Statistical Optimization of Bioprocess Parameters for Improved Production of L-Asparaginase from Lactobacillus plantarum

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - L-asparaginase (ASNase), a tetrameric enzyme, holds comprehensive applications in food industries as a...     

In Vitro Selection of Turmeric Somaclone Resistant to Fusarium oxysporum f.sp. Zingiberi

Fusarium wilt disease tolerant clones of Curcuma longa L. cv. Suroma were isolated using continuous in vitro selection technique against pure culture filtrate of Fusarium oxysporum f.sp.zingiberi. In vitro shoot buds were challenged with pure culture filtrate of F. oxysporoum to isolate viable plants within 30 days of culture, which were further subjected to pure culture filtrate treatment. After four cycles of treatment, 15 cell lines, tolerant to culture filtrate were isolated through continuous in vitro selection and subcultured on Murashige and Skoog basal medium with Benzylaminopurine (3 mg/l) along with the control plants. Both tolerant and control plants were screened for disease tolerance by adopting in vitro sick plot technique. The data obtained from this experiment revealed a ratio of 188:68 tolerant: susceptible in vitro clones retrieved from tolerant plants. However, plants from T1a₁ and control were susceptible under in vitro sick plot technique. The Fusarium wilt disease tolerant clones were hardened and established in soil with 90 % survival frequency.     

Evaluations of shorter exposures of contact lens cleaning solutions against Fusarium oxysporum species complex and Fusarium solani species complex to simulate inappropriate usage

An outbreak of Fusarium keratitis in contact lens users resulted in withdrawal of ReNu with MoistureLoc solution, although the exact cause of the outbreak remains enigmatic. We evaluated current and discontinued multipurpose cleaning solutions (MPSs; MoistureLoc, Equate, MultiPlus, and OptiFree Express) against plankton- and biofilm-derived cells of Fusarium oxysporum species complex (FOSC) and F. solani species complex (FSSC). The methods included a traditional assay based on CFU counts and a novel flow cytometry (FC) assay based on percent cell subpopulation (PCS) stained with two fluorochromes (Sytox Red and 5-chloromethylfluorescein diacetate). The tests were done with the respective manufacturers' recommended cleaning regimens (240 to 360 min) and under shorter exposures (15 to 60 min) to simulate inappropriate usage by the customers. FC assay measured PCS, which was available rapidly, in 5 to 7 h, whereas 24 to 48 h was needed for CFU counts, and there was good correlation between the two methods (r2=0.97). FC assays allowed identification of injured fungal cells, which are likely to be missed with growth assays. In general, a time- and inoculum-dependent survival pattern was seen for both FOSC and FSSC cells, and biofilm-derived cells were more resistant than plankton-derived cells. MultiPlus and Equate produced 100% sterilization of fungi even under shorter exposures. However, biofilm FOSC and FSSC cells survived for up to 4 h in MoistureLoc solution and up to 6 h in OptiFree Express solution under shorter exposure times. This finding was enigmatic, as OptiFree Express is not associated with any outbreak of Fusarium keratitis. This study provides additional support for possible roles that improper lens cleaning regimens and fungal biofilms could play as predisposing factors for Fusarium keratitis.     

Optimization of Targeted Cell Replacement Therapy: A New Approach for Lung Disease

Cell replacement therapy is a promising approach for treatment of lung disease such as cystic fibrosis, although rates of engraftment need to be improved. We previously showed improved cell retention in the lung using transtracheal delivery compared to intravenous injection. Here, we optimized other parameters of cell delivery using 7-day cultured bone marrow cells (BMCs). Retention of BMC in the lung was dose-dependent. Naphthalene treatment had maximal effects on BMC retention when given 2 days before cell delivery. Naphthalene treatment of the donor amplified a CCSP⁺ population and increased retention efficiency in the recipient. Repeated naphthalene treatment and repeated cell delivery both resulted in greater retention. The contribution of the second cell dose was minimal suggesting that a second delivery of BMC promotes proliferation of the first. Busulfan-induced myelosuppression augmented retention of exogenous BMC by up to 20-fold. These BMC helped CCSP reconstitution. Using the optimal delivery techniques and cytokeratin-18-driven green fluorescent protein (GFP) reporter mice, we detected threefold more GFP suggesting more BMC differentiated to epithelial cells. We propose that improved engraftment in the lung will increase cell replacement and thus be a more efficient therapeutic approach for various lung diseases.     

An Optimization Approach to Signal Extraction from Noisy Multivariate Data

We consider a problem of blind signal extraction from noisy multivariate data, in which each datum represents a system's response, observed under a particular experimental condition. Our prototype example is multipixel functional images of brain activity in response to a set of prescribed experimental stimuli. We present a novel multivariate analysis technique, which identifies the different activity patterns (signals) that are attributable to specific experimental conditions, without a priori knowledge about the signal or the noise characteristics. The extracted signals, which we term the generalized indicator functions, are optimal in the sense that they maximize a weighted difference between the signal variance and the noise variance. With an appropriate choice of the weighting parameter, the method returns a set of images whose signal-to-noise ratios satisfy some user-defined level of significance. We demonstrate the performance of our method in optical intrinsic signal imaging of cat cortical area 17. We find that the method performs effectively and robustly in all tested data, which include both real experimental data and numerically simulated data. The method of generalized indicator functions is related to canonical variate analysis, a multivariate analysis technique that directly solves for the maxima of the signal-to-noise ratio, but important theoretical and practical differences exist, which can make our method more appropriate in certain situations.     

Research Fundamentals: Statistical Considerations in Research Design: A Simple Person's Approach

A basic understanding of statistical methodology is essential, both for designing quality research projects and for evaluating the medical literature. Careful statistical planning, including the selection of study endpoints, the determination of the required sample size, and the selection of statistical tests to be used in the data analysis, is important to ensure a successful research project. The purpose of this article is to provide a basic review of statistical terms and methods for both the researcher and the clinician, as well as to clarify questions that need to be answered prior to embarking on an experimental study. The advantages of collaborating with statistical consultants, and some guidelines for such collaborations, are discussed as well.     

Co-inoculation of an antibiotic-producing bacterium and a lytic enzyme-producing bacterium for the biocontrol of tomato wilt caused by Fusarium oxysporum f. sp. lycopersici

The antifungal compound 2,4-diacetylphloroglucinol-producing bacterium, Pseudomonas fluorescens strain LRB3W1, inhibits the growth of Fusarium oxysporum f. sp. lycopersici, and controls Fusarium wilt of tomato caused by F. oxysporum f. sp. lycopersici. On the other hand, Serratia marcescens strain B2, which produces cell wall-degrading enzyme chitinases, did not inhibit fungal growth and the suppressive effect of strain B2 against tomato Fusarium wilt was less than that of strain LRB3W1. Combined inoculation of strain LRB3W1 with strain B2 was more effective than treatment with strain LRB3W1 alone. When 2,4-diacetylphloroglucinol and the chitinolytic enzymes were applied in combination, a synergistic inhibitory effect against the pathogen was observed. It was possible that bacteria which produce cell wall-degrading enzymes enhanced the biocontrol effect of the antibiotic-producing bacterium against tomato Fusarium wilt.     

Statistical Optimization of Terminalia chebula Fruit Extraction for Improved Antibacterial Activity Against Odour-Causing Bacteria

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - The antibacterial effect of plant extract majorly depends on the process parameters of herbal extraction. In...     

消化酶制剂治疗消化不良的系统评价

目的系统评价不同消化酶制剂治疗消化不良的疗效、安全性及经济性。方法计算机检索PubMed、Cochrane图书馆临床对照试验资料库、CBM、VIP及CNKI等数据库,收集各种消化酶制剂治疗消化不良的随机对照试验(RCT),检索时限均从建库至2010年6月。按纳入标准选择文献、提取资料和进行方法学质量评价后,采用RevMan 5.0软件进行Meta分析。结果共纳入8个RCT,1 092例患者。文献质量为B级3个,C级5个。Meta分析结果显示:米曲菌胰酶片、复方消化酶胶囊、复方阿嗪米特肠溶片治疗各种原因引起的消化不良总症状有效率均优于安慰剂组或空白对照组[OR=49.70,95%CI(17.16,143.96),P<0.000 01;OR=7.71,95%CI(3.88,15.33),P<0.000 01;OR=16.27,95%CI(6.85,38.66),P<0.000 01],同时在治疗食欲不振、腹胀、腹痛、腹泻及嗳气等方面也优于安慰剂或空白对照组。米曲菌胰酶在治疗胆囊切除术后并发消化不良的总症状及各症状的疗效差于复方消化酶胶囊。复方阿嗪米特肠溶片与复方消化酶胶囊在治疗慢性胰腺炎化学性消化不良总症状的疗效方面无明显差异。此外,所有纳入研究均未报道与治疗药物相关的不良反应,也无相关经济学评价。结论各种消化酶制剂均可有效治疗各种原因引起的消化不良;与安慰剂或空白对照组的间接对照结果显示,米曲菌胰酶片的疗效优于其他消化酶制剂。     

Statistical Modeling for the Optimization of Bioluminescence Production by Newly Isolated Photobacterium sp. NAA-MIE

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - The utilization of bioluminescent bacteria has served as a powerful bioassay in environmental monitoring as a...     

Statistical feature extraction for artifact removal from concurrent fMRI-EEG recordings

We propose a set of algorithms for sequentially removing artifacts related to MRI gradient switching and cardiac pulsations from electroencephalography (EEG) data recorded during functional magnetic resonance imaging (fMRI). Special emphasis is directed upon the use of statistical metrics and methods for the extraction and selection of features that characterize gradient and pulse artifacts. To remove gradient artifacts, we use channel-wise filtering based on singular value decomposition (SVD). To remove pulse artifacts, we first decompose data into temporally independent components and then select a compact cluster of components that possess sustained high mutual information with the electrocardiogram (ECG). After the removal of these components, the time courses of remaining components are filtered by SVD to remove the temporal patterns phase-locked to the cardiac timing markers derived from the ECG. The filtered component time courses are then inversely transformed into multi-channel EEG time series free of pulse artifacts. Evaluation based on a large set of simultaneous EEG-fMRI data obtained during a variety of behavioral tasks, sensory stimulations and resting conditions showed excellent data quality and robust performance attainable with the proposed methods. These algorithms have been implemented as a Matlab-based toolbox made freely available for public access and research use.     

Quantile Regression: A Statistical Tool for Out-of-hospital Research

The performance of out-of-hospital systems is frequently evaluated based on the times taken to respond to emergency requests and to transport patients to hospital. The 90th percentile is a common statistic used to measure these indicators, since they reflect performance for most patients. Traditional regression models, which assess how the mean of a distribution varies with changes in patient or system characteristics, are thus of limited use to researchers in out-of-hospital care. In contrast, quantile regression models estimate how specified quantiles (or percentiles) of the distribution of the outcome variable vary with patient or system characteristics. The authors examined the performance of traditional linear regression vs. that of quantile regression to assess the association between hospital transport interval and patient and system characteristics. They demonstrate that richer inferences can be drawn from the data using quantile regression, utilizing data drawn from a study of ambulance diversion and out-of-hospital delay. The results demonstrate that the effect of ambulance diversion upon out-of-hospital transport intervals is not uniform, but is worse on the right tail of the distribution of transport intervals. In other words, ambulance diversion disproportionately affects those patients who already have longer transport intervals. Second, the distribution of transport intervals, conditional on a given set of variables, is positively skewed, and not uniformly or symmetrically distributed. The flexibility of quantile regression models makes them particularly well suited to out-of-hospital research, and they may allow for more relevant evaluation of out-of-hospital system performance.     

A Combined Molecular Approach to Screen for mec Gene Variants from Methicillin-resistant Staphylococcus aureus

Previous reports have suggested a common origin for all methicillin resistance (mec) genes from methicillin-resistant Staphylococcus aureus (MRSA) isolates examined so far. The purpose of this study was to explore several molecular methods for screening MRSA isolates from different sources and, in some cases, with varying phenotypes. Eighty MRSA isolates from three teaching hospitals in the University of Louisville Medical Center were compared with MRSAs from a hospital in southern California and with methicillin-sensitive S. aureus isolates. The methods were used to detect the presence of mec gene and to screen for any polymorphisms in these genes for the respective strains. The mec gene for each isolate was amplified via the polymerase chain reaction, and each polymerase chain reaction product was compared to the others by restriction enzyme digestion, denaturing-gradient gel electrophoresis, and mutation detection enhancement. By these criteria, the mec genes from the 80 MRSA strains in this study seemed to be identical. Such a finding was not unexpected and supported the existing hypothesis of a common ancestor for all mec genes isolated in MRSA isolates. However, the combination of methods used in this study may facilitate screening of MRSA strains in population studies as mec gene variants begin to emerge.     

酶免疫法对沙眼衣原体诊断价值的Meta分析

目的系统评价酶免疫法诊断沙眼衣原体的准确性。方法计算机检索PubMed（1966～2011．12）、TheCochraneLibrary（2011．12）、EMbase（1974～2011．12）、CNKI（1994—2011．12）、VIP（1989—2011．12）和CBM（1978—2011．12）,并辅助手工检索和其他检索,收集EIA诊断沙眼衣原体的试验研究。由两名评价者依据QUADAS质量评价标准评价纳入研究的质量后,采用MetaAnalyst和RevMan5．0软件进行Meta分析。结果最终共纳入17个研究,9461例受试者。Meta分析结果显示：酶免疫法诊断沙眼衣原体的合并敏感度、特异度、阳性似然比、阴性似然比、诊断比值比和SROC曲线下面积分别为O．847[95％CI（O．571,O．995）]、0．964[95％CI（0．890,0．994）j、25．972195％CI（18．587,36．293）j、0．156[95％CI（0．114,0．212）j、228．875[95％CI（127．136,412．028）]和0．953。结论酶免疫法对诊断沙眼衣原体具有较高的敏感度和特异度,推荐酶免疫法用于沙眼衣原体的初筛及确诊高度疑似病例或症状体征不明显的患者。     

Cognitive-Behavioral Therapy for Migraine Headaches: A Minimal-Therapist-Contact Approach Versus a Clinic-Based Approach

The efficacy of a clinic-based cognitive-behavioral program for the treatment of common migraine was compared to the same approach using a minimal-therapist-contact format by means of a randomized controlled trial. Forty-eight subjects between 18 and 50 years of age completed the program. Following four weeks of recording headache activity, subjects were randomly assigned to a waiting list control condition or to one of the two treatment conditions. Treatment was followed by four weeks of recording of headache activity immediately posttreatment and again six months later. Multivariate analysis of variance indicated that there was a significant reduction in headache frequency, duration and peak intensity following treatment for both treated groups. These reductions were maintained at six months follow-up. Treatment for the minimal-contact group was significantly more cost-effective than for the clinic group.     

Statistical 4D graphs for multi-organ abdominal segmentation from multiphase CT

The interpretation of medical images benefits from anatomical and physiological priors to optimize computer-aided diagnosis applications. Diagnosis also relies on the comprehensive analysis of multiple organs and quantitative measures of soft tissue. An automated method optimized for medical image data is presented for the simultaneous segmentation of four abdominal organs from 4D CT data using graph cuts. Contrast-enhanced CT scans were obtained at two phases: non-contrast and portal venous. Intra-patient data were spatially normalized by non-linear registration. Then 4D convolution using population training information of contrast-enhanced liver, spleen and kidneys was applied to multiphase data to initialize the 4D graph and adapt to patient-specific data. CT enhancement information and constraints on shape, from Parzen windows, and location, from a probabilistic atlas, were input into a new formulation of a 4D graph. Comparative results demonstrate the effects of appearance, enhancement, shape and location on organ segmentation. All four abdominal organs were segmented robustly and accurately with volume overlaps over 93.6% and average surface distances below 1.1mm.     

Enzyme replacement therapy for Fabry disease: lessons from two alpha-galactosidase A orphan products and one FDA approval

Two virtually identical products have been developed for enzyme replacement therapy for the treatment of Fabry disease, which is a rare and debilitating genetic disease caused by decreased activity of the lysosomal enzyme alpha-galactosidase A. Lack of this enzyme results in progressive tissue accumulation of globotriaosylceramide (GL-3), resulting in life-threatening renal, cardiac and cerebrovascular complications. Both enzyme replacement products, agalsidase alfa (Replagal; Transkaryotic Therapies, Cambridge, MA, USA) and agalsidase beta (Fabrazyme; Genzyme Corporation, Cambridge, MA, USA), were approved by the European Agency for the Evaluation of Medicinal Products in 2001; agalsidase alfa at a recommended dose of 0.2 mg/kg and agalsidase beta at a recommended dose of 1 mg/kg. In the US, however, orphan drug laws dictated that only one of these products could be approved. In April 2003, after a rigorous evaluation of both products by the US FDA, this approval was granted to agalsidase beta. This decision reflected clinical trial design, how dosages were determined, antibody effects and the ability of each product to demonstrate either clinical efficacy or reduction of tissue storage of GL-3 in major organs of pathology when administered at the recommended dosage. The process also highlighted important issues in the evaluation of drugs to treat life-threatening genetic diseases for which the pathological basis is well-defined.