BioSCOOP - Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks.

Dynamic development of biobanking industry (both business and science) resulted in an increased number of IT systems for samples and data management. The most difficult and complicated case for the biobanking community was cooperation between institutions, equipped with different IT systems, in the field of scientific research, mainly data interchange and information flow. Tools available on the market relate mainly to the biobank or collection level. Efficient and universal protocols including the detailed information about the donor and the sample are still very limited. Here, we have developed BioSCOOP, a communication protocol in the form of a well documented JSON API. The main aim of this study was to harmonize and standardize the rules of communication between biobanks on the level of information about the donor together with information about the sample. The purpose was to create a communication protocol for two applications: to transfer the information between different biobanks and to allow the searching and presentation of the sample and data sets.

Concurrent pulmonary adenocarcinoma and silicate pneumoconiosis in a red-legged partridge (Alectoris rufa).

An adult red-legged partridge (Alectoris rufa) presented with concurrent pulmonary carcinoma and severe silicosis. The animal was submitted to the Veterinary Teaching Hospital of the University of Córdoba (Spain) because of respiratory signs, and it died during clinical examination. At postmortem examination, numerous firm, whitish to yellowish nodules involving the lungs, mainly the right lobe, were found. The histopathologic study revealed numerous peribronchiolar large granulomatous lesions composed of macrophages, which showed abundant cytoplasm containing numerous birefringent crystals identified as silicates by transmission electron microscopy. An epithelial neoplasm showing papillary, acinar, and solid patterns occupied large areas of the pulmonary parenchyma. The histopathologic and immunohistochemical features were consistent with a pulmonary carcinoma. Small tumor nests were often located close to the granulomatous lesions. This is the first report of concurrent pneumoconiosis and pulmonary carcinoma in a nonhuman species.

Non-lethal freezing effects on seed degreening in Brassica napus.

The effects of a non-lethal freezing stress on chlorophyll content, moisture level and distribution, and abscisic acid (ABA) levels were examined in siliques and seeds of Brassica napus (canola). A non-lethal freezing stress resulted in the retention of chlorophyll in seed at harvest that was most pronounced for seeds 28, 32 and 36 days after flowering (DAF). This increase was primarily due to an increased retention of chlorophyll a relative to chlorophyll b. Chlorophyll retention in seeds exposed to a non-lethal freezing stress correlated with an increased ABA catabolism, as measured 1, 3 or 7 days after the stress treatment. Although the non-lethal freezing stress had no significant effect on moisture content in seeds of siliques stressed at 28-44 DAF, moisture distribution, as viewed by magnetic resonance imaging, showed an uneven drying of 32 and 40 DAF siliques after exposure to the non-lethal freezing stress. Moisture was initially lost more rapidly from the silique wall between seeds, than in control non-stressed siliques. Increased moisture loss was not due to structural changes in the vasculature of the silique/seed of stressed tissues. These results are consistent with the hypothesis that a non-lethal freezing stress-induced decrease in ABA level, during seed maturation, effects an inhibition of normal chlorophyll a catabolism resulting in mature but green B. napus seed.

Ferrocenoyl amino acids and peptides: probing peptide structure.

Recent studies clearly show the utility of the carbodiimide protocol to attach the redox-active Fc moiety to the N-terminal side of amino acids and peptides under mild conditions, resulting in stable and often crystalline products that afford themselves to structural analysis by X-ray crystallography. Electrochemical studies of Fc-peptides show that there is a significant influence of the redox potential depending on the amino acid sequence. The Fc moiety is sensitive to structural changes that occur in the peptide to which it is attached. For helical Fc-oligoprolines, the redox potential of the Fc group makes it easier to oxidize as the oligoproline chain increases in length. Nonhelical peptides, having a similar primary but different secondary structure, give rise to very different redox potentials. The ramifications of these findings to biological systems are significant in that they provide further evidence that the redox properties of a metal center are influenced by factors that go beyond the primary ligand sphere and thus for the involvement of long-range interactions. The Fc group is clearly sensitive to the shape of the peptide. These effects are currently under more detailed investigation [45] in order to gain further insight into the electronic structure of these ferrocenoyl peptides. Although we are not yet in a position to distinguish between "sensing" coordination or "sensing" conformation changes, this effect is of interest because it may allow the development of peptidic sensors.

Avian pox infection in Spanish Imperial eagles (Aquila adalberti).

A cutaneous lesion, previously known as "warts", affecting the featherless parts of face and legs has long been recognized in juvenile Spanish Imperial eagles (Aquila adalberti). This paper describes the presentation, microbiological, histopathological, and electron microscopic findings of lesions and diagnosis of poxvirus infection in nine juveniles. Lesions consisted of single or multiple nodules with a crust and surrounded by skin swelling. Seventy-eight percent of the swabs taken from lesions yielded bacterial growth, with Escherichia coli being the most common bacterium isolated. Histopathology revealed typical pox lesions in all cases. Histopathological changes found consisted of proliferative epithelium, with ballooning degeneration of keratinocytes and lymphocyte infiltrates extending into underlying dermis. Avianpox virus was confirmed by the presence of eosinophilic intracytoplasmatic inclusion bodies in the affected cells on light microscopy, and diagnosis confirmation was performed by electron microscopy of biopsies from all nine eagles.

Bovine tuberculosis and the endangered Iberian lynx.

We report the first case of bovine tuberculosis in a free-living Iberian lynx (Lynx pardina), an extremely endangered feline, from Doñana National Park in Spain. The isolate (Mycobacterium bovis) correlates by molecular characterization with other isolates from wild ungulates in the park, strongly suggesting an epidemiologic link. Mycobacterium bovis infects many animal species, with wild and free-ranging domestic ungulates being the main reservoirs in nature (1).

Alpha-2 agonist dissociative anesthetic combinations in fallow deer (Cervus dama).

Three anesthetic protocols, each using an alpha-2 agonist sedative in combination with a dissociative anesthetic, were evaluated in 17 captive fallow deer (Cervus dama). The alpha-2 agonist was given first in two of the three protocols: 1) detomidine (0.1-0.2 mg/kg i.m.) followed by tiletamine-zolazepam (3.0-6.3 mg/kg i.m.) and 2) xylazine (0.6-0.9 mg/kg i.m.) followed by tiletamine-zolazepam (4-5 mg/kg i.m.). In the third protocol, xylazine (1.0-6.2 mg/kg i.m.) and ketamine (2.5-5.1 mg/kg i.m.) were given simultaneously. Each of the sedative/anesthetic combinations produced acceptable immobilization in fallow deer and both provide an alternative to narcotic anesthesia.

FT-Raman, FT-IR spectroscopy and PIXE analysis applied to gallstones specimens.

Fourier transform Raman (FT-Raman) spectroscopy and Fourier transform infrared spectroscopy (FT-IR) were used as the main analytical techniques for the determination of human gallstone structural composition. These techniques provide rapid, qualitative and quantitative information about stone structure. The gallstones were obtained from. 40 patients during both surgical operations and laparoscopy. The results of FT-Raman and FT-IR analysis allowed to distinguish of four main groups of gallstones according their cholesterol and bilirubinate salt content. Our studies were extended to trace element analysis by means of proton induced X-ray emission (PIXE). On 14 elements detected, six elements Ca, Mn, Fe, Cu, Zn and Br were chosen for quantitative analysis. The concentration levels of these elements varied depending the chemical structure of the gallstones. The relationship between Ca and Cu appears to be of particular significance. In this paper a correlation between stone structure and trace element concentrations is presented.

The effect of dihydrotestosterone on transcription of prostatic acid phosphatase mRNA in human hyperplastic gland.

The effect of 5alpha-dihydrotestosterone (DHT) on the level of human prostatic acid phosphatase (hPAP) mRNA was studied using tissue slices from various benign prostatic hyperplastic glands. The absence of DHT in the incubation medium led to a gradual, significant decrease of the hPAP mRNA level. Addition of the hormone induced hPAP mRNA in a time- and dose-dependent manner. The maximal 2-4-fold induction by 10(-9) M DHT was observed after 3-5 h of incubation, and then the hPAP mRNA level was 6-20-fold higher than that in a parallel sample incubated without DHT. The results suggest that DHT is necessary to sustain the expression of hPAP in hyperplastic prostates.

A comparison of the effectiveness of Therevac SB and bisacodyl suppositories in SCI patients' bowel programs.

The evaluation described in this article compared the Therevac SB "mini-enema" with bisacodyl suppositories in the bowel management programs of patients with spinal cord injury (SCI). Of particular interest were (a) determining whether the additional costs of Therevac SB could be justified and (b) identifying the degree of bowel program improvement possible. Fourteen SCI patients were selected from the SCI inpatient unit and the clinic of a Department of Veterans Affairs facility. All patients experienced a delay of at least 45 minutes between insertion of a suppository and the beginning of stool evacuation. Each patient used bisacodyl suppositories for five bowel programs, then Therevac SB for five programs, finally repeating the bisacodyl suppositories for five more programs. Each patient maintained a bowel program log. Ten patients completed the evaluation. Using a MANOVA, the authors found a significant difference between bisacodyl and Therevac SB mean evacuation times for this group. An analysis of direct and indirect costs related to bowel care with the two regimens is also presented.

Back injury prevention program on a spinal cord injury unit.

A back injury prevention program was developed for the Spinal Cord Injury (SCI) nursing staff at the San Diego Veterans Affairs Medical Center (SDVAMC). This preventive program has the following components: 1. All nursing staff are sent to a one hour "back school" in order to learn and practice proper body mechanics. This program is held in the therapy clinic and conducted by a kinesiotherapist. In addition, each nurse must be certified in transfer techniques by our clinical nurse specialist, before performing transfers on patients. 2. All nursing staff participate in 5-10 minutes of stretching, warm-up exercises at the beginning of their shift. These exercises are helpful as injuries are less likely to occur when muscles have been warmed up prior to lifting and moving patients. 3. All nursing staff wear a lumbar sacral back support while on duty. This device will offer physical support to the lower back as well as provide a mental reminder to use proper body mechanics when transferring patients. This back injury prevention program has been in effect since the opening of the SCI unit in March 1989. The rate of low-back injuries on the SCI unit from October 1989 to September 1990 was compared to the rate of low-back injuries on the other hospital units. As a result of this program, there were only four low-back injuries with six lost work days on the SCI unit. This rate compares favorably with the incidence of low-back injuries in other patient care areas.

Properties of low-molecular-weight acid phosphatases isolated from cytosol and chromatin of rat liver.

1. Acid phosphatases (orthophosphoric-monoester phosphohydrolases, acid optimum, EC 3.1.3.2) of low molecular weight were isolated from cytosol and chromatin of rat liver cells. The cytosolic enzyme was homogeneous on SDS-polyacrylamide-gel electrophoresis at pH 8.3 (mol. wt. 16 000+/-3000). Both enzymes showed similar electrophoretic mobility and molecular weight but they differed in substrate specificity, response to inhibitors and susceptibility to SH-protecting reagents.

Familial hypospadias in three generations.

Retroglandular hypospadias has been observed in five males in three generations of the same family. Cytogenetic studies of peripheral blood lymphocytes and buccal smears revealed in all investigated patients normal karyotypes 46,XY with elongation of the long arm of chromosome Y (Yq+).

Operative repair of retroglandular hypospadias.

The operative repair of retroglandular hypospadias should be individualized. In some cases only resection of hooded foreskin and meatotomy are required. In a small number of properly selected cases a one-stage operation may be performed. In most cases a three-stage repair was carried out by the authors.

Comparative studies on immobilization of human prostatic acid phosphatase.

Acid phosphatase (othophosphoric monoester phosphohydrolase (acid optimum), EC 3.1.3.2) from the human prostate was immobilized by its protein moiety on cyanogen bromide-activated Sepharose, by carbohydrate moiety on Concanavalin-A-Sepharose, and by Schiff base formation with partially oxidized carbohydrate groups on ethylenediamine-Sepharose. The highest retention of enzyme activity, 80%, was found for the noncovalent immobilization on Concanavalin-A-Sepharose. It was demonstrated that the optimal pH changes for the Concanavalin-A-Sepharose and CNBr-Sepharose-enzyme complexes are electrostratic in character. In all cases of immobilization the enzyme has higher thermostability than that for the native enzyme under the same conditions. The effects of the enzyme stabilization were interpreted in terms of the multipoint interaction between the enzyme molecule and the carrier.