Towards effective machine learning in medical imaging analysis: A novel approach and expert evaluation of high-grade glioma 'ground truth' simulation on MRI.

PURPOSE/OBJECTIVE(S): Gliomas are uniformly fatal brain tumours with significant neurological and quality of life detriment to patients. Improvement in outcomes has remained largely unchanged in nearly 20 years. MRI (magnetic resonance imaging) is often used in diagnosis and management. Machine learning analyses of large-scale MRI data are pivotal in advancing the diagnosis, management and improve outcomes in neuro-oncology. A common challenge to robust machine learning approaches is the lack of large 'ground truth' datasets in supervised learning for building classification and prediction models. The creation of these datasets relies on human-expert input and is time-consuming and subjective error-prone, limiting effective machine learning applications. Simulation of mechanistic aspects such as geometry, location and physical properties of brain tumours can generate large-scale ground-truth datasets allowing for comparison of analysis techniques in clinical applications. We aimed to develop a transparent and convenient method for building 'ground truth' presentations of simulated glioma lesions on anatomical MRI. MATERIALS/METHODS: The simulation workflow was created using the Feature Manipulation Engine (FME®), a data integration platform specializing in the spatial data processing. By compiling and integrating FME's functions to read, integrate, transform, validate, save, and display MRI data, and experimenting with ways to manipulate the parameters concerning location, size, shape, and signal intensity with the presentations of glioma, we were able to generate simulated appearances of high-grade gliomas on gadolinium-based high-resolution 3D T1-weighted MRI (1 mm3). Data of patients with canonical high-grade tumours were used as real-world tumours for validating the accuracy of the simulation. Twenty raters who are experienced with brain tumour interpretation on MRI independently completed a survey, designed to distinguish simulated and real-world brain tumours. Sensitivity and specificity were calculated for assessing the performance of the approach with the binary classification of simulated vs real-world tumours. Correlation and regression were used in run time analysis, assessing the software toolset's efficiency in producing different numbers of simulated lesions. Differences in the group means were examined using the non-parametric Kruskal-Wallis test. RESULTS: The simulation method was developed as an interpretable and useful workflow for the easy creation of tumour simulations and incorporation into 3D MRI. A linear increase in the running time and memory usage was observed with an increasing number of generated lesions. The respondents' accuracy rate ranged between 33.3 and 83.3 %. The sensitivity and specificity were low for a human expert to differentiate simulated lesions from real gliomas (0.43 and 0.58) or vice versa (0.65 and 0.62). The mean scores ranking the real-world gliomas did not differ between the simulated and real tumours. CONCLUSION: The reliable and user-friendly software method can allow for robust simulation of high-grade glioma on MRI. Ongoing research efforts include optimizing the workflow for generating glioma datasets as well as adapting it to simulating additional MRI brain changes.

MMP-9 as a potential biomarker for carcinoma of oral cavity: a study in eastern India.

Carcinoma of oral cavity have a high risk of recurrence after initial treatment with surgery, radiotherapy, surgery with adjuvant radiotherapy, or radio-chemotherapy.The present study investigated the changes in expression, activity and regulation of matrix metalloproteinases (MMP) -2 and -9 in oral squamous cell carcinoma (OSCC) which might help to ascertain the invasive potential of the tumor . Tumor tissues and adjacent normal tissues of OSCC patients [N,37; either sex; 20-70 yrs] were subjected to clinico-pathology, histopathology and TNM grading. The enzyme activity and associated signalling was observed with gelatin zymography, immunohistochemistry, ELISA, western blot and semi quantitative reverse transcriptase PCR. OSCC tissues were observed with elevated MMP-9 activity, enhanced expression of fibronectin (FN), phosphorylated focal adhesion kinase (FAK Try 397), phosphatidyl inositol 3­kinase (PI3K), protein kinase B (AKT) and reduced expression of tissue inhibitor of metalloproteinase- 1(TIMP-1) than the control tissues.OSCC patients elicited a predominance of MMP-9 activity via up regulated FAK/PI3K/AKT pathway. A routine MMP-9 analysis may ascertain the invasiveness of the tumor and therefore may be professed as a suitable biomarker for metastatic potential of oral cancer.

The IML3/MCM19 gene of Saccharomyces cerevisiae is required for a kinetochore-related process during chromosome segregation.

The mcm19 mutation in budding yeast affects minichromosome maintenance. In this work we have shown that this mutation leads to defects in the segregation of minichromosomes and chromosomes. The mutant cells show defective kinetochore function as judged by three criteria-- relaxation of the transcriptional block normally associated with a CEN box, stable maintenance of a dicentric plasmid in mutant cells, and mild sensitivity to the antimicrotubule drug benomyl. The MCM19 gene has been cloned and found to be the same as IML3, which codes for the ORF YBR107C. Deletion of the gene was not lethal, nor did it confer any growth defects on the mutant cells. However, the mcm19 null mutation conferred growth defects in the presence of a mutation in the TUB1 gene coding for alpha-tubulin. Two-hybrid experiments showed an interaction between Im13p/Mcm19p and the kinetochore protein Ch14, indicating that the Im13/Mcm19 protein has a role in kinetochore function.

A highly chemoselective oxidation of alcohols to carbonyl products with iodosobenzene diacetate mediated by chromium(III)(salen) complexes: synthetic and mechanistic aspects.

[reaction: see text] The catalytic oxidation of the allylic alcohols 1d-n with iodosobenzene diacetate, mediated by the [Cr(III)(salen)]X complex, affords the respective enones in excellent chemoselectivity for Cl(-) as counterion [complex A(Cl)], while for the counterions TfO(-) [complex A(TfO)] and PF(6)(-) [complex A(PF(6)())] nearly equal amounts of enone and epoxide are observed. This counterion-dependent oxidation of allylic alcohols by Cr(III)(salen) complexes is rationalized in terms of Lewis acid catalysis by the complex A(Cl) and redox catalysis for A(TfO) and A(PF(6)()).

Efficacy of single-dose ROM therapy plus low-dose convit vaccine as an adjuvant for treatment of paucibacillary leprosy patients with a single skin lesion.

The recent World Health Organization multicentric field study on the treatment of paucibacillary (PB) leprosy patients with single skin lesion (SSL) and a single dose of rifampin-ofloxacin-minocycline (ROM) brought new hope to those who are engaged in the eradication of leprosy from India. Being encouraged by the WHO report, we undertook the present hospital-based study and found that PB leprosy patients with SSL were morphologically and histopathologically heterogeneous. The histological spectrum of SSL ranged from indeterminate through tuberculoid (TT) to borderline tuberculoid (BT) leprosy, and most patients had active BT leprosy. Ninety new, untreated PB leprosy patients with SSL were included in the present study for comparative assessment of the efficacies of ROM and ROM plus Convit vaccine therapies. Children, pregnant women, lactating mothers and patients with any thickening of nerves were excluded. All patients were bacteriologically negative (skin-smear test) but lepromin reactive. The patients were divided into two groups after proper matching for morphological and histological status of SSL: a) The test group included 60 patients and the control group included 30 patients. The test group was given a single dose of ROM initially and two injections of low-dose Convit vaccine, one initially and the other at the end of 3 months. b) The control group was given only a single dose of ROM initially. Both groups were followed clinically every 2 weeks for 6 months and retested for histological, bacteriological and lepromin status at the end of 6 months. Thereafter, they were followed clinically every month for another 6 months. In the test group, the SSL resolved in 33.3%, regressed in 48.3%, and remained active in 18.3% of the patients, while the granuloma disappeared in 70% of the cases. Only one patient developed neuritis, and in another patient the disease relapsed on the eighth month. On the other hand, the SSL in the control patients resolved, regressed and remained active in 13.3%, 63.3% and 23.3% of the cases, respectively, while the granuloma disappeared in 53.3% of the cases. In the seven patients who remained active, the disease course was progressive, and two of them developed neuritis. The clinical outcome of the patients treated with ROM plus low-dose Convit vaccine was statistically superior to those treated with single-dose ROM therapy alone.

Why relapse occurs in PB leprosy patients after adequate MDT despite they are Mitsuda reactive: lessons form Convit's experiment on bacteria-clearing capacity of lepromin-induced granuloma.

It is amazing how after years of scientific research and therapeutic progress many simple and basic questions about protective immunity against Mycobacterium leprae remain unanswered. Although the World Health Organization (WHO) has recommended short-term multidrug therapy (WHO/MDT) for the treatment of paucibacillary (PB) leprosy patients, from time to time several workers from different parts of the globe have reported inadequate clinical responses in a few tuberculoid and indeterminate leprosy patients following adequate WHO/MDT despite the fact that they are Mitsuda responsive. A few borderline tuberculoid patients harbor acid-fast bacilli (AFB) in their nerves for many years even though they become clinically inactive following MDT, a fact which has been ignored by many leprosy field workers. Keeping these patients in mind, we have attempted to investigate the cause of the persistence of AFB in PB cases and have looked into the question of why Mitsuda positivity in tuberculoid and indeterminate leprosy patients, as well as in healthy contacts, is not invariably a guarantee for protectivity against the leprosy bacilli. We have: a) analyzed the histological features of lepromin-induced granulomas, b) studied the bacteria-clearing capacity of the macrophages within such granulomas, and c) studied the in vitro leukocyte migration inhibition factor released by the blood leukocytes of these subjects when M. leprae sonicates have been used as an elicitor. The results of these three tests in the three groups of subjects have been compared and led us to conclude that the bacteria-clearing capacity of the macrophages within lepromin-induced granuloma (positive CCB test) may be taken as an indicator of the capability of elimination of leprosy bacilli and protective immunity against the disease. This important macrophage function is not invariably present in all tuberculoid and indeterminate leprosy patients or in all contacts even though they are Mitsuda responsive and are able to show a positive leukocyte migration inhibition (LMI) test. It is likely but not certain that this deficit of the macrophage is genetically predetermined and persists after completion of short-term WHO/MDT. Thus, after discontinuation of treatment slow-growing, persisting M. leprae multiply within macrophages leading to relapse.

Immunotherapy of lepromin-negative borderline leprosy patients with low-dose Convit vaccine as an adjunct to multidrug therapy; a six-year follow-up study in Calcutta.

The present report, which describes management of lepromin-negative borderline leprosy patients with low-dose Convit vaccine, is an extension of our earlier study on the treatment of lepromatous leprosy patients with low-dose Convit vaccine as an adjunct to multidrug therapy (MDT). The test Group I, consisting of 50 lepromin-negative, borderline leprosy patients, were given low-dose Convit vaccine plus MDT. The control group II consisted of 25 lepromin-negative, borderline leprosy patients given BCG vaccination plus MDT and 25 lepromin-negative, borderline leprosy patients given killed Mycobacterium leprae (human) vaccine plus MDT. The control group III consisted of 50 lepromin-positive, borderline leprosy patients not given any immunostimulation but given only MDT. Depending upon the lepromin unresponsiveness, the patients were given one to four inoculations of the various antileprosy vaccines and were followed up every 3 months for 2 years for clinical, bacteriological and immunological outcome. All patients belonging to the test and control groups showed clinical cure and bacteriological negativity within 2 years. However, immunologic potentiation, assessed by lepromin testing and the leukocyte migration inhibition test (LMIT), was better in the test patients receiving low-dose Convit vaccine plus MDT than in the control patients receiving BCG vaccine plus MDT or killed M. leprae vaccine plus MDT or MDT alone. But the capacity of clearance bacteria (CCB) test from the lepromin granuloma showed poor bacterial clearance in the test patients. However, there was no relapse during 6 years of follow up. Two mid-borderline (BB) patients had severe reversal reactions with lagophthalmos and wrist drop during immunotherapy despite being given low-dose Convit vaccine.

Binding of water and solute to protein-mixture and protein-coated alumina.

Extent of water vapour adsorption (n1) of gelatin and bovine serum albumin and their mixtures in different proportion respectively has been measured by isopiestic vapour pressure methods at various values of water activity (a1) ranging between zero and unity. Similar measurements have also been carried out with gelatin and BSA coated alumina powder. At a given value of a1, n1 for the protein mixture is found to be significantly less than their ideal value obtained from the additivity rule. Such decrease is probably due to the protein-protein interaction as a result of which some of the water binding sites become unavailable for water vapour adsorption. On the other hand when a protein is mixed with alumina powder, the water vapour adsorption of the protein coated alumina surface at a given water activity is found to be 2 to 3 times larger than its ideal value obtained from the additivity rule. The standard free energy changes for hydration of protein mixtures and protein-coated alumina have been evaluated using Bull equation. The extent of excess hydration of these proteins and their mixtures as well as protein-coated alumina in the presence of excess neutral salts and urea respectively have been evaluated using the isopiestic method. In all cases, the moles of water and solute respectively bound in absolute amount to biopolymers, biopolymer mixtures and protein-coated alumina have been evaluated in the limited range of solute concentrations in the medium. Based on the Gibbs-Duhem equations, a rigorous expression for the standard free energy change for binding of excess solute and solvent to biopolymer have been evaluated with reference to unit solute mole fraction as standard state. Free energies of excess hydration of different biopolymer systems have been evaluated using this equation.

Immunotherapy of far-advanced lepromatous leprosy patients with low-dose convit vaccine along with multidrug therapy (Calcutta trial).

This report describes a promising mode of treatment of lepromin-unresponsive, far-advanced, lepromatous (LL) leprosy patients with antileprosy vaccines as an adjunct to multidrug therapy (MDT). The Trial Groups included 50 highly bacilliferous, lepromin-negative, untreated LL patients. They were given MDT for 2 years. Of them, 30 patients were administered a mixed antileprosy vaccine containing killed Mycobacterium leprae of human origin plus M. bovis BCG. The remaining 20 patients were given M. bovis BCG. Depending on the severity of lepromin unresponsiveness, they were given one to six inoculations at 3-month intervals. Another 20 similar LL patients were taken in the Control Group. They were given only MDT for 2 years. From the start of the study, all patients belonging to the Trial and Control Groups were followed every 3 months for clinical, bacteriological and immunological outcomes. Within 2 years all 50 patients of the Trial Groups and 19 of the 20 patients of the Control Group became clinically inactive and bacteriologically negative. However, the clinical cure and the falls of the bacterial and morphological indexes were much faster in those patients receiving the mixed vaccine therapy than in those patients who were given BCG plus MDT or only MDT. The immunological improvements in the patients of the Trial and Control Groups were assessed by: a) lepromin testing at the beginning of the study and at 3-month intervals and also by b) the in vitro leukocyte migration inhibition (LMI) test at both the beginning and end of the study. As the patients were given more and more vaccinations, the incidence of lepromin conversion increased, more so in the patients receiving the mixed vaccine. Thus, 63%, 15% and 5% of the patients became lepromin positive in those patients receiving the mixed vaccine, BCG, and MDT only, respectively. Lamentably, the vaccine-induced lepromin positivity was temporary and faded away within several months. At the beginning of the study, the LMI test against specific M. leprae antigen was negative in all patients of both the Trial and Control Groups. After the end of the chemo-immunotherapy schedule, the LMI test became positive in 50% and 20% of LL patients receiving the mixed vaccine and BCG, respectively. None of the Control Group could show LMI positivity after completion of the MDT schedule. These results show that treatment of LL patients with the mixed vaccine and MDT could quickly reverse the clinical course of the disease, remove immunologic anergy in some patients, and induce a rapid decrease in the bacterial load in them.

Protein adsorption at solid-liquid interfaces: Part IV--Effects of different solid-liquid systems and various neutral salts.

Adsorption isotherms of BSA at the solid-water interfaces have been studied as a function of protein concentration, ionic strength of the medium, pH and temperature using silica, barium sulphate, carbon, alumina, chromium, ion-exchange resins and sephadex as solid interfaces. In most cases, isotherms for adsorption of BSA attained the state of adsorption saturation. In the presence of barium sulphate, carbon and alumina, two types in the isotherms are observed. Adsorption of BSA is affected by change in pH, ionic strength and temperature of the medium. In the presence of metallic chromium, adsorbed BSA molecules are either denatured or negatively adsorbed at the metallic interface. Due to the presence of pores in ion-exchange resins, adsorption of BSA is followed by preferential hydration on resin surfaces in some cases. Sometimes two steps of isotherms are also observed during adsorption of BSA on the solid resins in chloride form. Adsorption of BSA, beta-lactoglobulin, gelatin, myosin and lysozyme is negative on Sephadex surface due to the excess adsorption of water by Sephadex. The negative adsorption is significantly affected in the presence of CaCl2, KSCN, LiCl, Na2SO4, NaI, KCl and urea. The values of absolute amounts of water and protein, simultaneously adsorbed on the surface of different solids, have been evaluated in some cases on critical thermodynamic analysis. The standard free energies (delta G0) of excess positive and negative adsorption of the protein per square meter at the state of monolayer saturation have been calculated using proposed universal scale of thermodynamics. The free energy of adsorption with reference to this state is shown to be strictly comparable to each other. The magnitude of standard free energy of transfer (delta G0B) of one mole of protein or a protein mixture at any type of physiochemical condition and at any type of surface is observed to be 38.5 kJ/mole.

Protein adsorption at solid-liquid interfaces: Part III--Adsorption from ternary protein mixture.

Simultaneous adsorption of bovine serum albumin (BSA), beta-lactoglobulin and gelatin from aqueous solutions of their ternary mixture to the alumina-water interface has been studied as a function of protein concentration at different values of pH, ionic strength, temperature and weight fraction ratios of proteins. At a fixed weight fraction of beta-lactoglobulin, preferential adsorption (gamma w(lac)) of this protein significantly depends on the amounts of BSA and gelatin present in the solution before adsorption. At higher ranges of protein concentrations, extent of adsorption (gamma w(ser)) of BSA decreases sharply with increase of gamma w(lac) until gamma w(ser) becomes significantly negative, thereby indicating that beta-lactoglobulin and water preferentially adsorbed at the interface are responsible for complete displacement of BSA from the surface. On the other hand, adsorption (gamma w(gel)) of gelatin under similar situation increases mutually with increase in the values of gamma w(lac) in many systems. In few systems, gamma w(gel) also decreases with increase of gamma w(lac) depending upon solution parameters. At pH 5.2, increase of ionic strength and temperature, respectively, increases the extent of adsorption of each protein in the mixture considerably. Extents of adsorption of all proteins are observed to increase when pH is changed from 5.2 to 6.4. The affinities of different proteins in the mixture are expressed in unified scales either in terms of maximum extents of total adsorption or in terms of standard free energies of adsorption of protein mixtures with respect to surface saturation.

Protein adsorption at solid-liquid interfaces: Part I--Affinities of proteins for alumina surface.

Extent of adsorption (gamma pw) of bovine serum albumin, beta-lactoglobulin, gelatin and myosin at the alumina-water interface has been measured as function of protein concentration (Cp) at several temperatures, pH, and ionic strengths of the medium. gamma pw for proteins in most cases increases with increase of protein concentration but it attains maximum value gamma pw(m) when Cp is high. Values of maximum adsorption have been examined in terms of molecular orientation, molecular size and shape and unfolding of the packed proteins at the interface. In few cases, gamma pw increases with increase of Cp without reaching a real state of saturation as a result of aggregation of molecules or extensive unfolding of the protein at the interface. In the case of beta-lactoglobulin at pH 5.2 and ionic strength 0.05, gamma pw in high concentration region decreases to zero value when Cp increases. For myosin at 45 degrees C and pH 6.4, and also at 27 degrees and pH 7.8, the values of gamma pw are all negative and these negative values increase with increase of Cp. All these results have been explained in terms of significant competitions of water and protein for binding to the surface sites of the powdered alumina. Adsorption of myosin has also been found to be affected in the presence of NaCl, KCl, CaCl2, KI, Na2SO4, LiCl and urea. The relative affinities of the adsorption of various proteins for the surface of alumina at different physical conditions of the system have been compared in terms of maximum values of adsorption attained when gamma pw is varied with Cp. The affinities are shown to be compared more precisely in terms of the standard free energy decrease for the saturation of the surface by protein as a result of the change in its concentration from zero to unity in the mole fraction scale.

Protein adsorption at solid-liquid interfaces: Part II--Adsorption from binary protein mixture.

Extent of adsorption of proteins at alumina-water interface from solutions containing binary mixture of beta-lactoglobulin and bovine serum albumin (BSA), beta-lactoglobulin and gelatin, and gelatin and bovine serum albumin has been estimated as functions of protein concentrations at varying pH, ionic strength, temperature and weight fraction ratios of protein mixture. The extent of adsorption (gamma lacw) of lactoglobulin in the presence of BSA increases with increase of protein concentration (Clac) until it reaches a maximum but a fixed value gamma lacw(m). Extent of adsorption gamma serw also initially increases with increase of protein concentrations until it reaches maximum value gamma serw(m). Beyond these protein concentrations, adsorbed BSA is gradually desorbed due to the preferential adsorption of lactoglobulin from the protein mixture. In many systems, gamma serw at high protein concentrations even becomes negative due to the strong competition of BSA and water for binding to the surface sites in the presence of lactoglobulin. For lactoglobulin-gelatin mixtures, adsorption of both proteins is enhanced as protein concentration is increased until limiting values for adsorption are reached. Beyond the limiting value, lactoglobulin is further accumulated at the interface without limit when protein concentration is high. For gelatin-albumin mixtures, extent of gelatin adsorption increases with increase in the adsorption of BSA. The limit for saturation of adsorption for gelatin is not reached for many systems. At acid pH, adsorbed BSA appears to be desorbed from the surface in the presence of gelatin. From the results thus obtained the role of electrostatic and hydrophobic effects in controlling the adsorption process has been analysed.

Once-monthly rifampicin plus daily dapsone in initial treatment of lepromatous leprosy.

In an international multicentre controlled single-blind trial of 93 previously untreated lepromatous leprosy patients the therapeutic effects of adding rifampicin, 450 mg/day orally or 1,200 mg once monthly in a single oral dose, to dapsone (50 mg/day orally) for the first 6 months of treatment were compared. Clinical and histopathological improvements and bacteriological regression, indicated by the decreases in the bacterial and morphological indices of the skin and nose-blow smears, were satisfactory and practically identical after 6 months' treatment. The once-monthly rifampicin schedule was better tolerated than the daily one. In view of the good therapeutic efficacy and tolerability, the much lower cost of treatment (about one-tenth of that of the daily rifampicin regimen) and the possibility of administration under supervision, once-monthly rifampicin given in a single oral 1,200 mg dose should be recommended, along with a standard dapsone regimen, for large-scale, initial, and intensive combination treatment of patients with lepromatous and borderline-lepromatous leprosy, to help prevent an increase in dapsone resistance. A third antileprosy drug (e.g., clofazimine) may be added to this initial dual-treatment regimen.

Lepromin conversion after repeated lepromin administration

Out of 265 contacts of bacillary positive lepromatous leprosy patients 92 were lepromin positive...