Comparative analysis of molecular fingerprints in prediction of drug combination effects.

Application of machine and deep learning methods in drug discovery and cancer research has gained a considerable amount of attention in the past years. As the field grows, it becomes crucial to systematically evaluate the performance of novel computational solutions in relation to established techniques. To this end, we compare rule-based and data-driven molecular representations in prediction of drug combination sensitivity and drug synergy scores using standardized results of 14 high-throughput screening studies, comprising 64 200 unique combinations of 4153 molecules tested in 112 cancer cell lines. We evaluate the clustering performance of molecular representations and quantify their similarity by adapting the Centered Kernel Alignment metric. Our work demonstrates that to identify an optimal molecular representation type, it is necessary to supplement quantitative benchmark results with qualitative considerations, such as model interpretability and robustness, which may vary between and throughout preclinical drug development projects.

Comparison of Finnish meat inspection records and average daily gain for cattle herds differing in Mycoplasma bovis test-status.

Detecting Mycoplasma bovis on cattle farms represents a challenge in the absence of an outbreak or cases of M. bovis mastitis, yet identification of an infection is essential to control the spread of the disease successfully. The objectives of this study were: (1) to determine whether meat inspection records can aid identification of cattle farms supporting M. bovis infection, and (2) to compare the average daily weight gain estimated from carcass weight for cattle originating from farms differing in M. bovis test-status. Meat inspection records were collected from two abattoirs in 2015; 80 677 animals in total. All the dairy and mixed breed cows and bulls used for meat production were categorized according to known M. bovis infection status of the farms from which the cattle were derived; positive, contact or control farms. The associations between animals from different M. bovis categories and lung lesions of bulls and cows (pneumonia and pleuritis), identified during meat inspection, and estimated average daily gain (ADG) of bulls, were investigated. The odds ratios for lung lesions, especially pleuritis, were higher in M. bovis test-positive or contact farms compared with control farms. Additionally, odds ratios for pleuritis were higher among animals from M. bovis test-positive farms and animals from contact slaughtering farms originating from M. bovis-free rearing farms. Bulls originating from M. bovis test-positive farms had higher estimated average daily gain than cattle from control farms. Meat inspection records can be used alongside other methods to detect M. bovis-positive farms where M. bovis causes lung lesions.

Identification of 33 candidate oncogenes by screening for base-specific mutations.

BACKGROUND: Genes with recurrent codon-specific somatic mutations are likely drivers of tumorigenesis and potential therapeutic targets. Hypermutable cancers may represent a sensitive system for generation and selection of oncogenic mutations. METHODS: We utilised exome-sequencing data on 25 sporadic microsatellite-instable (MSI) colorectal cancers (CRCs) and searched for base-specific somatic mutation hotspots. RESULTS: We identified novel mutation hotspots in 33 genes. Fourteen genes displayed mutations in the validation set of 254 MSI CRCs: ANTXR1, MORC2, CEP135, CRYBB1, GALNT9, KRT82, PI15, SLC36A1, CNTF, GLDC, MBTPS1, OR9Q2, R3HDM1 and TTPAL. A database search found examples of the hotspot mutations in multiple cancer types. CONCLUSIONS: This work reveals a variety of new recurrent candidate oncogene mutations to be further scrutinised as potential therapeutic targets.

Improvement of immunoglobulin M capture immunoassay specificity: toxoplasma antibody detection method as a model.

In the Toxoplasma gondii immunoglobulin M (IgM) capture fluorometric enzyme immunoassay used as a model, nonspecific responses due to the binding of human IgM to horseradish peroxidase (HRP) conjugates were observed despite the removal of the Fc portion of the immunoglobulin. This interaction may be mediated through the binding of human IgM to the HRP moiety of the conjugate. Addition of polymerized HRP into the reaction mixture reduced nonspecific signals in the majority of low false-positive serum reactions. Other plausible sites of interaction are conserved epitopes of mouse immunoglobulins presenting antigenic similarities with the allotopes of other species. Fragmentation of mouse antimicrobial IgG to Fab' and selection of proper conjugation procedure improved assay specificity.

Metabolic syndrome is associated with changes in D-mannose metabolism.

Serum mannose concentration increases in diabetic patients and correlates closely with blood glucose. In patients with glomerulonephritis, serum mannose and mannose/glucose ratio positively correlate with dyslipidemia and the extent of urinary protein excretion. We investigated whether changes in serum mannose mark subjects with features of metabolic syndrome, including obesity, hypertension, glucose intolerance, and dyslipidemia. The study comprised 20 patients with mean age of 68 (SD 11) years, body mass index 27.2 (SD 5.1) kg/m2, blood glucose 6.2 (SD 1.6) mmol/L, serum total cholesterol 6.3 (SD 1.2) mmol/L, triglyceride 2.0 (SD 0.08) mmol/L, uric acid 320 (SD 109) micromol/L, mannose 60.0 (SD 17) micromol/L, and mannose/glucose ratio 9.7 (SD 1.8) micromol/mmol. Serum mannose correlated with blood glucose (r=0.758, p=0.012), triglyceride (r=0.478, p=0.023), and HDL-cholesterol (r = approximately 0.427, p=0.022). Mannose/glucose ratio correlated with BMI (r=0.581, p=0.033), mannose (r=0.491, p=0.035), and uric acid (r=0.608, p=0.027). The rate of VLDL lipoprotein turnover may be instrumental in the regulation of serum mannose concentration. We conclude that an altered mannose metabolism is a novel consideration among the metabolic abnormalities in the metabolic syndrome.

Enzymatic determination of unbound D-mannose in serum.

Mannose is an aldohexose component of a number of glycoproteins in cellular membranes and blood plasma. Free (unbound) mannose is a normal blood plasma constituent and its concentration is elevated in diabetes mellitus and chronic glomerulonephritis. We devised an enzymatic method for the determination of free mannose in which mannose is converted to glucose-6-phosphate and measured spectrophotometrically using glucose-6-phosphate dehydrogenase and nicotinamide adenine dinucleotide phosphate (NADP). Accumulation of reduced NADP in the assay was verified by spectral analysis and by finding rapid disappearance of absorbance at 340 nm on addition of glutathione reductase and oxidized glutathione into the reaction mixture. The method necessitates prior removal of glucose from the samples. This we accomplished using glucose-6-phosphate dehydrogenase and a surplus amount of NADP, followed by elimination of reduced NADP by acidification of the reaction mixture. The assays may be run in parallel for expediency. Concentration of free mannose in serum was 18.5 +/- 5.5 mumol/l in healthy fasting female adults. The analytical recovery was 90.2 +/- 10.2% and the between-run imprecision was 13.5% (18.5 +/- 5.5 mumol/l, mean +/- SD) and 10.4% (75.3 +/- 10.3 mumol/l). The assay showed rectilinearity up to 220 mumol/l, which covers the measuring range to which the mannose concentrations in normal and clinical samples may be expected to fall.

Mannose, mannitol, fructose and 1,5-anhydroglucitol concentrations measured by gas chromatography/mass spectrometry in blood plasma of diabetic patients.

Gas chromatography/mass fragmentography was applied to measure sugars in the plasma of patients with diabetes mellitus (DM). The isotope-dilution technique was used in the calculation of 1,5-anhydro-D-glucitol (1,5-AG), whereas reductive deuterization of the samples and regression analysis of the reduction products were used to calculate the concentrations of mannose, fructose and mannitol. The concentrations of mannose and glucose were closely and positively correlated both in insulin-dependent (IDDM; r = 0.74, P = 0.001) and non-insulin-dependent (NIDDM; r = 0.89, P = 0.001) DM. The close correlation was also encountered in serial samples taken from patients with widely fluctuating plasma glucose concentrations. The mannose/glucose ratio was increased in NIDDM (P = 0.007). The concentration of 1,5-AG was decreased in both types of DM, but more markedly in IDDM. The concentration was negatively correlated with glucose concentration (r = 0.071, P = 0.02) and HbAtc (r = 0.84, P = 0.001) in NIDDM. It was postulated that both mannose and glucose, by competing with 1,5-AG of renal tubular sugar carrier sites, contribute to the high urinary excretion of 1,5-anhydroglucitol leading to depletion of the sugar in the diabetic organism. The high concentrations of circulating mannose suggested further that the contribution of mannose to the adverse effects of hyperglycaemia should be examined. The study demonstrated that parallel use of the isotope-dilution and reductive deuterization techniques is quite useful in the analysis of monosaccharides in biological fluids.

Proteinuria and plasma hexosugars in early-stage glomerulonephritis.

Marked changes in the plasma concentration of several non-glucose monosaccharides have been detected among patients++ with end-stage renal disease. To find changes specific to renal disease and not caused by a failing urinary excretion, we studied the plasma monosaccharide concentration in patients with early-stage glomerulonephritis whose renal function was normal or only mildly compromised. Plasma mannose, fructose and 1,5-anhydroglucitol (1,5-AG) concentrations were measured using gas chromatography/mass spectrometry and isotope-labelled sugar standard additions. The daily urinary protein excretion was positively correlated with the plasma cholesterol (r = 0.785), mannose (r = 0.550), triglyceride (r = 0.531 ) and fructose (r = 0.401) concentrations, while the correlation with 1,5-AG (r = -0.581) was inverse. The correlations were statistically significant. As previous studies have revealed a close positive correlation between the plasma mannose and glucose concentrations, we calculated the mannose/glucose concentration ratio to find out whether the increase in mannose concentration was or was not explained by ambient glucose. There was a strong correlation between the ratio and the urinary protein excretion (r = 0.704). It is inferred that the metabolic syndrome associated with glomerulonephritis and characterised by hyperlipidemia also involves a derangement in mannose and 1,5-AG metabolism.

Determination of mannose and fructose in human plasma using deuterium labelling and gas chromatography/mass spectrometry.

We used gas chromatography/mass spectrometry to measure mannose and fructose in human blood plasma. The plasma samples were treated with sodium borodeuteride. Characteristic ion fragments for (1-d)mannitol, (2-d)mannitol and (1-d,2-13C)mannitol were selected for use in sugar fragmentography and to build an algorithm for calculation of the sugar concentrations. The analytical recovery of mannose and fructose and the precision of the mannose assay were satisfactory. The measurement of fructose was marked by poor precision, which was accounted for, at least in part, by the low fructose content of the plasma samples. The method may prove useful in profiling monosaccharides in biological fluids. The method leans on the measurement of polyols but it can also provide auxiliary information on the occurrence of aldoses and ketoses.

The involvement of fructose 2,6-bisphosphate in substrate cycle control in the nonoxidative stage of the pentose phosphate pathway. A phosphorus magnetic resonance spectroscopy study.

The role of fructose 2,6-bisphosphate in the interconversion of sedoheptulose 7-phosphate and sedoheptulose 1,7-bisphosphate in rat liver cytosol fractions was studied by means of phosphorus magnetic resonance spectroscopy. When the activity of 6-phosphofructo-1-kinase was inhibited by a high concentration of ATP, the addition of fructose 2,6-bisphosphate led to a marked decrease in sedoheptulose 7-phosphate levels, accompanied by an increased concentration of ADP. Fructose 2,6-bisphosphate essentially inhibited both the decrease in sedoheptulose 1,7-bisphosphate concentration and the accumulation of Pi in the incubation mixture. The data provided evidence that fructose 2,6-bisphosphate can regulate the substrate cycle: sedoheptulose 7-phosphate<-->sedoheptulose 1,7-bisphosphate in the liver, and thus control the flux through the nonoxidative stage of the pentose phosphate pathway.

Renal tubular reabsorption of 1,5-anhydro-D-glucitol and D-mannose in vivo in the rat.

1,5-Anhydro-D-glucitol (AG) is efficiently reabsorbed in renal tubuli by a mechanism that is saturated at high AG concentrations. To gain insight into the stereospecific requirements of the mechanism, we employed an in vivo loading test technique in which rats were injected with anhydrosugars and aldohexoses in doses that led to excretion of the sugar injected, thus saturating tubular reabsorption. Administration of AG elicited an increase in the excretion of D-mannose (P less than 0.0005), while D-mannose caused AG to appear in urine. Administration of 1,5-anhydro-D-mannitol led to increased excretion of D-mannose (P less than 0.0005) and the appearance of AG in urine. The effects of 1,5-anhydro-D-mannitol on the excretion of D-mannose and AG, and the effect of D-mannose on AG were dependent on the dose. Myoinositiol, mannitol and C-3-C-6 epimers of AG did not interfere with the reabsorption. The mechanism was highly phlorizin-sensitive. Repeated administration of 1,5-anhydro-D-mannitol rapidly depleted the rat organism from mobilizable AG. The AG space calculated (53% of body weight) suggested the presence of considerable cellular stores of AG. D-Mannose and AG are regular components of the plasma monosaccharide profile. The data suggest that the two sugars are reabsorbed in renal tubuli by a common mechanism, which is distinct from the main D-glucose reabsorption system. The presence of a glucose-type C-3-C-6 and pyranose structure is required for a sugar to be transported by the system.(ABSTRACT TRUNCATED AT 250 WORDS)

[The role of the clinical laboratory in the evaluation of the tubular function of the kidneys]. / Rol' klinicheskoi laboratorii v otsenke kanal'tsevoi funktsii pochek.

Renal tubules contribute to maintenance of the body equilibrium by regulating urinary excretion of electrolytes and low molecular mass components. Many transport mechanisms for regulation of concentrations of various components of the tubular fluid are situated in the renal tubules. Studies on the specification and localization of subcellular mechanisms functioning in the renal tubules is a progressive borderline trend of investigation. A new approach has been used to solve the problems of clinical nephrology and maintenance of the body balance. Processes of calcium, sodium, and monosaccharide reabsorption in the tubular fluid are described in brief.

1,5-Anhydro-D-glucitol--a novel type of sugar in the human organism.

1,5-Anhydroglucitol is a six-carbon chain monosaccharide in C1-chair conformation with an oxygen ring in pyran position. The compound is a component of normal human blood serum. The concentration in serum fluctuates within a narrow range in a normal population. Very low serum concentrations are found in patients with diabetes mellitus. In insulin-dependent (type 1) diabetes with a long history of disease the concentration of 1,5-anhydroglucitol remains low in spite of improvement of glycaemic control by intensification of treatment, whereas in non-insulin dependent (type 2) diabetes the concentration gradually increases towards normal levels concomitantly with improvement in glycaemic control. The serum 1,5-anhydroglucitol concentration may be useful as an indicator of glycaemic control in patients with non-insulin dependent diabetes. Urinary excretion of 1,5-anhydroglucitol in normal subjects is very low inferring that the compound is efficiently reabsorbed by tubular cells. During glucosuria, induced by glucose tolerance test in human or streptozotocin administration in rats the 1,5-anhydroglucitol excretion is temporarily increased, which may be attributable to a competition between 1,5-anhydroglucitol and glucose for renal tubular transporters. Data so far obtained indicate that 1,5-anhydroglucitol may be either actively or passively transported through the cell membrane, depending on the cell type. Gas-liquid chromatography is the method of choice in the measurement of the low concentrations of 1,5-anhydroglucitol present in biological samples.

Plasma 1,5-anhydroglucitol in experimental galactosemia in the rat.

Feeding with a galactose-rich diet induced a substantial drop in blood plasma 1,5-anhydroglucitol concentration. The decline was proportional to the dose of galactose. The decline was less marked in xylose-fed rats.

Correction of haemodialysis-associated anaemia by deferoxamine. Effects on serum aluminum and iron overload.

Aluminium and iron overload is often seen among long-term haemodialysis patients. Untreated non-de-aluminized dialysis water or the intake of large amounts of aluminium hydroxide as phosphate binders are the most common reasons for hyper-aluminaemia. Iron overload is mainly a result of multiple blood transfusions given to correct renal anaemia. In chronic dialysis patients, hypochromic anaemia is one of the clinical manifestations of a long-term overload of aluminium and perhaps of other metals, e.g. iron. We used deferoxamine (DFO) to chelate aluminium and excessive iron in 17 patients on chronic haemodialysis. Two grams of DFO was administered weekly in the form of an i.v. infusion during the last hour of the dialysis session. The mean serum aluminum concentration decreased from 407.3 micrograms/l to 184.2 micrograms/l within 3 years of treatment, the mean serum ferritin concentration from 1,563 micrograms/l to 487 micrograms/l within 2 years. Anaemia was corrected concomitantly with an increase in the haemoglobin level, which rose from 71.7 g/l to 80.8 g/l. The mean corpuscular volume increased from 83.8 fl to 91.3 fl. The need for blood transfusion also decreased significantly in all patients after the institution of DFO therapy. The clinical manifestations of aluminium and iron overload disappeared and the quality of life improved. No major side-effects were observed.

Evaluation of an immunoturbidimetric microalbuminuria assay.

We have evaluated an immunoturbidimetric method for the estimation of urinary albumin. The method, besides being easy to perform and cost-effective, was sensitive enough to detect an even slightly increased albumin excretion (detection limit 5 mg/l). Within-run reproducibility was 1.8 and 2.1%, and between-run reproducibility 2.9 and 4.3% in samples containing 16.1-17.8 mg/l and 50.6-54.0 mg/l of albumin, respectively. The recovery of albumin added to the samples was 98.6-106.6%. Results obtained by this method correlated well with the results obtained by radial immunodiffusion (r = 0.980, n = 44) and radioimmunoassay (r = 0.982, n = 41). The immunoturbidimetric method can be easily adapted for several clinical chemistry analysers.

Bioaerosols and office building ventilation systems.

Becterial and fungal spore samples were collected from twelve office building ventilation systems. Measurements were done both with and without humidification. Ventilation or humidification systems were not found to act as bioaerosol sources in any case. No difference was observed between bioaerosol counts in offices with and without humidification. The microbial levels decreased in all ventilation systems.

Nephelometry of acute-phase glycoproteins by binding to concanavalin A.

Nephelometry of serum acute-phase glycoproteins by binding to concanavalin A (con-A) was compared with assays for haptoglobin and alpha 1-acid glycoprotein, and for C-reactive protein. The cutoff points for positive reactions were determined on the basis of results for a random sample (n = 130) from a middle-aged population. The sensitivity of the con-A binding assay compared favorably with that of individual acute-phase glycoproteins in a follow-up cohort of 198 patients with inflammatory joint diseases. Unlike the case in many individual acute-phase glycoprotein assays, the distribution of con-A binding values in healthy subjects is remarkably symmetrical, allowing an easy distinction between abnormal and normal values.

Serum beta-N-acetylglucosaminidase and beta-glucuronidase activities in silicosis patients and in workers exposed to silica dust.

The serum activities of two lysosomal enzymes, beta-N-acetylglucosaminidase (EC 3.2.1.30; NAG) and beta-glucuronidase (EC 3.2.1.31; GLU) were analysed in 116 male patients with silicosis. Twenty-eight of the patients were matched with controls of similar sex, age and exposure to silica dust but with no radiographical evidence of silicosis. A control group which had not been exposed to silica dust consisted of male blood donors. The mean activity of NAG in serum was higher in the silicosis patients than in the blood donors (P less than 0.01). Similarly, the NAG level in the silicosis patients with matched controls was higher than that in the silica-exposed controls (P less than 0.05). The silicosis patients who showed a progression of small opacities by one or more subcategories had a slightly higher mean NAG activity in their sera than the patients with no progression but this difference did not reach statistical significance; the activity was higher than in silica-exposed controls (P less than 0.05). We suggest that these findings may be related to the effects of silica on macrophages which have been observed experimentally in vitro and in vivo and might indicate an increased turnover of macrophages caused by silica dust and active, progressive silicotic fibrosis.

The elimination of 1,5-anhydroglucitol administered to rats.

Rat serum contains natural 1,5-anhydroglucitol. Injected or orally administered 1,5-anhydroglucitol was efficiently reabsorbed by the renal tubuli via a mechanism which had a saturation point at high serum 1,5- anhydroglucitol levels. The compound had a slow turnover rate in the body; its half-life is approximately 3 days. The compound was readily absorbed in the gut when administered orally.