Analysis of DNMT1 gene variants in progression of neural tube defects-an in silico to in vitro approach.

Neural tube defects (NTDs) are significant congenital deformities of the central nervous system among which spina bifida is the most common form that occurs due to defect in the neurulation process of embryogenesis. NTDs are among the most common type of birth defects occurring at a range of 0.5-10 in every 1000 live births worldwide and are thought to have multifactorial etiology, including multigenetic and epigenetic notions. Epigenetic regulations control differential gene expression in normal and disease phenotypes. DNA methylation is a significant epigenetic process, guided by DNMT1, one of the most important maintenance methylating agents. However, the relationship between DNMT1 and NTDs had always been inconclusive and poorly understood. In the present study, by utilizing in silico methodologies we tried to figure out potent single nucleotide variants (SNVs) that could play roles in generating functional differences in DNMT1 expression and we also tried to check (by in vitro method) if there is any connection between DNMT1 expression and spina bifida condition. A number of coding and non-coding (both intragenic and intergenic) SNVs of DNMT1 were found (using the in silico methods) that have potentials to alter its expression. From the in vitro experimentations, differential DNMT1 RNA expressions were found between spina bifida affected newborns and their respective mothers when compared with controls. It is the first report of NTD from Eastern India precisely showing inverse correlation between DNMT1 expression and occurrence of NTD. The findings of the present study could be further considered for early prognosis and future experimental designs.

Remediating textbook deficiencies by leveraging community question answers.

The paper presents a method for recommending augmentations against conceptual gaps in textbooks. Question Answer (QA) pairs from community question-answering (cQA) forums are noted to offer precise and comprehensive illustrations of concepts. Our proposed method retrieves QA pairs for a target concept to suggest two types of augmentations: basic and supplementary. Basic augmentations are suggested for the concepts on which a textbook lacks fundamental references. We identified such deficiencies by employing a supervised machine learning-based approach trained on 12 features concerning the textbook's discourse. Supplementary augmentations aiming for additional references are suggested for all the concepts. Retrieved QA pairs were filtered to ensure their comprehensiveness for the target students. The proposed augmentation system was deployed using a web-based interface. We collected 28 Indian textbooks and manually curated them to create gold standards for assessing our proposed system. Analyzing expert opinions and adopting an equivalent pretest-posttest setup for the students, the quality of these augmentations was quantified. We evaluated the usability of the interface from students' responses. Both system and human-based evaluations indicated that the suggested augmentations addressed the concept-specific deficiency and provided additional materials to stimulate learning interest. The learning interface was easy-to-use and showcased these augmentations effectively.

Dichotomy in Growth and Invasion from Low- to High-Grade Glioma Cellular Variants.

Glial dysfunction outraging CNS plasticity and integrity results in one of the most dangerous cancers, namely glioma, featuring little median survival period and high recurrence. The hallmark properties of proliferation, invasion and angiogenesis with the infiltrated macrophages in glioma are expected to be tightly coupled or cross-linked, but not properly related so far. The present study is aimed to find a relationship between this featured quadrangle from lower to higher grades (HG) of post-operative glioma tissues and their invading subsets. Elevated Ki67-associated proliferation in lower grades (LG) was supported with VEGF dependent angiogenic maintenance which found a decrease unlikely in HG. In contrast, MMP 2 and 9-associated invasions augmented high in HG with the dominant presence of CD204+ M2 polarized macrophages and a general increase in global DNMT1-associated methylation. Marked differences found in ECM invading cellular subsets of HG showing high proliferative capacity indicating rationally for recurrence, contrasting the nature of gross tumor tissue of the same grade. Thus in LG, the neoplastic lesion is more inclined to its growth while in higher grade more disposed towards tissue wreckage in support with cellular environmental milieu whereas the cellular variants and subsets of invaded cells showed different trends. Therefore, some operational dichotomy or coupling among cellular variants in glioma is active in determining its low- to high-grade transition and aggressive progression.

Quantifying and visualizing site performance in clinical trials.

BACKGROUND: One of the keys to running a successful clinical trial is the selection of high quality clinical sites, i.e., sites that are able to enroll patients quickly, engage them on an ongoing basis to prevent drop-out, and execute the trial in strict accordance to the clinical protocol. Intuitively, the historical track record of a site is one of the strongest predictors of its future performance; however, issues such as data availability and wide differences in protocol complexity can complicate interpretation. Here, we demonstrate how operational data derived from central laboratory services can provide key insights into the performance of clinical sites and help guide operational planning and site selection for new clinical trials. METHODS: Our methodology uses the metadata associated with laboratory kit shipments to clinical sites (such as trial and anonymized patient identifiers, investigator names and addresses, sample collection and shipment dates, etc.) to reconstruct the complete schedule of patient visits and derive insights about the operational performance of those sites, including screening, enrollment, and drop-out rates and other quality indicators. This information can be displayed in its raw form or normalized to enable direct comparison of site performance across studies of varied design and complexity. RESULTS: Leveraging Covance's market leadership in central laboratory services, we have assembled a database of operational metrics that spans more than 14,000 protocols, 1400 indications, 230,000 unique investigators, and 23 million patient visits and represents a significant fraction of all clinical trials run globally in the last few years. By analyzing this historical data, we are able to assess and compare the performance of clinical investigators across a wide range of therapeutic areas and study designs. This information can be aggregated across trials and geographies to gain further insights into country and regional trends, sometimes with surprising results. CONCLUSIONS: The use of operational data from Covance Central Laboratories provides a unique perspective into the performance of clinical sites with respect to many important metrics such as patient enrollment and retention. These metrics can, in turn, be used to guide operational planning and site selection for new clinical trials, thereby accelerating recruitment, improving quality, and reducing cost.

Microglial Contribution to Glioma Progression: an Immunohistochemical Study in Eastern India.

Human glioma, arising from glial cells of the central nervous system, accounts for almost 30%of all brain tumours , neoplasms with a poor prognosis and high mortality rates worldwide. In the present study we assessed tissue architectural modifications associated with macrophage lineage cells, controversial major immune effector cells within the brain, in human glioma tissue samples from eastern India. Ethically cleared post-operative human glioma samples from our collaborative neurosurgery unit with respective CT/MRI and patient history were collected from the Nodal Centre of Neurosciences in Kolkata, over 9 months. Along with conventional histopathology, samples were subjected to silver-gold staining and fluorescence tagged immunophenotyping for the detection of electron dense brain macrophage/microglia cells in glioma tissue, followed by immune-phenotyping of cells. With higher grades, CD11b+/Iba-1+ macrophage/microglia architecture with de-structured boundaries of glioma lesions indicated malfunction and invasive effector state. Present study documented a contribution of microglia to glioma progression in Eastern India.

Reliability and Validity of Prototype Diagnosis for Adolescent Psychopathology.

The current study investigated the interrater reliability and validity of prototype ratings of 5 common adolescent psychiatric disorders: attention-deficit/hyperactivity disorder, conduct disorder, major depressive disorder, generalized anxiety disorder, and posttraumatic stress disorder. One hundred fifty-seven adolescent inpatient participants consented to participate in this study. We compared ratings from 2 inpatient clinicians, blinded to each other's ratings and patient measures, after their separate initial diagnostic interview to assess interrater reliability. Prototype ratings completed by clinicians after their initial diagnostic interview with adolescent inpatients and outpatients were compared with patient-reported behavior problems and parents' report of their child's behavioral problems. Prototype ratings demonstrated good interrater reliability. Clinicians' prototype ratings showed predicted relationships with patient-reported behavior problems and parent-reported behavior problems. Prototype matching seems to be a possible alternative for psychiatric diagnosis. Prototype ratings showed good interrater reliability based on clinicians unique experiences with the patient (as opposed to video-/audio-recorded material) with no training.

Prospective microglia and brain macrophage distribution pattern in normal rat brain shows age sensitive dispersal and stabilization with development.

The monocytic lineage cells in brain, generally speaking brain macrophage and/or microglia show some dissimilar distribution patterns and disagreement regarding their origin and onset in brain. Here, we investigated its onset and distribution/colonization pattern in normal brain with development. Primarily, early and late embryonic stages, neonate and adult brains were sectioned for routine H/E staining; a modified silver-gold staining was used for discriminating monocytic lineage cells in brain; and TEM to deliver ultramicroscopic details of these cells in brain. Immunofluorescence study with CD11b marker revealed the distribution of active microglia/macrophage like cells. Overall, in early embryonic day 12, the band of densely stained cells are found at the margin of developing ventricles and cells sprout from there dispersed towards the outer edge. However, with development, this band shrunk and the dispersion trend decreased. The deeply stained macrophage like cell population migration from outer cortex to ventricle observed highest in late embryonic days, continued with decreased amount in neonates and settled down in adult. In adult, a few blood borne macrophage like cells were observed through the vascular margins. TEM study depicted less distinguishable features of cells in brain in early embryo, whereas from late embryo to adult different neuroglial populations and microglia/macrophages showed distinctive features and organization in brain. CD11b expression showed some similarity, though not fully, with the distribution pattern depending on the differentiation/activation status of these macrophage lineage cells. This study provides some generalized spatial and temporal pattern of macrophage/microglia distribution in rat brain, and further indicates some intrigue areas that need to be addressed.

Formal modeling of a system of chemical reactions under uncertainty.

We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

Construct validity of the Schwartz Outcome Scale: validation using a 28-day inpatient chemical rehabilitation patient sample.

The Schwartz Outcome Scale-10 (SOS-10) is a 10-item self-report that measures quality of life and psychological well-being. It is easy to administer and score, and past research has revealed its utility, validity, and reliability with different samples (i.e., clinical and nonclinical) and in different clinical settings (i.e., inpatient, outpatient, nonpsychiatry medical settings). The present study looks to investigate the utility of the SOS-10 in measuring psychological well-being and quality of life with the 28-day inpatient chemical dependency sample. In addition, the current study looks to investigate its ability to be used as a treatment outcome measure for chemical-dependent inpatients. The results revealed that the SOS-10 was associated with aspects of interpersonal dependency and alexithymia in predicted ways. The SOS-10 was positively associated to "Healthy Dependence" and negatively related to alexithymia and "Destructive Overdependence" and "Dysfunctional Detachment." The results also showed that the SOS-10 showed healthy change from admission to discharge and that this change was paralleled by healthy change in interpersonal dependency and alexithymia.

Quality-by-design case study: investigation of the role of poloxamer in immediate-release tablets by experimental design and multivariate data analysis.

The role of poloxamer 188, water and binder addition rate, on retarding dissolution in immediate-release tablets of a model drug from BCS class II was investigated by means of multivariate data analysis (MVDA) combined with design of experiments (DOE). While the DOE analysis yielded important clues into the cause-and-effect relationship between the responses and design factors, multivariate data analysis of the 40+ variables provided additional information on slowdown in tablet dissolution. A steep dependence of both tablet dissolution and disintegration on the poloxamer and less so on other design variables was observed. Poloxamer was found to increase dissolution rates in granules as expected of surfactants in general but retard dissolution in tablets. The unexpected effect of poloxamer in tablets was accompanied by an increase in tablet-disintegration-time-mediated slowdown of tablet dissolution and by a surrogate binding effect of poloxamer at higher concentrations. It was additionally realized through MVDA that poloxamer in tablets either acts as a binder by itself or promotes binder action of the binder povidone resulting in increased intragranular cohesion. Additionally, poloxamer was found to mediate tablet dissolution on stability as well. In contrast to tablet dissolution at release (time zero), poloxamer appeared to increase tablet dissolution in a concentration-dependent manner on accelerated open-dish stability. Substituting polysorbate 80 as an alternate surfactant in place of poloxamer in the formulation was found to stabilize tablet dissolution.

Alzheimer's disease - not an exaggeration of healthy aging.

The world population is becoming older now. The boom of the elderly population comes from public health efforts to improve living conditions and prevent disease, and from improved medical interventions. People more than 65-year-old who are representing 12.9% of the population now is expected to grow to be 19% of the population by 2030. Very few numbers of diseases will have such socioeconomic burden on society in the newer world. Although Alzheimer's disease (AD) has been studied very well recently, still its exact etiopathogenesis is unknown. Currently there are no available tests for the definitive diagnosis of AD. So the clinical diagnosis of AD remains a diagnosis of exclusion. This limits the potential for early intervention. The difference between normal degenerative processes of brain and preclinical changes of AD is a gray zone and there is no particular way to distinguish between the two. Now several modalities like functional magnetic resonance imaging (fMRI), positron emission tomography (PET) scan, electrophysiological tests and cerebrospinal fluid (CSF) biomarkers for tauopathy and Aß have shown to be promising in the development of early diagnostic tools for neurodegenerative changes and help us to differentiate between healthy aging and pathological aging. In this article we tried to discuss about the differences between pathological and physiological aging process from radiological, pathological, biochemical, and electrophysiological point of view. However, differentiating between physiological and pathological dementia still remains a challenge.

A Quality by Design approach to investigate tablet dissolution shift upon accelerated stability by multivariate methods.

This paper presents the use of experimental design, optimization and multivariate techniques to investigate root-cause of tablet dissolution shift (slow-down) upon stability and develop control strategies for a drug product during formulation and process development. The effectiveness and usefulness of these methodologies were demonstrated through two application examples. In both applications, dissolution slow-down was observed during a 4-week accelerated stability test under 51°C/75%RH storage condition. In Application I, an experimental design was carried out to evaluate the interactions and effects of the design factors on critical quality attribute (CQA) of dissolution upon stability. The design space was studied by design of experiment (DOE) and multivariate analysis to ensure desired dissolution profile and minimal dissolution shift upon stability. Multivariate techniques, such as multi-way principal component analysis (MPCA) of the entire dissolution profiles upon stability, were performed to reveal batch relationships and to evaluate the impact of design factors on dissolution. In Application II, an experiment was conducted to study the impact of varying tablet breaking force on dissolution upon stability utilizing MPCA. It was demonstrated that the use of multivariate methods, defined as Quality by Design (QbD) principles and tools in ICH-Q8 guidance, provides an effective means to achieve a greater understanding of tablet dissolution upon stability.

Genomics Portals: integrative web-platform for mining genomics data.

BACKGROUND: A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. RESULTS: Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. CONCLUSION: The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Quality by design case study: an integrated multivariate approach to drug product and process development.

To facilitate an in-depth process understanding, and offer opportunities for developing control strategies to ensure product quality, a combination of experimental design, optimization and multivariate techniques was integrated into the process development of a drug product. A process DOE was used to evaluate effects of the design factors on manufacturability and final product CQAs, and establish design space to ensure desired CQAs. Two types of analyses were performed to extract maximal information, DOE effect & response surface analysis and multivariate analysis (PCA and PLS). The DOE effect analysis was used to evaluate the interactions and effects of three design factors (water amount, wet massing time and lubrication time), on response variables (blend flow, compressibility and tablet dissolution). The design space was established by the combined use of DOE, optimization and multivariate analysis to ensure desired CQAs. Multivariate analysis of all variables from the DOE batches was conducted to study relationships between the variables and to evaluate the impact of material attributes/process parameters on manufacturability and final product CQAs. The integrated multivariate approach exemplifies application of QbD principles and tools to drug product and process development.

Application of robotics to steady state enzyme kinetics: analysis of tight-binding inhibitors of dipeptidyl peptidase IV.

Using available commercial robotics and instrumentation, we developed a fully automated and rigorous steady state enzyme kinetic assay for dipeptidyl peptidase IV (DPP IV; E.C. 3.4.14.5). The automated assay was validated with isoleucyl thiazolidide, a potent inhibitor of DPP IV with K(is)=110nM. Signal window analysis indicated that the assay had a 98% probability of detecting an inhibitor yielding 15% inhibition, with a predicted false positive rate of 0.13%. A mechanistic inhibition version of the automated assay was validated with isoleucyl 4-cyanothiazolidide, a very potent inhibitor of DPP IV. Isoleucyl 4-cyanothiazolidide was a competitive inhibitor of purified porcine DPP IV with K(is)=1 nM. Similar K(is) values were obtained for purified rat DPP IV and for DPP IV activity in human plasma from normal and diabetic donors. The pH dependence of K(is) for isoleucyl 4-cyanothiazolidide yielded a bell-shaped profile, with pK(a)=5.0 and pK(b)=7.6. To date, over 100,000 data points have been generated in profiling targeted compound libraries and in the analysis of tight-binding inhibitors of DPP IV. The data also show that robotic analysis is capable of producing full mechanistic inhibition analysis in a timely fashion to support drug discovery.