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High-throughput sequencing produces an extraordinary amount of genomic data that is organized into a number of high-dimension datasets. Accordingly, visualization of genomic data has become essential for quality control, exploration, and data interpretation. The Variant Call Format (VCF) is a text file format generated during the variant calling process that contains genomic information and locations of variants in a group of sequenced samples. The current workflow for visualization of genomic variant data from VCF files requires use of a combination of existing tools. Here, we describe VIVA (VIsualization of VAriants), a command line utility and Jupyter Notebook based tool for evaluating and sharing genomic data for variant analysis and quality control of sequencing experiments from VCF files. VIVA combines the functionality of existing tools into a single command to interactively evaluate and share genomic data, as well as create publication quality graphics.

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An experiment was carried out to study the effect of acute stress on cortisol concentration in goat milk (milk cortisol; MC) and its suitability for stress assessment. Additional variables studied were plasma cortisol (PC), blood glucose (BG), and somatic cell count (SCC). Ten goats free of mastitis at 2 mo of lactation were divided into 2 groups. One group of animals was exposed to acute stress (visual and auditory, but not physical, contact with a barking dog for 3 min) immediately before the 1000 h sampling (STR), and the other group was considered as the control group, not exposed to acute stress (CON). The animals were gradually accustomed to the sampling schedule for 1 wk before the stress treatment (pre-experimental period). The variables PC, MC, BG, SCC, and milk composition (fat, lactose, whey protein, true protein, and casein) were recorded at 0600, 1000, 1130, 1400, 1800, 2200, and 0200 h. Milk variables were recorded in both glands separately. The right gland (n=10) was completely milked and the left gland (n=10) was milked to 30 mL at every sampling except at 1000 h, when complete milking was carried out on both glands. Variables were analyzed by using a linear mixed model. Both PC and MC concentrations varied throughout the day, with values being highest in the morning. Higher PC levels were recorded in the STR group immediately after treatment compared with CON (36.9 vs 16.3 ng/mL). For MC, differences between treatments were noted 1.5h after STR treatment (1.27 vs 0.25 ng/mL). Blood glucose increased immediately after treatment in STR animals, being different from CON until 1.5h after treatment sampling (101 vs. 58 mg/dL). The SCC was not increased by STR treatment, showing higher values in the morning and afternoon compared with evening and night (5.6±0.13 to 5.87±0.13 log10 SCC). The STR treatment had no significant effect on milk composition, and overall milk yield of a complete day after stress stimulus of both groups was similar (STR: 2,067±280 g/d; CON: 2,134±427 g/d). We conclude that plasma and milk cortisol concentrations in control dairy goats varied throughout the day; MC showed significant differences in the STR group if samples were taken 1.5h after the stressing stimulus, whereas PC showed significant differences in samples taken immediately after the stressing stimulus. Additionally, MC sampling has the advantage of being noninvasive compared with blood sampling.

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AIM: The aim of our study was to describe clinical data, frequency of the findings, sonographic patterns, confirmation of diagnosis, and differential diagnosis of focal echorich splenic lymphoma involvement. PATIENTS: During the last 20 years a focal splenic lesion was found in 178 patients with malignant lymphoma. Echorich splenic lesions were seen in 11 out of 178 cases (6.2%). METHODS: Splenic size, echomorphology of lesions, size and number of lesions, and presentation during sonographic follow-up examination were presented. RESULTS: Echorich infiltrates of the spleen were predominantly seen in patients with low grade Non-Hodgkin-Lymphoma (9 out of 11), the size of lesions mostly was less than 3 cm in diameter (9 out of 11), the underlying splenic size was over 8 x 20 cm in 9 out of 11 patients. Diagnosis was confirmed by sonographic follow-up (n = 11) and autopsy (n = 1). CONCLUSION: Echorich splenic lymphoma involvement is a rare event and is characterised by a variable presentation during follow-up. Up to date the clinic significance of our observation is still unclear.

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The synthesis and subsequent purification of several hydrophobic peptides is described. These peptides include the 24-residue M3 transmembrane domain of the rat connexin 32 protein, a peptide sequence that contains only seven amino acids with hydrophilic side-chains (71% hydrophobic). Moreover, for comparison, a much smaller hydrophobic octapeptide, designed to exist with alpha-helical secondary structure, was also studied. Optimum conditions for the RP-HPLC purification of these peptides was dependent on peptide length and solubility properties.

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Two hundred and ten patients with exudative pleural effusion were studied by ultrasound for sonographic signs of pleural carcinomatosis. Images were evaluated for echoes within the fluid, septations, sheet-like or nodular pleural masses, and associated lesions of the lung. Our results showed that sonographic findings of echogenic or septated fluid were unspecific for malignancy. Only the evidence of pleural masses was characteristic of malignant effusion. Ultrasound of the chest should therefore be carried out before invasive diagnostic procedures are planned.

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Abdominal sonography is now the most frequently used screening method for the detection of abdominal lymph node enlargement. For proper classification, size, localisation and infiltration pattern must be known. The definitive determination whether lymph nodes are benign or malignant cannot be made by the size of the lesion alone. The localisation (parietal/visceral) of enlarged lymph nodes has been shown to be of significance in the staging of abdominal carcinomas. Different infiltration patterns (diffuse small nodular, focal small nodular, focal large nodular, bulky formations) show the broad spectrum of abdominal lymphomas detected by ultrasound. Knowledge of these different infiltration patterns together with clinical information often helps to discriminate between lymph node enlargement caused by inflammation, metastasis, or malignant lymphoma. The definitive diagnosis is made via laparotomy, ultrasound guided biopsy or sonographic follow-up studies.

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Sonographic findings in 19 patients with proved adrenal pheochromocytomas observed over a 10 year period were evaluated retrospectively. Adrenal tumors were analyzed by number, size, echogenicity, internal echogenicity, and biologic behavior. There were 16 benign and 3 malignant pheochromocytomas, all of which were well marginated or encapsulated and ranged from 1.4 to 11 cm in greatest diameter (mean, 4.8 +/- 2.2 cm). A broad spectrum of sonographic appearances has been noted, including purely solid tumors (68%), complex masses (16%), and cystic lesions (16%). Compared with renal parenchyma as a reference tissue, 10 (77%) of 13 solid pheochromocytomas were isoechoic or hypoechoic, whereas three (23%) were hyperechoic. Six (46%) of the solid tumors were homogeneously echogenic, and seven (54%) were heterogeneous. Ultrasonic discrimination between benign and malignant pheochromocytoma on the basis of acoustic features alone has proved impossible. Abdominal sonography, however, provided evidence of malignancy in all three patients with malignant tumors by disclosing regional or distant metastases. In conclusion, rather than showing a specific uniform ultrasonographic appearance, pheochromocytoma is associated with a broad spectrum of possible sonographic presentations.

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This report summarizes the results of ultrasound-guided percutaneous drainage procedures in eight patients with solitary (n = 6) and multiple (n = 2) splenic abscesses. Seven patients underwent a total of 15 closed-needle aspirations with local installation of antibiotic solution. In one case, catheter drainage was performed. All patients received parenteral broad-spectrum antibiotic therapy. Seven (88%) of the eight patients with splenic abscesses recovered completely following percutaneous drainage procedures and none of these required splenectomy later. In one patient with multiple splenic abscesses, repetitive needle aspiration was ineffective, necessitating splenectomy. The only complication associated with nonsurgical percutaneous interventions was a pleural empyema that resolved with chest tube drainage (complication rate, 13%). These results and those reported in the literature indicate that pyogenic splenic abscesses can be treated effectively by (repetitive) closed aspiration technique or catheter drainage with a relatively low rate of complications. From our experience, splenectomy should only be performed in splenic abscesses that are not accessible percutaneously and in those cases with percutaneous drainage failure.

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PURPOSE: To determine the role of intrarenal Doppler ultrasound (US) in detection of moderate to severe (> 50%) renal artery stenosis (RAS). MATERIALS AND METHODS: In 72 patients, 142 kidneys were examined with conventional angiography and color duplex US. Renal size, mean intrarenal-arterial resistive index (RI), and difference of mean RIs between both kidneys (delta RI) were determined and compared with severity of RAS as determined with quantitative angiography. RESULTS: In 32 patients, angiography showed mild RAS < or = 50% in 13, moderate RAS in 10, and severe RAS in nine. Both renal size and mean RI values were decreased significantly (P < .001) only for severe RAS compared with values in 40 control subjects. For delta RI, no significant difference was noted between controls and patients with mild RAS; highly significant differences, however, were noted for both moderate and severe RAS (P < .001). Sensitivity and specificity of a cutoff delta RI of > 5% were 82% and 92% for RAS > 50% and 100% and 94% for moderate RAS and RAS > 60%. CONCLUSION: Color Doppler US and analysis of intrarenal Doppler spectra are recommended as a useful method for noninvasive diagnosis and grading of RAS. In bilateral RAS > 50%, however, calculation of delta RI is potentially biased by undergrading of stenosis.

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In a prospective study on 60 healthy adults, 38 men and 22 women (age range, 20-70 years), semiquantitative analyses of intrarenal arterial Doppler waveforms were performed by means of colour duplex sonography under standardised conditions. Furthermore, the effect of heart rate on calculation of renoparenchymal arterial Doppler spectra was evaluated. A total of 115 normal kidneys were studied, giving the following normal values (mean +/- standard deviation): resistance index (RI): 57 +/- 4.5%, pulsatility index (PI): 89 +/- 13%, pulsatile flow index (PFI): 65 +/- 6%. There were no different values for men and women. The normal renal resistance indices, however, were found to be age dependent, with increasing trend of RI and PI and decreasing trend of PFI with increasing age, most probably due to a corresponding increase of vascular resistance and mean arterial blood pressure. In an experimental study, we found a significant decrease of RI and PI and an increase of PFI paralleling the increase of heart rate. To eliminate the effect of heart rate on renal resistance indices, i.e. for interindividual comparison of data or intraindividual follow-up, measurements of indices can be corrected for a standardised heart rate by using regression equations. The results of our studies emphasise that interpretations of semiquantitative calculations of renal Doppler waveforms should be performed in consideration of extrarenal factors, for example the patient's age and heart rate.

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