Hierarchical Re-estimation of Topic Models for Measuring Topical Diversity

A high degree of topical diversity is often considered to be an important characteristic of interesting text documents. A recent proposal for measuring topical diversity identifies three elements for assessing diversity: words, topics, and documents as collections of words. Topic models play a central role in this approach. Using standard topic models for measuring diversity of documents is suboptimal due to generality and impurity. General topics only include common information from a background corpus and are assigned to most of the documents in the collection. Impure topics contain words that are not related to the topic; impurity lowers the interpretability of topic models and impure topics are likely to get assigned to documents erroneously. We propose a hierarchical re-estimation approach for topic models to combat generality and impurity; the proposed approach operates at three levels: words, topics, and documents. Our re-estimation approach for measuring documents' topical diversity outperforms the state of the art on PubMed dataset which is commonly used for diversity experiments.Comment: Proceedings of the 39th European Conference on Information Retrieval (ECIR2017

Studies on the quantitative and qualitative characters of cocoons and silk from methoprene and fenoxycarb treated Bombyx mori (L) larvae

Juvenile hormone analogues (JHA s) are known to prolong larval life in insects, and these have been tried for the improvement of silk production in the silkworm, Bombyx mori (L). In the cocoons and silk from 5thinstar B. mori treated with selected doses of methoprene and fenoxycarb, quantitative parameters like cocoon weight, shell weight, shell percentage, filament length and denier followed by qualitative charactersof the silk like non-breakable filament length, reelability, winding capacity, tenacity, elongation percentage, cohesiveness, sericin and fibroin contents were determined. The cocoon from 1.0 mg methoprene and 3.0fg/larvae treated on days one and two showed improved quantitative characters of cocoons followed by qualitative characters of the silk over the control. The use of juvenile hormone like methprene and fenoxycarb during summer season will help to get improved cocoon yiel

Fermentatative production of itaconic acid by Aspergillus terreus using Jatropha seed cake

Fermentation process for the production of itaconic acid was carried out using jatropha seed cake. Itaconic acid is commercially produced by the cultivation of Aspergillus terreus with molasses. Jatropha seed cake is one of the best carbon sources among various carbohydrates, because it is pure, inexpensive and available in a mass supply. The reaction was carried out at various temperatures, agitations and pH. The samples were collected at 24 h time intervals. Itaconic acid concentration wasmeasured by the rapid spectroscopic method. Jatropha seed cake shows maximum yield of 24.45g/lafter 120 h

A standing-wave thermoacoustic engine driven by liquid nitrogen

Thermoacoustic oscillation at cryogenic temperatures, such as Taconis oscillation, has been typically suppressed in the former studies, and few efforts have been made to enhance it. We proposed a standing-wave thermoacoustic engine (TE) driven by liquid cryogens instead of the conventional heat to enhance the thermoacoustic effects and utilize the cold energy. Experimental and theoretical work has been performed on a self-made standingwave TE to demonstrate the feasibility and the operating characteristics of the engine driven by the liquid nitrogen. Experiments show that with nitrogen at 0.5 MPa as a working gas, a pressure ratio of 1.21 is obtained on the TE driven by liquid nitrogen with a much lower temperature difference along the stack compared to that of the conventional TE. The onset temperature difference decreases by 28.9% with helium at 0.63 MPa as a working gas, compared to that of the conventional TE. This study verifies the feasibility of enhancing the thermoacoustic oscillation at cryogenic temperatures. The TEs driven by liquid cryogens such as liquid nitrogen and liquefied nature gas (LNG), may be an alternative for recovering the cold energy

Microcystic cyanobacteria extract induces cytoskeletal disruption and intracellular glutathione alteration in hepatocytes.

Microcystins are a group of highly liver-specific toxins, although their exact mechanisms of action remain unclear. We examined the effects of microcystic cyanobacteria extract (MCE) collected from a contaminated water source on the organization of cellular microtubules (MTs) and microfilaments (MFs) in hepatocytes. We also investigated the effects on lactate dehydrogenase (LDH) leakage and intracellular glutathione (GSH). Primary cultured rat hepatocytes exposed to MCE (equivalent to 125 microg/mL lyophilized algae cells) showed a characteristic disruption of MTs and MFs in a time-dependent manner. Under these conditions, MCE caused aggregation of MTs and MFs and a severe loss of MTs in some cells. Moreover, MCE-induced cytoskeletal alterations preceded the LDH leakage. On the other hand, the treatment of cells with MCE led to a dose-dependent increase of intracellular GSH. However, time-course study showed a biphasic change of intracellular GSH levels with a significant increase in the initial stage followed by a decrease after prolonged treatment. Furthermore, pretreatment with N-acetylcystein (NAC), a GSH precursor, significantly enhanced the intracellular GSH level and decreased the MCE-induced cytotoxicity as well as cytoskeleton changes. In contrast, buthionine-(S, R)-sulfoximine, a specific GSH synthesis inhibitor, increased the cell susceptibility to MCE-induced cytotoxicity by depleting the intracellular GSH level. These findings suggest that intracellular GSH plays an important role in MCE-induced cytotoxicity and cytoskeleton changes in primary cultured rat hepatocytes. Increasing intracellular GSH levels protect cells from MCE-induced cytotoxicity and cytoskeleton changes

Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy

Background: Urine proteome analysis is rapidly emerging as a tool for diagnosis and prognosis in disease states. For diagnosis of diabetic nephropathy (DN), urinary proteome analysis was successfully applied in a pilot study. The validity of the previously established proteomic biomarkers with respect to the diagnostic and prognostic potential was assessed on a separate set of patients recruited at three different European centers. In this case-control study of 148 Caucasian patients with diabetes mellitus type 2 and duration >= 5 years, cases of DN were defined as albuminuria >300 mg/d and diabetic retinopathy (n = 66). Controls were matched for gender and diabetes duration (n = 82). Methodology/Principal Findings: Proteome analysis was performed blinded using high-resolution capillary electrophoresis coupled with mass spectrometry (CE-MS). Data were evaluated employing the previously developed model for DN. Upon unblinding, the model for DN showed 93.8% sensitivity and 91.4% specificity, with an AUC of 0.948 (95% CI 0.898-0.978). Of 65 previously identified peptides, 60 were significantly different between cases and controls of this study. In <10% of cases and controls classification by proteome analysis not entirely resulted in the expected clinical outcome. Analysis of patient's subsequent clinical course revealed later progression to DN in some of the false positive classified DN control patients. Conclusions: These data provide the first independent confirmation that profiling of the urinary proteome by CE-MS can adequately identify subjects with DN, supporting the generalizability of this approach. The data further establish urinary collagen fragments as biomarkers for diabetes-induced renal damage that may serve as earlier and more specific biomarkers than the currently used urinary albumin

Estimating Small Area Income Deprivation: An Iterative Proportional Fitting Approach

Small area estimation and in particular the estimation of small area income deprivation has potential value in the development of new or alternative components of multiple deprivation indices. These new approaches enable the development of income distribution threshold based as opposed to benefit count based measures of income deprivation and so enable the alignment of regional and national measures such as the Households Below Average Income with small area measures. This paper briefly reviews a number of approaches to small area estimation before describing in some detail an iterative proportional fitting based spatial microsimulation approach. This approach is then applied to the estimation of small area HBAI rates at the small area level in Wales in 2003-5. The paper discusses the results of this approach, contrasts them with contemporary ‘official’ income deprivation measures for the same areas and describes a range of ways to assess the robustness of the results

Chronic NMDA administration to rats increases brain pro-apoptotic factors while decreasing anti-Apoptotic factors and causes cell death

<p>Abstract</p> <p>Background</p> <p>Chronic <it>N</it>-Methyl-d-aspartate (NMDA) administration to rats is reported to increase arachidonic acid signaling and upregulate neuroinflammatory markers in rat brain. These changes may damage brain cells. In this study, we determined if chronic NMDA administration (25 mg/kg i.p., 21 days) to rats would alter expression of pro- and anti-apoptotic factors in frontal cortex, compared with vehicle control.</p> <p>Results</p> <p>Using real time RT-PCR and Western blotting, chronic NMDA administration was shown to decrease mRNA and protein levels of anti-apoptotic markers Bcl-2 and BDNF, and of their transcription factor phospho-CREB in the cortex. Expression of pro-apoptotic Bax, Bad, and 14-3-3ζ was increased, as well as Fluoro-Jade B (FJB) staining, a marker of neuronal loss.</p> <p>Conclusion</p> <p>This alteration in the balance between pro- and anti-apoptotic factors by chronic NMDA receptor activation in this animal model may contribute to neuronal loss, and further suggests that the model can be used to examine multiple processes involved in excitotoxicity.</p

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation

Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium _Escherichia coli_, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the _in vivo_ MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally