Determinants of two-year mortality among HIV positive patients with Cryptococcal meningitis initiating standard antifungal treatment with or without adjunctive dexamethasone in Uganda

Globally, early initiation of antiretroviral therapy for HIV led to a reduction in the estimated mortality from cryptococcal meningitis (CCM) from 624,700 in 2009 to 181,100 in 2014. However, CCM remains one of the leading causes of mortality among HIV infected patients especially in sub-Saharan Africa where 75% of the deaths occur. Most of the studies evaluating mortality have reported short-term mortality (at or before 10 weeks of therapy). We determined mortality and associated factors among patients treated for CCM in the CryptoDex trial (ISRCTN59144167) in Uganda, and the effect of dexamethasone adjunctive therapy on mortality at two years. We conducted a retrospective cohort study between May 2017 and July 2017 to determine the long term survival (up to 2 years post-randomization) of all patients who had been enrolled into the CryptoDex trial in Uganda. The CryptoDex trial recruited between April 2013 and February 2015. We estimated mortality rates and determined factors affecting mortality at two years using Cox regression. The study followed up 211 participants, 127 (60.2%) of whom were male. Sixteen participants (7.58%) were diagnosed with HIV at the same admission when CCM was diagnosed. By two years following randomization 127 (60%) participants had died, a mortality rate of 67 deaths per 100 person-years. Mortality was associated with Glasgow coma score (GCS) below 15 (adjusted Hazard ratio (aHR) 1.77, 95% CI: 1.02–2.44), p = 0.040; weight (aHR 0.97, per 1 Kg increase; 95% CI: 0.94–0.99), p = 0.003; and presence of convulsions (aHR 2.31, 95% CI: 1.32–4.04), p = 0.004, while dexamethasone use and fungal burden had no effect. Long-term mortality in CCM patients remains high even among patients receiving recommended therapy. Strategies to improve long-term survival in CCM patients are urgently needed, especially targeting those with reduced GCS, low weight, and convulsions.     

Selection of antibiotic-resistant standard plate count bacteria during water treatment.

Standard plate count (SPC) bacteria were isolated from a drinking-water treatment facility and from the river supplying the facility. All isolates were identified and tested for their resistance to six antibiotics to determine if drug-resistant bacteria were selected for as a consequence of water treatment. Among the isolates surviving our test procedures, there was a significant selection (P less than 0.05) of gram-negative SPC organisms resistant to two or more of the test antibiotics. These bacteria were isolated from the flash mix tank, where chlorine, alum, and lime are added to the water. Streptomycin resistance in particular was more frequent in this population as compared with bacteria in the untreated river water (P less than 0.01). SPC bacteria from the clear well, which is a tank holding the finished drinking water at the treatment facility, were also more frequently antibiotic resistant than were the respective river water populations. When 15.8 and 18.2% of the river water bacteria were multiply antibiotic resistant, 57.1 and 43.5%, respectively, of the SPC bacteria in the clear well were multiply antibiotic resistant. Selection for bacteria exhibiting resistance to streptomycin was achieved by chlorinating river water in the laboratory. We concluded that the selective factors operating in the aquatic environment of a water treatment facility can act to increase the proportion of antibiotic-resistant members of the SPC bacterial population in treated drinking water.     

Explorations in statistics: standard deviations and standard errors

Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This series in Advances in Physiology Education provides an opportunity to do just that: we will investigate basic concepts in statistics using the free software package R. Because this series uses R solely as a vehicle with which to explore basic concepts in statistics, I provide the requisite R commands. In this inaugural paper we explore the essential distinction between standard deviation and standard error: a standard deviation estimates the variability among sample observations whereas a standard error of the mean estimates the variability among theoretical sample means. If we fail to report the standard deviation, then we fail to fully report our data. Because it incorporates information about sample size, the standard error of the mean is a misguided estimate of variability among observations. Instead, the standard error of the mean provides an estimate of the uncertainty of the true value of the population mean.     

On ROC analysis with nonbinary reference standard

Statistical methods for the evaluation of the accuracy of diagnostic tests usually assume a binary true disease status. However, this assumption may not be realistic in practical settings in which “disease” is defined by dichotomizing continuous or ordinal categorical measures using a pre‐specified threshold value. In this paper, we focus on the analysis of studies in which both the diagnostic test and the reference standard are reported as continuous measures. We propose a semiparametric model for estimating the sensitivity, specificity, and the ROC curve as functions of reference standard thresholds. Under suitable order restrictions on the mean of the test result variable, fitting is done via two alternative approaches: isotonic regression and monotone smoothing splines. The model provides the basis to assess the effect of varying reference standard threshold on the performance of a diagnostic test. An example to evaluate the ability of the maximal SUV‐lean (standardized uptake value normalized to lean body mass) in predicting axillary node involvement in women diagnosed with breast cancer is presented.     

Detection of ABCC1 expression in classical Hodgkin lymphoma is associated with increased risk of treatment failure using standard chemotherapy protocols

ABSTRACT: BACKGROUND: The mechanisms responsible for chemoresistance in patients with refractory classical Hodgkin lymphoma (CHL) are unknown. ATP-binding cassette (ABC) transporters confer multidrug resistance in various cancers and ABCC1 overexpression has been shown to contribute to drug resistance in the CHL cell line, KMH2. FINDINGS: We analyzed for expression of five ABC transporters ABCB1, ABCC1, ABCC2, ABCC3 and ABCG2 using immunohistochemistry in 103 pre-treatment tumor specimens obtained from patients with CHL. All patients received first-line standard chemotherapy with doxorubicin (Adriamycin(R)), bleomycin, vinblastine, and dacarbazine (ABVD) or equivalent regimens. ABCC1 was expressed in Hodgkin and Reed-Sternberg (HRS) cells in 16 of 82 cases (19.5%) and ABCG2 was expressed by HRS cells in 25 of 77 cases (32.5%), respectively. All tumors were negative for ABCB1, ABCC2 and ABCC3. ABCC1 expression was associated with refractory disease (p = 0.01) and was marginally associated with poorer failure-free survival (p = 0.06). Multivariate analysis after adjusting for hemoglobin and albumin levels and age showed that patients with CHL with HRS cells positive for ABCC1 had a higher risk of not responding to treatment (HR = 2.84, 95%, CI: 1.12-7.19 p = 0.028). CONCLUSIONS: Expression of ABCC1 by HRS cells in CHL patients predicts a higher risk of treatment failure and is marginally associated with poorer failure-free survival using standard frontline chemotherapy regimens.     

Comparisons of several dosages of a GnRH analog with the standard dose of hCG in the treatment of follicular cysts in dairy cows

Two experiments were carried out to examine therapeutic effect of a gonadotropin-releasing hormone analog, buserelin, on ovarian follicular cysts in dairy cows. Follicular cysts were diagnosed by palpation per rectum as well as by milk progesterone assay. Luteinization of the follicular cysts following treatment was judged by an increase in milk progesterone. In Experiment 1, 35 cows were diagnosed to have follicular cysts on the basis of palpations and low milk progesterone concentrations 1 week before treatment. Another 19 cows which were clinically diagnosed with follicular cysts but showed high milk progesterone levels before treatment were excluded. Sixty-two percent (11 18 ) of cows with follicular cysts treated with 20 mug of buserelin and 82% (14 17 ) of cows treated with 10,000 IU of human chorionic gonadotropin (hCG) showed luteinization of follicular cysts within 4 to 5 days after the treatments. The percentage of cows conceiving within 100 days after treatment and the average interval in days between treatment and conception were 44% and 42+/-18 (SD) days for the buserelin-treated cows and 47% and 42+/-18 days for the hCG-treated cows. In Experiment 2, the effects of treatment doses (6, 10, 20 and 30 mug of buserelin and 10,000 IU of hCG) on follicular cysts were compared using 103 cows. An additional 23 cows which were clinically diagnosed as having follicular cysts and which were given treatment showed a high milk progesterone concentration on the day of treatment and were therefore excluded. Fifty to 64% of the cows responded with luteinization of follicular cysts after treatment. There was no significant difference in response among cows given either the different dosages of buserelin or the hCG. However, the percentage of the total number of cows that conceived after a single or a repeated treatment with 6 mug buserelin was lower than that of cows after a single or a repeated treatment with 10 mug buserelin (P<0.05). An increase in the dose of buserelin from 10 to 30 mug did not improve the therapeutic effect of the drug. Thus, it is concluded that a single intramuscular injection of buserelin at a dose of 10 mug or higher is as effective as 10,000 IU hCG, and is, therefore, recommended for the treatment of ovarian follicular cysts in cows.     

Multiple testing to establish superiority/equivalence of a new treatment compared with k standard treatments for unbalanced designs

In clinical studies, multiple superiority/equivalence testing procedures can be applied to classify a new treatment as superior, equivalent (same therapeutic effect), or inferior to each set of standard treatments. Previous stepwise approaches (Dunnett and Tamhane, 1997, Statistics in Medicine16, 2489-2506; Kwong, 2001, Journal of Statistical Planning and Inference 97, 359-366) are only appropriate for balanced designs. Unfortunately, the construction of similar tests for unbalanced designs is far more complex, with two major difficulties: (i) the ordering of test statistics for superiority may not be the same as the ordering of test statistics for equivalence; and (ii) the correlation structure of the test statistics is not equi-correlated but product-correlated. In this article, we seek to develop a two-stage testing procedure for unbalanced designs, which are very popular in clinical experiments. This procedure is a combination of step-up and single-step testing procedures, while the familywise error rate is proved to be controlled at a designated level. Furthermore, a simulation study is conducted to compare the average powers of the proposed procedure to those of the single-step procedure. In addition, a clinical example is provided to illustrate the application of the new procedure.     

Total body irradiation for standard treatment rooms: a robust sweeping beam technique with respect to the body shape

BackgroundThe purpose of this work is to improve a sweeping beam technique for total body irradiation (TBI) on a low flat couch using a varying patient thickness model. We designed a flat couch for total body irradiation in supine and prone position. Three generic arcs with rectangular segments for a patient torso thickness of 16, 22 and 28 cm were generated with respect to varying patient thickness of four particular parts of the body: head, torso, thighs and calves.Materials and methodsLongitudinal and transversal dose profiles were measured using an ionization chamber and the EBT3 gafchromic film in a solid water slab phantom. The robustness of the method was examined in phantoms of different thicknesses.ResultsMeasured dose homogeneity stays within ±10% of prescribed dose for all of the three patient thickness models. The robustness of the method was evaluated as the increase in dose in the phantom center of 0.7% per 1 cm reduction in phantom thickness.ConclusionThe method is applicable for the broad range of patient sizes, comfortable for patients, robust and suitable for standard treatment rooms with a standard linear accelerator. It requires minimal investments into equipment.     

Surface charging by large multivalent molecules. Extending the standard Gouy-Chapman treatment.

Traditionally, Gouy-Chapman theory has been used to calculate the distribution of ions in the diffuse layer next to a charged surface. In recent years, the same theory has found application to adsorption (incorporation, partitioning) of charged peptides, hormones, or drugs at the membrane-water interface. Empirically it has been found that an effective charge, smaller than the physical charge, must often be used in the Gouy-Chapman formula. In addition, the large size of these molecules can be expected to influence their adsorption isotherms. To improve evaluation techniques for such experiments, comparatively simple extensions of the standard Gouy-Chapman formalism have been studied which are based on a discrete charge virial expansion. The model allows for the mobility of charged groups at the interface. It accounts for finite size of the adsorbed macromolecules and for discrete charge effects arising from pair interactions in the interface plane. In contrast to previous discrete charge treatments this model nearly coincides with the Gouy-Chapman formalism in the case where the adsorbing molecules are univalent. Large discrepancies are found for multivalent molecules. This could explain the reduced effective charges needed in the standard Gouy-Chapman treatment. The reduction factor can be predicted. The model is mainly limited to low surface coverage, typical for the adsorption studies in question.     

Structural modifications and thermal transitions of standard maize starch after DIC hydrothermal treatment

Standard maize starch was hydrothermally treated by Instantaneous Controlled Pressure Drop (DIC) process at three pressure levels (1, 2 and 3 bar) corresponding to the temperatures of 100, 122 and 135 °C (at 13–27% moisture), respectively. The structural effects of various hydrothermal conditions were examined with differential scanning calorimetry (DSC) and wide-angle X-ray diffraction. In order to understand the changes that occur during DIC treatment, melting endotherms of native maize starch at various moisture contents were determined. The gelatinization temperatures of DIC treated standard maize starch increased with DIC treatment. The transition temperatures (T_o, T_p) are closely related to the combined effect of pressure and processing time. At approximately 10 min of processing time, T_o and T_p were 65.7 and 72.3, 68.8 and 73.6 °C, 74.8 and 79.8 °C for pressure levels of 1, 2 and 3 bar, respectively (against 63.1 and 69.6 °C for native starch). DIC treatment narrowed the gelatinization temperature range and decreased gelatinization enthalpy (ΔH), as the severity of processing conditions increased. ΔH decreased from 11.4 J g⁻¹ (native) to 11.0 (1 bar), 9.0 (2 bar) and 1.7 J g⁻¹ (3 bar) for treated maize starch during approximately 10 min. Relative crystallinity of hydrothermally treated starch decreased with increasing DIC conditions. The A-type crystalline pattern was progressively lost (at pressure level 2 bar) and substituted by the V_h-type X-ray diffraction pattern, corresponding to the formation of amylose–lipid complexes. For severe DIC conditions (pressure level of 3 bar), the substitution was completed. Microscopic observations revealed progressive loss of the birefringence of DIC treated starch granules except at low pressure (1 bar), while the integrity of starch granules was preserved for all the conditions. These modifications that reveal important changes in the crystalline organization of the starch granules are related to their functional properties.     

Quantification of phosphoproteins with global internal standard technology

Global internal standard technology (GIST) is being developed for the quantification of all primary structure and post-translational variants of proteins in a proteome. This paper is directed at an analysis of phosphorylation, primarily of serine and threonine. Quantification was achieved by acylation of primary amino groups in peptide cleavage fragments of proteins with isotopically coded derivatizing agents. Peptides from controls were globally coded with an isotopically "light" form of the reagent while those from experimental samples were coded with a "heavy" form of the reagent. The two types coding reagents used in this work were N-hydroxyl succinimide derivatives of acetate and 4-trimethylammoniumbutyrate. Heavy isotope forms were produced by deuteration of methyl groups. Subsequent to coding and mixing, the two samples were passed through a Ga(III) immobilized metal affinity chromatography (IMAC) column and the selected peptide fraction was further resolved by reversed-phase chromatography (RPC) and analyzed by mass spectrometry (MS). Relative differences in phosphopeptide concentration between samples were derived from isotope ratio measurements of the peptide isoforms observed in mass spectra. The method was validated with model peptides.     

Dot-ELISA in detection of filarial antibodies: comparison with standard ELISA

The present study deals with the preliminary results of two assays, standard ELISA and dot ELISA compared for their sensitivity in measuring humoral immune responses in filarial patients and normals residing in an area of bancroftian filariasis using a heterologous antigen. Responses were more vigorous in filarial patients than in endemic normals by both assays. Higher percentage of positivity and reciprocal titre of antibody were observed in dot ELISA showing more sensitivity than the standard ELISA. The dot ELISA method required only nanogram amounts of antigen.     

Nonconformance of standard metabolic rate with body mass in Hawaiian Honeycreepers

Summary Among four species of Hawaiian Honeycreepers, three from Hawaii (Vestiaria coccinea, 15.0 g; Himatione sanguinea, 12.9 g; Loxops virens, 10.7 g) and one from Kauai (Loxops parva, 7.9 g), standard metabolic rate (in ml O₂/g·h) was positively related to body mass, the opposite of that predicted by conventional endothermic allometry. SMR of V. coccinea conformed to the predicted value, but in the remaining species was progressively reduced below expected levels as body mass decreased. All four species occur predominantly in Metrosideros collina forests, where their preferred food is the nectar of its blooms. At least on Hawaii and during periods of moderate bloom the species are aligned along a dominance hierarchy, with the largest species most dominant and most successful at nectar exploitation. I believe that nonconformancy of SMR with body mass in the smaller species reflects an energy-conserving measure, the degree of which is dictated by social position and relative success in nectar exploitation.