Usability and Suitability of the Omics-Integrating Analysis Platform tranSMART for Translational Research and Education.

BACKGROUND: Platforms like tranSMART assist researchers in analyzing clinical and corresponding omics data. Usability is an important, yet often overlooked, factor affecting the adoption and meaningful use. Analyses on the specific needs of translational researchers and considerations about the application of such platforms for education are rare. OBJECTIVES: The aim of this study was to test whether tranSMART can be used in education and how well medical students and professional researchers can handle it; to identify which kind of translational researchers-in terms of skills, experienced limitations, and available data-can take advantage of tranSMART; and to evaluate the usability and to generate recommendations for improvements. METHODS: An online-based test has been done by medical students (N = 109) and researchers (N = 26). The test comprised 13 tasks in the context of four typical research scenarios based on experimental and clinical data. A web questionnaire was provided to identify both the needs and the conditions of research as well as to evaluate the system's usability based on the "System Usability Scale" (SUS). RESULTS: Students and researchers were able to handle tranSMART well and coped with most scenarios: cohort identification, data exploration, hypothesis generation, and hypothesis validation were answered with a rate of correctness between 82 and 100%. Of the total, 72.2% of the teaching researchers considered tranSMART suitable for their lessons and 84.6% of the researchers considered the platform useful for their daily work; 65.4% of the researchers named the nonavailability of a platform like tranSMART as a restriction on their research. The usability was rated "acceptable" with a SUS of 70.8. CONCLUSION: tranSMART is potentially suitable for education purposes and fits most of the needs of translational researchers. Improvements are needed on the presentation of analysis results and on the guidance of users through the analysis, especially to ensure the compliance of the analysis with the requirements of statistical testing.

Non-uniform fine structural alteration in the sinus node after cessation or reduction of blood flow.

The sinus node of the dog was examined, using a large-specimen resin-embedding method for combined light and electron microscopy, after 30-240 min of total in vitro ischaemia and after 15-180 min of reduced blood flow in hearts with 2:1 AV block. Although progressive fine structural alteration was observed in the in vitro series, not all cells developed changes at the same rate. Complete loss of glycogen stores and swelling of organelles could be seen in many after only 30 min, whilst others retained their glycogen and showed minimal alteration even after 90 min. Despite relatively severe alteration throughout the node after 120 or more min, some groups of cells showed more extreme degrees of swelling and surface bleb formation than others. In the partially ischaemic in vivo series focal alteration, consisting chiefly of mitochondrial swelling and/or gross dilatation of sarcoplasmic reticulum vesicles, was detectable after 20 min and increased little in extent or degree during longer periods of reduced blood flow. This non-uniform response of sinus nodal cells to ischaemic injury parallels that of contractile atrial muscle cells.

Fine structural alteration in the atrioventricular junctional conduction tissues of the dog heart during severe ischaemia.

To define the fine structural changes produced in the atrioventricular junctional conduction tissues by severe ischaemia, 3 sets of specimens from 37 dogs were examined by light and electron microscopy using a large specimen resin-embedding method. Surgical control material was taken from 18 open-chest animals maintained under anaesthesia for up to 6 h, autolysis control material from 10 excised normal hearts maintained at 37 degrees C in vitro for up to 4 h, and ischaemic material from 8 animals in which the septal and distal left circumflex coronary arteries were occluded for 15 min to 3 h. Surgical control material was found to be within normal limits, whereas both autolysed and ischaemic showed initially mild fine structural alteration, which increased progressively in severity with time and was comparable in both sets. All cell types showed loss of glycogen granules, mitochondrial swelling, dilatation of sarcoplasmic reticulum vesicles, clumping of nuclear chromatin and ultimately varying degrees of generalised cell swelling. Intramitochondrial dense inclusions also were prominent in autolysis but not ischaemia. These changes progressed faster in nodal cells than in His bundle/bundle branch cells, which retained considerable quantities of glycogen for at least 60 min. The slower development of irreversible alteration in His-Purkinje cells suggests that they may be relatively more resistant to ischaemia, whilst the low incidence of intramitochondrial dense inclusions in vivo suggests a beneficial effect of collateral blood flow.

The fate of fetal Leydig cells during the development of the fetal and postnatal rat testis.

The ultrastructure and developmental fate of the fetal generation of Leydig cells of the rat testis was studied from the 17th day of fetal life up to 100 days after birth. The number of fetal Leydig cells per testis was determined by light microscopic morphometric analysis of semithin plastic sections. In fetal testes (days 17-22 postconception), Leydig cells exhibited a characteristic ultrastructure, containing smooth endoplasmic reticulum, many lipid inclusions and glycogen. Testes of 17-day-old fetuses contained about 25 x 10(3) fetal Leydig cells, rapidly increasing to 90 x 10(3) per testis in 21-day-old fetuses. After birth, fetal Leydig cells per testis remained relatively constant up to 2 weeks (80-90 x 10(3) per testis) and were identified by light and electron microscopy which showed their numerous lipid inclusions, their tendency for clustering and their association with interstitial tissue fibroblasts which partly encapsulated the fetal Leydig cells. From 21-100 days after birth, fetal Leydig cell numbers were quite variable with a mean of 45-60 x 10(3) per testis. These results are the first to show that the fetal generation of Leydig cells persist in the adult testis and do not undergo early postnatal degeneration or dedifferentiation into other interstitial cells. The simultaneous occurrence of the fetal Leydig cells and the adult population of Leydig cells indicates that these cells are distinct cell generations which are developmentally unrelated.

Effect of unilateral cryptorchidism on the intertubular tissue of the adult rat testis: evidence for intracellular changes within the Leydig cells.

Adult male rats were made unilaterally cryptorchid for 1, 2 or 4 weeks, and the morphological response of the Leydig cells was then studied using morphometric assessment of total Leydig cell volume and number per testis in abdominal and scrotal testes. Serum hormone levels were measured and the steroidogenic properties of isolated Leydig cells were evaluated by in-vitro stimulation with hCG and interstitial fluid (IF) obtained from normal rat testes. Total Leydig cell volume and number per testis were not altered in abdominal vs scrotal testes, although the volume of the abdominal testis was 46, 29 and 21%, respectively, of the volume of the contralateral scrotal testis after 1, 2 and 4 weeks. This reduction was accompanied by significant (P less than 0.05) elevation of the serum levels of FSH and LH, although serum testosterone levels were unchanged from the normal range. Despite the lack of quantitative alterations in Leydig cell morphology, hCG- and IF-stimulated testosterone production was significantly (P less than 0.01) greater by abdominal Leydig cells when compared with scrotal Leydig cells derived from the same animals. Ultrastructural examination of Leydig cells in situ suggested an increase in volumetric density of mitochondria in abdominal Leydig cells. Together with the enhanced steroidogenic responses of these cells, these findings suggest that disruption of spermatogenesis in the cryptorchid testis is accompanied by intracellular activation of Leydig cells. Since these effects were not exhibited by Leydig cells from the scrotal testis it is concluded that local factors within the cryptorchid testis are responsible, at least in part, for regulation of Leydig cell activity.

Stimulation of interstitial cell growth after selective destruction of foetal Leydig cells in the testis of postnatal rats.

Five-day-old male rats received a single treatment of ethane dimethanesulphonate (EDS), and the response of the testis on days 6-10 and 21 was examined by light microscopy and morphometry, supplemented by measurement of peripheral testosterone levels. One day after treatment, foetal Leydig cells degenerated, showing fragmentation, condensation and nuclear pyknosis. Macrophages phagocytosed the foetal leydig cells resulting in their disappearance by day 7. Destruction of foetal Leydig cells was followed by an arrest of testicular growth in comparison to testes of intact age-matched control rats. In testes of EDS-treated rats, gonocytes and spermatogonia also degenerated, forming pyknotic bodies within the seminiferous cords. In contrast, interstitial fibroblasts and mesenchymal cells showed proliferative activity, which on days 4 and 5 after treatment resulted in peritubular hyperplasia surrounding each seminiferous cord. Thereafter, on day 21 after EDS administration, the previously depressed serum testosterone levels became markedly elevated coincident with the development of many immature-type Leydig cells, of which the total volume per testis was similar to that of Leydig cells in control testes, despite a four- to five-fold difference in testicular volumes. The results indicate that, although EDS destroys the foetal Leydig cells and impairs spermatogenesis, the interstitial tissue exhibits increased cell growth. The latter probably occurs in response to altered gonadotrophic stimulation and/or disturbances in the interaction between the seminiferous cords and the interstitial tissue.

Ultrastructural analysis of the effect of ethane dimethanesulphonate on the testis of the rat, guinea pig, hamster and mouse.

The morphological response of the testis of rats, guinea pigs. Syrian hamsters and mice to treatment with the cytotoxin ethane dimethanesulphonate was examined using light and electron microscopy. One to two days after a single administration of ethane dimethanesulphonate to adult rats, guinea pigs, and hamsters, the Leydig cells showed marked ultrastructural alterations suggestive of degeneration and cell death. The former alterations included karyopyknosis, cytoplasmic vesiculation and accumulation of lipid inclusions and large lipofuscin bodies. Fragments of necrotic Leydig cells were often engulfed by the interstitial tissue macrophages. The morphology of the seminiferous epithelium of these three species was unchanged from the morphology observed in vehicle-injected control animals. In contrast, multiple injections of ethane dimethane-sulphonate given to mice produced no ultrastructural alternation to Leydig cells yet the seminiferous epithelium exhibited disruption of spermatogenesis. Although the Leydig cells of the mouse appear resistant to ethane dimethanesulphonate, this agent exerts a selective cytotoxic action upon leydig cells of the rat, guinea pig and hamster thus identifying ethane dimethanesulphonate as a useful chemical for future endocrine and physiological studies of testicular function in three common laboratory species.

Ultrastructure and possible function of giant crystalloids in the Sertoli cell of the juvenile and adult koala (Phascolarctos cinereus).

Sertoli cells of the juvenile and adult koala testis exhibit a unique morphology due to their large nuclei and in particular, a remarkable abundance of large cytoplasmic crystalloid inclusions. Numerous crystalloid subunits in immature Sertoli cells are aggregated into distinct clusters where by assembly and union, they form large slender crystalloids consisting of an ordered substructure of filaments and tubules. Adult Sertoli cells contain large numbers of basally-positioned crystalloids up to 60 micron in length and the observations suggest a possible mechanism for their growth from collections of tubules assembled together within membrane-bound inclusions. The trunk and adluminal cytoplasm of the adult Sertoli cell also contains crystalloids, usually single, positioned between germ cells or their excess residual cytoplasm. Following sperm release, crystalloids are not shed from the seminiferous epithelium but are retained within the apical Sertoli cell cytoplasm. Although their subsequent fate could not be determined crystalloids did not show evidence of breakdown or phagocytosis by the Sertoli cell, suggesting that they may be reutilized and possibly function to stabilize the association between Sertoli cell cytoplasm and the developing germ cells.

The regenerative capacity of testicular interstitial tissue : A recurrent pattern of experimental destruction and regeneration of rat Leydig cells.

A single intraperitoneal injection of ethane dimethanesulphonate (EDS) destroys all Leydig cells in the adult rat testis but 1-2 weeks later new foetal-type Leydig cells begin to regenerate within the interstitial tissue. A further EDS treatment at 4 weeks failed to kill the new population of foetal-type Leydig cells. Between 10-20 weeks, the new Leydig cells exhibited the characteristics of adult-type Leydig cells. These cells responded to another EDS treatment by exhibiting a second phase of complete degeneration followed by regeneration of a foetal-type and subsequently an adult-type cell population. The results indicate that the testis retains the ability to replenish its supply of Leydig cells despite successive phases of total degradation of Leydig cells.

Structural alterations in cardiac conducting cells in oxygen deficiency.

The fine structural effects of oxygen deficiency on the cardiac conduction system were studied in the dog and the rat, using various in vitro and in vivo models. Observations did not support the concept that conducting cells are inherently more resistant to ischaemia and anoxia than contractile myocardial cells. Nodal cells altered more rapidly than His-Purkinje cells in the dog, but not in the rat, which has less clearly-defined cell differences in these regions and a greater glycogen content in the atrioventricular node. Cellular alteration was uniform in global ischaemia in the isolated rat heart, but focal in high-flow, glucose-free anoxia. Comparison of in vitro and in vivo observations in the dog indicated that better collateral blood flow is chiefly responsible for preservation of conducting elements in the context of myocardial infarction.

The effects of raised phosphate level on the energy metabolism, contractile function, and fine structure of oxygenated and oxygen-deficient myocardium.

The possible role of inorganic phosphate (Pi) in depressing the contractility of oxygen-deficient myocardium was investigated by examining the effects of 30 mM Pi on the cardiac function and myocardial biochemistry and fine structure in normoxic and anoxic Langendorff-perfused isolated rat hearts. In normoxia, the intracellular Pi level increased three-fold, the ATP content remained normal, and there was moderate loss of glycogen only. Contractile performance (as assessed from systolic pressure recordings) was significantly depressed, as was the heart rate for the first 10 min. The myocardial fine structure showed persistent glycogen, marked relaxation of myofibrils, and a higher incidence of vacuolation than in hearts with normal Pi. In anoxia, the intracellular Pi level was comparable with that of the perfusate and both ATP and glycogen were severely depleted. Contractile performance and heart beat ceased completely at 15 min, although in anoxic controls both persisted at low levels for at least 25 min. In anoxia, Pi also depressed coronary flow rate. In the inner half of the ventricular wall of oxygen-depleted hearts, where flow became reduced after 15 or more min, Pi markedly reduced the formation of intramitochondrial densities and augmented mitochondrial swelling and ischaemic contracture, which extended out through the mid-myocardium. In the outer half of the wall, where flow remained high, it promoted severe dilatation of the sarcoplasmic reticulum vesicles and undifferentiated regions of the intercalated discs. The observed effects in normoxia are probably attributable at least in part to the lowering of the free Ca2+ concentration of the perfusate by the increased Pi level.(ABSTRACT TRUNCATED AT 250 WORDS)