A systematic method for diagnosis of hepatitis disease using machine learning

Hepatitis is among the deadliest diseases on the planet. Machine learning approaches can contribute toward diagnosing hepatitis disease based on a few characteristics. On the UCI dataset, authors assessed distinct classifiers' performance in order to develop a systematic strategy for hepatitis disease diagnosis. The classifiers used are support vector machine, logistic regression (LR), K-nearest neighbor, and random forest. The classifiers were employed without class balancing and in conjunction with class balancing using SMOTE strategy. Both studies, classification without class balancing and with class balancing, were compared in terms of different performance parameters. After adopting class balancing, the efficiency of classifiers improved significantly. LR with SMOTE provided the highest level of accuracy (93.18%).

Host biology and genomic properties of Plumeria mosaic virus, a tobamovirus discovered in a temple tree in India co-infecting with frangipani mosaic virus

Temple tree (Plumeria rubra f. acutifolia), an important fragrant-flower tree extensively used in the urban landscaping is known to be infected with a tobamovirus, frangipani mosaic virus (FrMV). In this study, we describe another tobamovirus, Plumeria mosaic virus (PluMV) infecting temple tree in India. PluMV was isolated from an old temple tree co-infected with FrMV. The presence of another tobamovirus was initially realized based on the distinct symptoms on Gomphrena globosa (globe amaranth), a non-host of FrMV. PluMV was highly transmissible through simple rub-inoculation. In host-range study, brinjal (Solanum melongena), chilli (Capsicum annuum), datura (Datura stramonium), globe amaranth and tobacco (Nicotiana benthamiana, N. glutinosa, N. tabacum cv. Xanthi) could differentiate PluMV from FrMV. The complete genome sequence of PluMV was determined (6,688 nucleotides [nt], GenBank KJ395757), which showed the genome structure typical of tobamovirus encoding four proteins: small replicase (3,549 nt/130 kDa), large replicase (5,061 nt/188 kDa), movement protein (770 nt/29 kDa) and coat protein (527 nt/19 kDa). The 5' and 3' UTR of PluMV contained 91 and 284 nt, respectively. The PluMV genome was 45 nts longer than that of FrMV and shared only 71.4-71.6% sequence identity with FrMV and  < 50% sequence identity with the rest of the other members of the genus Tobamovirus. PluMV shared a close but a divergent evolutionary relationship with FrMV. Based on the species demarcation guidelines of ICTV (<90% genome sequence identity), PluMV was considered as a new tobamovirus species. As PluMV was serologically related with FrMV, differential diagnostic assays such as simplex and duplex RT-PCR were developed, which revealed that PluMV naturally existed in both the species of temple tree, P. rubra f. acutifolia and P. rubra f. obtusa in India either alone or in mixed infection with FrMV.

A CGMMV genome-replicon vector with partial sequences of coat protein gene efficiently expresses GFP in Nicotiana benthamiana

A highly infectious clone of Cucumber green mottle mosaic virus (CGMMV), a cucurbit-infecting tobamovirus was utilized for designing of gene expression vectors. Two versions of vector were examined for their efficacy in expressing the green fluorescent protein (GFP) in Nicotiana benthamiana. When the GFP gene was inserted at the stop codon of coat protein (CP) gene of the CGMMV genome without any read-through codon, systemic expression of GFP, as well as virion formation and systemic symptoms expression were obtained in N. benthamiana. The qRT-PCR analysis showed 23 fold increase of GFP over actin at 10days post inoculation (dpi), which increased to 45 fold at 14dpi and thereafter the GFP expression was significantly declined. Further, we show that when the most of the CP sequence is deleted retaining only the first 105 nucleotides, the shortened vector containing GFP in frame of original CP open reading frame (ORF) resulted in 234 fold increase of GFP expression over actin at 5dpi in N. benthamiana without the formation of virions and disease symptoms. Our study demonstrated that a simple manipulation of CP gene in the CGMMV genome while preserving the translational frame of CP resulted in developing a virus-free, rapid and efficient foreign protein expression system in the plant. The CGMMV based vectors developed in this study may be potentially useful for the production of edible vaccines in cucurbits.

Characterisation and diagnosis of frangipani mosaic virus from India

Frangipani mosaic virus (FrMV) is known to infect frangipani tree (Plumeria rubra f. acutifolia) in India but the virus has not been characterized at genomic level and diagnosis is not available. In the present study, an isolate of FrMV (FrMV-Ind-1) showing greenish mosaic and vein-banding symptoms in P. rubra f. acutifolia in New Delhi was characterized based on host reactions, serology and genome sequence. The virus isolate induced local symptoms on several new experimental host species: Capsicum annuum (chilli), Nicotiana benthamiana, Solanum lycopersicum and S. melongena. N. benthamiana could be used as an efficient propagation host as it developed systemic mottle mosaic symptoms all round the year. The genome of FrMV-Ind-1 was 6643 (JN555602) nucleotides long with genome organization similar to tobamoviruses. The Indian isolate of FrMV shared a very close genome sequence identity (98.3 %) with the lone isolate of FrMV-P from Australia. FrMV-Ind-1 together with FrMV-P formed a new phylogenetic group i.e. Apocynaceae-infecting tobamovirus. The polyclonal antiserum generated through the purified virus preparation was successfully utilized to detect the virus in field samples of frangipani by ELISA. Of the eight different tobamoviruses tested, FrMV-Ind-1 shared distant serological relationships with only cucumber green mottle mosaic virus, tobacco mosaic virus, bell pepper mottle virus and kyuri green mottle mosaic virus. RT-PCR based on coat protein gene primer successfully detected the virus in frangipani plants. This study is the first comprehensive description of FrMV occurring in India.

Clinical profile of pulmonary aspergilloma complicating residual tubercular cavitations in Northen Indian patients

BACKGROUND

Little is known regarding the clinical profile of Aspergilloma in Indian patients. Such a study was undertaken at Hospital for Chest and TB, Jaipur.

MATERIALS AND METHODS

Old, treated patients of pulmonary tuberculosis showing ball like lesion/s inside cavity/ies or a recent thickening of cavity wall were enrolled. Morning sputa samples were collected in the patients who were able to raise sputum and were examined by KOH mount and fungal culture. Serum anti-aspergillus antibodies were estimated in all the patients. Twenty normal healthy subjects were included to serve as control. All patients showing a positive or borderline positive serology were diagnosed as pulmonary aspergilloma (PA group). The remaining patients formed the non-aspergilloma group (Non PA group).

RESULTS

A total of 98 study patients could be classified as PA group (54 patients by serology alone, 44 patients by serology as well as sputum culture). The remaining 152 patients were classified as non PA group. Hemoptysis alone or along with other chest symptoms was significantly more common in PA group as compared to non PA group patients (P<0.001), more so in those with ball like lesions. But chest symptoms other than hemoptysis were more common in non PA group. Within the PA group, 21 (13 with ball like lesions and 8 with thickening of cavity wall) had clinical symptoms suggestive of CNPA and two patients (one each with ball like lesions and thickening of cavity wall) had clinical symptoms suggestive of ABPA.

CONCLUSION

The clinical profile of pulmonary Aspergilloma in Indian patients is very protean ranging from saprophytic disease to CNPA and less commonly to ABPA.

Elevated circulating levels of matrix metalloproteinase-9 and -2 in patients with symptomatic coronary artery disease

BACKGROUND

Matrix metalloproteinases (MMP-9 and MMP-2) have been implicated in development of atherosclerosis and plaque rupture in acute coronary syndromes (ACS).

AIM

To determine the relationship between circulating MMPs and symptomatic coronary artery disease.

METHODS

Plasma levels of MMP-9 and MMP-2 were measured in patients with ACS, stable angina (SA) and in controls, using a quantitative gelatin zymography. These measurements were correlated with markers of systemic inflammation (hs-CRP) in all subjects and myocardial injury (troponin T) in patients with ACS.

RESULTS

Plasma MMP-9 in ACS was greater than in SA, and was greater in SA than in controls (P < 0.01 ACS vs SA and controls, P < 0.01 SA vs control). Plasma MMP-2 was significantly greater in ACS than SA or controls (P < 0.01 vs SA and controls). There was strong overall relationship between hs-CRP and MMP-9 (r = 0.65, P < 0.0001) driven by a significant relationship in ACS patients (r = 0.58, P = 0.02), as there was no significant association in SA or controls. A weaker overall correlation was found between hs-CRP and MMP-2 (r = 0.39, P = 0.02), but no significant relationship was present for either of the two patient subgroups or controls. There was no correlation between levels of troponin T and MMP-9, MMP-2 or hs-CRP in ACS patients.

CONCLUSION

Quantitative gelatin zymography identifies increased circulating levels of MMP-9 and MMP-2 in patients with symptomatic coronary disease. MMP-9 and MMP-2 are higher in ACS than SA patients and might have use as markers of plaque rupture or instability. The strong relationship between MMP-9 and hs-CRP in ACS patients suggests MMP-9 might be an additional marker and/or consequence of the inflammatory component in ACS.

The reduction of tumor initiating activity and cell mediated mutagenicity of dimethylbenz[a]anthracene by a copper coordination compound

Cu(II) (3,5-diisopropyl salicylate)2 (CuDIPS) which is an anti-inflammatory copper coordination compound (mol. wt. 503) possessing superoxide dismutase (SOD) activity was tested to determine its effect on 7,12-dimethylbenz[a]anthracene (DMBA)-induced initiation of tumors in mouse skin and on mutagenicity to 6-thioguanine resistance in a mouse keratinocyte mediated Chinese hamster V-79 cell system. A single application of CuDIPS (0.4 mg/mouse) administered at a short interval before DMBA application when followed by 20 weeks of promotion by TPA reduced the mouse skin tumor yield by 55%. When DMBA-induced cell-mediated mutagenesis was tested in the presence of CuDIPS a significant reduction in the number of V-79 6-thioguanine resistant mutants was observed.

Effect of tunicamycin on receptors for tumor promoters

A progressive decline in the specific binding of [20-3H]phorbol 12,13-dibutyrate ([3H]PDBu) and glycoprotein synthesis was observed following treatment of primary mouse epidermal cells with tunicamycin, a specific inhibitor of dolichol-mediated glycosylation. Following 18 h of treatment, the specific binding of [3H]PDBu was reduced to 33-56% of the control value. The total protein synthesis determined by leucine incorporation into acid-insoluble material was not altered by this antibiotic drug. These results suggest that the receptor for phorbol diesters is, or is functionally linked to, a glycoprotein on the cell surface.

Decreased accumulation of cyclic adenosine 3',5'-monophosphate in "ischemic" skin after 12-0-tetradecanoyl-phorbol-13-acetate treatment

The effect of 12-0-tetradecanoyl-phorbol-13-acetate (TPA) on cyclic adenosine 3',5'-monophosphate (cyclic AMP) level in adult mouse skin in response to ischemia was examined. The incubation of skin pieces in a buffered salts medium at 37 degrees C resulted in a rapid accumulation of cyclic AMP. In mouse skin pieces maximum accumulation (about 6 times the basal level) occurred after 2 min incubation and was followed by a rapid decline in the cyclic AMP level. This "ischemic" rise in epidermal cyclic AMP was greatly reduced if skin was used 16 hr after a single application of 17 nmoles of TPA. The effect of TPA on cyclic AMP accumulation in response to ischemia was first observed at 1 hr after TPA treatment and was maximal at 4 hr. The lack of "ischemic" response in TPA-treated skin was not related to an increase in the activity of cyclic AMP phosphodiesterase after TPA application. In addition, the accumulation of cyclic AMP in skin in response to both ischemia and exposure to isoproterenol, adenosine, histamine, or prostaglandin E2 (PGE2) was not observed in skin treated with the tumor promoter TPA.

The effect of ischemia on cyclic adenosine 3',5'monophosphate accumulation in mouse skin

The incubation of adult mouse skin pieces in a buffered salts medium at 37 degrees C led to a rapid accumulation of cyclic adenosine 3'5-monophosphate (cyclic AMP) in the tissue. In mouse skin maximum accumulation occurred after 2 min incubation; levels reverted to near control levels after a further 7 min incubation. the increase in cyclic AMP contents of the skin pieces was probably not due to the release of materials which activate adenylate cyclase after binding to cellular receptors. Thus, cyclic AMP accumulation was unaffected by the inclusion of alpha- or beta-adrenergic antagonists, or by the pretreatment of adult mouse skin with indomethacin (an inhibitor of prostaglandin synthetase). Furthermore, adenosine, a known activator of epidermal adenylate cyclase, could not be detected in the incubation medium. The functional integrity of epidermal adenylate cyclase was maintained during the cyclic AMP accumulation in response to ischemia. Thus, adenosine, histamine, isoproterenol and prostaglandin E2 (PGE2) augmented the cyclic AMP response. Cyclic AMP accumulation at 37 degrees C was not observed in newborn mouse skin; this lack of cyclic AMP accumulation was probably not due to increased activity of low affinity cyclic AMP phosphodiesterase in newborn mouse skin.

Effect of tumor promoters on lipid peroxidation in mouse skin

Products of lipid peroxidation were measured in mouse epidermis. These were shown to increase with advancing age. Conversely, a decline in these products was observed on treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA), a potent tumor promoting agent. A decline in lipid peroxidation occurred within 4 h after application of 2 micrograms TPA and the maximum effect was seen at 22-24 h. A lesser active tumor promoter, phorbol dibenzoate; and ethyl phenylpropiolate, a purely hyperplastic agent, also lowered lipid peroxidation; while phorbol, a non-promoter, did not show any significant effect. Mezerein, a resiniferonal derivative with weak promoting activity but a potent stage II promoter, appeared to be more potent than TPA in lowering the basal levels of peroxidation. The TPA-induced decrease in lipid peroxidation could be prevented by fluocinolone acetonide, a potent antipromoting and antimitotic agent, but not by retinoic acid and tosylamino-2-phenylethylchlorimethyl-ketone which are relatively potent antipromoting agents but lack antimitotic activity, suggesting that the decrease of lipid peroxidation by tumor promoting agents is possibly related to their mitotic activity. Furthermore, skin papilloma and carcinoma contain lower levels of lipid peroxidation compared to epidermis from the same mice.

Specific binding of phorbol ester tumor promoters to intact primary epidermal cells from Sencar mice

The binding of [20-3H]phorbol 12,13-dibutyrate ([3H]PDB) to intact living epidermal cells in monolayer culture was characterized. At 37 degrees C, the maximum specific [3H]PDB binding (binding displaceable by 30 microM unlabeled PDB) was attained in 15--20 min and was followed by a rapid decrease (down regulation) of radioactivity bound to the cells. The activity lost by the cells during this decrease was found in the incubation medium. Prior exposure of cells to phorbol 12-myristate 13-acetate (PMA; 12-O-tetradecanoylphorbol 13-acetate) but not to phorbol for 2 hr at 37 degrees C caused approximately 55% reduction in the number of measurable binding sites for [3H]PDB. The down regulation was temperature sensitive; there was no loss of radioactivity after 1 hr at 4 degrees C. The specific binding of [3H]PDB at 4 degrees C reached equilibrium in 15--20 min and was saturable and freely reversible. At equilibrium, epidermal cells contained 1.2 x 10(5) binding sites per cell, and binding sites had a KD of 10 nM. Specificity of binding was shown by the observation that the biologically active phorbol esters PMA and 12-deoxyphorbol 13-decanoate inhibited the binding, whereas the inactive parent compound phorbol and the nonphorbol tumor promoter anthralin did not have any effect. The abilities of these compounds to inhibit [3H]PDB binding directly correlates with their tumor promoting activities. Epidermal cells exposed to retinoic acid or fluocinolone acetonide for 24 hr had similar [3H]PDB binding characteristics as untreated cells suggesting that inhibition of tumor promotion induced by these compounds is not mediated through alterations in the phorbol ester binding sites.

Down regulation of specific binding of [20-3H]phorbol 12,13-dibutyrate and phorbol ester-induced differentiation of human promyelocytic leukemia cells

Binding of [20-3H]phorbol 12,13-dibutyrate ([3H]PDB) to intact human promyelocytic leukemia cells susceptible (HL-60) or resistant (R-35) to phorbol ester-induced differentiation was characterized. Specific binding of [3H]PDB to both HL-60 and R-35 cells at 37 degrees C reached a maximum within 15-20 min. Maximal specific [3H]PDB binding to HL-60 cells was followed by a decline (down regulation) of radioactivity. This down regulation was temperature dependent, because no loss of radiolabel occurred by 1 hr at 4 degrees C. The down regulation of bound [3H]PDB seen in HL-60 cells at 37 degrees C was not observed with R-35 cells. Prior exposure of the HL-60 cells but not of R-35 cells to 1 microM phorbol 12-myristate 13-acetate for 90 min at 37 degrees C caused a marked reduction in the specific binding of [3H]PDB. When [3H]PDB binding was carried out at 4 degrees C, [3H]PDB bound to both cell types in a rapid, specific, and reversible manner. At equilibrium, HL-60 and R-35 cells were found to contain almost the same number of binding sites, which had dissociation constants of about 50 nM, indicating that the failure of R-35 cells to undergo PDB-induced differentiation was not associated with any change in the affinity or in the number of [3H]PDB binding sites. These results indicate that the down regulation of specific [3H]PDB binding may be a crucial early event in the control of phorbol ester-induced terminal differentiation in HL-60 cells. Furthermore, we suggest that such down regulation may be involved in other cellular and biochemical effects of phorbol diester tumor promoters.

Diminution of mouse epidermal superoxide dismutase and catalase activities by tumor promoters

The effects of phorbol ester tumor promoters and related compounds on superoxide dismutase (SOD) and catalase were examined. The treatment of adult mouse skin with 2 micrograms 12-O-tetradecanoylphorbol-13-acetate (TPA) resulted in a sustained decrease in the basal levels of both SOD and catalase activities in the epidermis. A decline in SOD activity occurred within 3 h after application and the maximum effect was seen at 16--17 h. The decrease in SOD activity was always accompanied by a similar decline in the epidermal catalase activity. The alterations in both enzymes occurred against a high background of enhanced protein synthesis which indicates that the effect of TPA is selective for SOD and catalase. Other tumor promoters such as phorbol 12,13-dibutyrate and the non-phorbol tumor promoter anthraline also lowered the activities of both the enzymes. Mezerein, a resiniferonol derivative with weak promoting activity but a potent stage-II promoter, appeared to be more potent than TPA in lowering the basal levels. These results indicate that damage which favors neoplastic progression could occur in TPA-treated mouse skin due to the accumulation of free radicals resulting from low levels of SOD and catalase activity. In addition, the TPA-caused decrease in the levels of SOD and catalase was not prevented by either retinoic acid, fluocinolone acetonide, tosyl amino-2-phenylethyl chloromethyl ketone, or butylated hydroxytoluene, suggesting that inhibition of tumor promotion by these agents is not mediated through alterations in the levels of enzymatic activities which decrease free radical concentrations.

Effects of cholera toxin on ornithine decarboxylase activity in mouse skin

The subcutaneous injection of cholera toxin into adult mice resulted in a sustained increase in cyclic AMP levels in mouse epidermis after a lag period of about 2 hr. An increase in ornithine decarboxylase activity occurred between 7 and 10 hr, which was maintained for at least 10 hr. The increase in decarboxylase activity was localized to the area of epidermis visually affected by cholera toxin and was unaffected by hypophysectomy, suggesting a direct effect of the toxin on the epidermal cells. The subcutaneous injection of cholera toxin also led to an increase in cyclic AMP levels in newborn mouse skin. In contrast to adult mice, newborn mouse skin contained high basal activities of ornithine decarboxylase in both the epidermal and dermal fractions. The activity in both fractions was markedly decreased following cholera toxin injection. The ability of cholera toxin to induce both epidermal and dermal ornithine decarboxylase activity developed between 10 and 21 days after birth.

The beta-adrenergic receptor of newborn mouse skin

Binding of the potent beta-adrenergic antagonist [125I]iodohydroxybenzylpindolol ([125I]IHYP) to particulate preparations from newborn mouse skin was characterized. A number of criteria were used to establish that binding occurred to specific, high affinity beta-adrenergic receptors in the skin preparations. Thus specific binding (that displaced by 10 micrometer concentrations of the beta-adrenergic antagonist (-)propranolol) reached equilibrium in 15--20 min, was saturable (ligand concentration for half-maximal saturation, 0.25 nM) and freely reversible. Stereoselectivity of binding was demonstrated by the observation that displacement of [125I]IHYP by (-)propranolol occurred at concentrations at least 100 times lower than with (+)isoproterenol. Displacement was also observed with the beta-adrenergic agonists (-)isoproterenol, (-)epinephrine and (-)norepinephrine, but not with the alpha-adrenergic antagonist phentolamine.

Accumulation of cyclic adenosine 3',5'-monophosphate in adult and newborn mouse skin: responses to ischemia and isoproterenol

Levels of cyclic adenosine 3',5'-monophosphate in adult mouse skin pieces were rapidly increased on incubation at 37 degrees C, or on exposure to isoproterenol. Accumulation of the cyclic nucleotide under both conditions was greatly decreased in newborn mouse skin, or in adult skin treated with the tumor promotor 12-0-tetradecanoyl-phorbol-13-acetate.