membrane by phospholipases A2, C and D as well as the partial depletion of cholesterol was shown to be accompanied by the change of the acetylcholinesterase (AChE) UV-sensitivity. The ability of UV-light to change the catalytic properties (Km) of the membrane-bound AChE not observed for free AChE (constant value of Km) and known as the phenomenon of photochemical allotopy, is retained in the cholesterol depleted membranes and disappears after an enzymatic treatment of the membranes by phospholipases. The possible non-photochemical influence of the membrane lipid phase in response to UV-damage of membrane-bound AChE is discussed.     

Manifestation of the neurotoxic effect of the organochlorine pesticide hexachlorobutadiene in the postnatal period of ontogeny in the rat

Daily peroral administration of chlororganic pesticide hexachlorobutadiene in doses 8.1 mg/kg (1/20 LD50) to pregnant rats results in certain ultrastructural changes of neurocytes and myelin fibers of the spinal cord both in the animals and their offspring (newborns and 1-2-month-old rats). By means of electron paramagnetic resonance (EPR) method, changes in intensity of the EPR-signals of free radicals in the spinal cord, ceruloplasmin of blood serum have been revealed in the experimental pregnant animals, as well as in 1-month-old rats (in the latter--in the brain, too). Gas-liquid chromatography reveals the preparation contents in the adrenals, heart, brain and spinal cord, in the uterus of the pregnant animals, as well as in corresponding organs of their offspring. Certain retardation in growth and decrease in body mass are noted in the offspring.     

Evaluation of the role of the adaptive result in the theory of the functional systems

The fundamental of the theory of the functional systems, i.e., the concept of the useful adaptive result as a universal system-forming factor is considered. It is suggested that the adaptive result is not system-forming in behaviors actualized exclusively due to activity of systems developed earlier. It is argued that positive mutations may serve as the system-forming factor for hereditary determined behavioral forms. In all other cases of goal-directed behavior (except conditioning) the aim of performance as a model of the future result plays the decisive role. Only in conditioning the classical concept of the system-forming role of the adaptive result seems to be undeniable. The refined ideas about the mechanisms of formation of the functional systems may be useful in analysis of a number of animal and human functions (learning, emotional stress, neuroses, etc.).     

Role of the thyroid in the involution of the mesonephric Malpighian corpuscles in the chick embryo

The mesonephros of the chick embryo normally begins to regress during the second half of embryonic life. Experimental methods, such as adenohypophysis grafting, hypophysectomy or use of antithyroid drugs, which stimulate or depress the thyroid function of the embryo, modified accordingly the regressive processes occurring in the mesonephric Malpighian corpuscles, particularly at the level of the glomerular basement laminae. These results as well as the known sensitivity of the mesonephros to thyroxine and the concordance between the steps of embryonic thyroid development and the mesonephric modifications show that the thyroid normally plays a major determining role in this phenomenon.     

Influence of testosterone on the development of the ischiocavernosus muscle of the rat

The mean area of the neuromuscular endplates and the acetylcholinesterase (AChE) activity at the myotendinous junction of the ischiocavernosus muscle were studied in normal, castrated and testosterone-treated castrated Wistar rats by the Koelle method. The mean endplate area was found to be smaller in castrated rats, compared to normal ones (p less than 0.001), while testosterone treatment restored its normal size (0.8 greater than p greater than 0.7). The terminal AChE activity in castrated rats was as strong and spread as in juvenile ones, while it was almost absent in normal and in testosterone-treated castrated rats. The same parameters were examined in the tibialis anterior muscle of the same rats, chosen as a specimen of 'nonhormone-dependent' muscle, without finding any difference among the single groups.     

Characterization of the channel constriction allowing the access of the substrate to the active site of yeast oxidosqualene cyclase

In oxidosqualene cyclases (OSCs), an enzyme which has been extensively studied as a target for hypocholesterolemic or antifungal drugs, a lipophilic channel connects the surface of the protein with the active site cavity. Active site and channel are separated by a narrow constriction operating as a mobile gate for the substrate passage. In Saccharomyces cerevisiae OSC, two aminoacidic residues of the channel/constriction apparatus, Ala525 and Glu526, were previously showed as critical for maintaining the enzyme functionality. In this work sixteen novel mutants, each bearing a substitution at or around the channel constrictions, were tested for their enzymatic activity. Modelling studies showed that the most functionality-lowering substitutions deeply alter the H-bond network involving the channel/constriction apparatus. A rotation of Tyr239 is proposed as part of the mechanism permitting the access of the substrate to the active site. The inhibition of OSC by squalene was used as a tool for understanding whether the residues under study are involved in a pre-catalytic selection and docking of the substrate oxidosqualene.     

On the fine structure of the perivascular cells in the neural lobe of rats

Summary The purpose of this study is to investigate the ultrastructural features of perivascular cells as found in the neural lobe of the hypophysis. In particular, an inquiry was made into the nature of the relationship of such cells to neurosecretory fibers and endings. The latter, in fact, are often invaginated within the perivascular cells and enveloped by their processes; furthermore, they often reveal a certain number of empty granules as well as characteristics of degenerative nature. In the course of this study the localization of the perivascular cells has been investigated as well as that of their processes within the extensive interlobular network typical of the hypophysial neural lobe of rodents. Based on the data gathered, the hypothesis is put forward that the perivascular cells play an important role in the turnover of neurosecretory endings, both under physiological and experimental conditions, contributing thereby to the release of post-hypophysial hormones.With the technical assistance of Vincenzo Panetta.     

Organization of the cavernous structures of the human rectum

By means of complex histological and injection methods, including roentgenovasography and morphometry, 140 preparations of the human rectum have been studied during the late and middle fetal period, as well as during all periods of the postnatal ontogenesis. On the lateral walls of the columnar zone of the anal canal, places where the internal haemorrhagic nodes occur especially often, peculiar incapsulated and nonincapsulated microglomal cavernous bodies have been revealed. A large vascular peduncle connects them with the superior rectal artery and vein (according to 2-4 and 8-10 o'clock on the clock face) as complexes consisting of 2-3 penicilli and glomeruli. They are connected with the portocaval anastomoses of the initial multicanal anal-columnar sources of the superior and inferior rectal veins. The latter have various obturative mechanisms represented as microvalves, subintimal muscular toruli and arteriol-venular shunts of the obturative glomal and combined type.