Gene Expression Induced by Cerebral Ischemia: An Apoptotic Perspective

The flow of new information on gene expression related to apoptosis has been relentless in the last several years. This has also been the case with respect to gene expression after cerebral ischemia. Many of genes associated with an apoptotic mode of cell death have now been studied in the context of experimental cerebral ischemia from the immediate early genes through modulating genes such as bcl-2 to genes in the final execution phase such as interleukin-1β converting enzyme (ICE)-related proteases. It was impossible to adequately cite all primary reports on these subjects. However, many excellent reviews have appeared in the last year, which together, cover all these areas of interest. In this review, we have elected to cite only reports published since January 1996 and use an extensive collection of reviews (indicated in italics) to guide the reader to the earlier literature. Our intent is to provide the reader with a timely and useful analysis of the current state of the art. It is hoped that this approach does not cause offense with our colleagues whose contributions before 1996 laid the foundation for much of this work.

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ON THE HARDNESS OF THE BORDER LENGTH MINIMIZATION PROBLEM ON A RECTANGULAR ARRAY

International Journal of Foundations of Computer Science ◽

10.1142/s0129054110007751 ◽

2010 ◽

Vol 21 (06) ◽

pp. 1089-1100 ◽

Cited By ~ 1

Author(s):

VAMSI KUNDETI ◽

SANGUTHEVAR RAJASEKARAN

Keyword(s):

Gene Expression ◽

Expression Profiling ◽

State Of The Art ◽

Combinatorial Problem ◽

Np Hard ◽

Microarray Technology ◽

Rectangular Grid ◽

Rectangular Array ◽

Current State ◽

Invaluable Tool

DNA microarray technology has proven to be an invaluable tool for molecular biologists. Microarrays are used extensively in SNP detection, genomic hybridization, alternative splicing and gene expression profiling. However the manufacturers of the microarrays are often stuck with the problem of minimizing the effects of unwanted illumination (border length minimization (BLM)) which is a hard combinatorial problem. In this paper we prove that the BLM problem on a rectangular grid is NP-hard – this however does not mean the BLM problem on a square grid is NP-hard. We also give the first integer linear programming (ILP) formulation to solve BLM problem optimally. Experimental results indicate that our ILP method produces superior results (both in runtime and cost) compared to the current state of the art algorithms to solve the BLM problem optimally.

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Sonoporation: Underlying Mechanisms and Applications in Cellular Regulation

BIO Integration ◽

10.15212/bioi-2020-0028 ◽

2021 ◽

Author(s):

Yue Li ◽

Zhiyi Chen ◽

Shuping Ge

Keyword(s):

Gene Expression ◽

Cell Membrane ◽

State Of The Art ◽

Cellular Functions ◽

Cellular Regulation ◽

Current State ◽

Cellular Apoptosis ◽

Ultrasonic Parameters ◽

Or Gene ◽

Underlying Mechanisms

Ultrasound combined with microbubble-mediated sonoporation has been applied to enhance drug or gene intracellular delivery. Sonoporation leads to the formation of openings in the cell membrane, triggered by ultrasound-mediated oscillations and destruction of microbubbles. Multiple mechanisms are involved in the occurrence of sonoporation, including ultrasonic parameters, microbubbles size, and the distance of microbubbles to cells. Recent advances are beginning to extend applications through the assistance of contrast agents, which allow ultrasound to connect directly to cellular functions such as gene expression, cellular apoptosis, differentiation, and even epigenetic reprogramming. In this review, we summarize the current state of the art concerning microbubble–cell interactions and sonoporation effects leading to cellular functions.

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Tooth Enamel: Current State of the Art

Journal of Dental Research ◽

10.1177/002203457905800220011 ◽

1979 ◽

Vol 58 (2_suppl) ◽

pp. 684-694 ◽

Cited By ~ 25

Author(s):

R.M. Frank

Keyword(s):

State Of The Art ◽

Tooth Enamel ◽

Predominant Role ◽

Growth Structure ◽

Current State ◽

New Information ◽

Hole Configuration ◽

And Function ◽

Important Progress

Important progress has been made relative to the growth, structure and function of enamel. Better understanding of the epithelial mesenchymal interactions during odontogenesis has been gained through tissue culture, and the predominant role of the dental papilla has been established. Differences between rodent and human amelogenesis have been demonstrated. With radioautography and cytochemistry, a significant amount of new information has been obtained on the metabolism of the ameloblasts, concerning the synthesis of proteins, glycoproteins and proteoglycans, as well as calcium transport. Numerous biochemical investigations have been devoted to developing and mature enamel matrix. The organic components of human adult enamel are mainly constituted of lipids and proteins, but further investigations are still needed to elucidate their precise nature. The so-called key-hole configuration of adult enamel can be questioned when amelogenesis is considered since the tissue does not develop in a prismatic head-tail fashion. The most important results have probably been obtained in the field of individual enamel apatite crystals shape and ultrastructure as well as in the description of the precise patterns of their carious dissolution which bears great similarities to the dissolution of synthetic apatites in acids.

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Methodology of Pilot Performance Measurements

MAD - Magazine of Aviation Development ◽

10.14311/mad.2017.02.04 ◽

2017 ◽

Vol 5 (2) ◽

pp. 25-30

Author(s):

Peter Kalavsky ◽

Róbert Rozenberg ◽

Luboš Socha ◽

Vladimír Socha ◽

Jindrich Gazda ◽

...

Keyword(s):

State Of The Art ◽

Flight Simulator ◽

Basic Information ◽

Performance Measurements ◽

Pilot Performance ◽

Research Project ◽

Training And Education ◽

Current State ◽

New Information ◽

Conducting Research

<p align="LEFT">The article is devoted to the development of the methodology of measuring pilot performance under real flight conditions. It provides the basic information on a research project realized to obtain new information regarding training and education of pilots. The introduction is focused on the analytical part of the project and the outputs in terms of the current state of the art. Detailed view is cast on the issue of measuring pilot performance under specific conditions of the cockpit or the flight simulator. The article is zooming in on the two selected and developed methods of pilot performance in terms of the defined indicators evaluated, conditions of compliance for conducting research and procedures of the methodology of pilot performance measurements.</p>

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Prognostic model for multiple myeloma progression integrating gene expression and clinical features

GigaScience ◽

10.1093/gigascience/giz153 ◽

2019 ◽

Vol 8 (12) ◽

Cited By ~ 1

Author(s):

Chen Sun ◽

Hongyang Li ◽

Ryan E Mills ◽

Yuanfang Guan

Keyword(s):

Gene Expression ◽

Multiple Myeloma ◽

Clinical Features ◽

Prognostic Model ◽

State Of The Art ◽

Cox Model ◽

Functional Enrichment ◽

Machine Learning Techniques ◽

Right Censored Data ◽

Current State

Abstract Background Multiple myeloma (MM) is a hematological cancer caused by abnormal accumulation of monoclonal plasma cells in bone marrow. With the increase in treatment options, risk-adapted therapy is becoming more and more important. Survival analysis is commonly applied to study progression or other events of interest and stratify the risk of patients. Results In this study, we present the current state-of-the-art model for MM prognosis and the molecular biomarker set for stratification: the winning algorithm in the 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3. Specifically, we built a non-parametric complete hazard ranking model to map the right-censored data into a linear space, where commonplace machine learning techniques, such as Gaussian process regression and random forests, can play their roles. Our model integrated both the gene expression profile and clinical features to predict the progression of MM. Compared with conventional models, such as Cox model and random survival forests, our model achieved higher accuracy in 3 within-cohort predictions. In addition, it showed robust predictive power in cross-cohort validations. Key molecular signatures related to MM progression were identified from our model, which may function as the core determinants of MM progression and provide important guidance for future research and clinical practice. Functional enrichment analysis and mammalian gene-gene interaction network revealed crucial biological processes and pathways involved in MM progression. The model is dockerized and publicly available at https://www.synapse.org/#!Synapse:syn11459638. Both data and reproducible code are included in the docker. Conclusions We present the current state-of-the-art prognostic model for MM integrating gene expression and clinical features validated in an independent test set.

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ElimiNet: A Model for Eliminating Options for Reading Comprehension with Multiple Choice Questions

Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence ◽

10.24963/ijcai.2018/594 ◽

2018 ◽

Cited By ~ 5

Author(s):

Soham Parikh ◽

Ananya Sai ◽

Preksha Nema ◽

Mitesh Khapra

Keyword(s):

Reading Comprehension ◽

Large Scale ◽

State Of The Art ◽

Multiple Choice ◽

Multiple Choice Questions ◽

Current State ◽

New Information ◽

Partial Elimination ◽

Maximum Similarity ◽

Option Selection

The task of Reading Comprehension with Multiple Choice Questions, requires a human (or machine) to read a given {passage, question} pair and select one of the n given options. The current state of the art model for this task first computes a question-aware representation for the passage and then selects the option which has the maximum similarity with this representation. However, when humans perform this task they do not just focus on option selection but use a combination of elimination and selection. Specifically, a human would first try to eliminate the most irrelevant option and then read the passage again in the light of this new information (and perhaps ignore portions corresponding to the eliminated option). This process could be repeated multiple times till the reader is finally ready to select the correct option. We propose ElimiNet, a neural network-based model which tries to mimic this process. Specifically, it has gates which decide whether an option can be eliminated given the {passage, question} pair and if so it tries to make the passage representation orthogonal to this eliminated option (akin to ignoring portions of the passage corresponding to the eliminated option). The model makes multiple rounds of partial elimination to refine the passage representation and finally uses a selection module to pick the best option. We evaluate our model on the recently released large scale RACE dataset and show that it outperforms the current state of the art model on 7 out of the 13 question types in this dataset. Further, we show that taking an ensemble of our elimination-selection based method with a selection based method gives us an improvement of 3.1% over the best-reported performance on this dataset.

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Implications, conflicts, and reductions for Steiner trees

Mathematical Programming ◽

10.1007/s10107-021-01757-5 ◽

2021 ◽

Author(s):

Daniel Rehfeldt ◽

Thorsten Koch

Keyword(s):

Steiner Tree ◽

State Of The Art ◽

The State ◽

Branch And Cut ◽

Steiner Tree Problem ◽

New Methods ◽

Current State ◽

Benchmark Instances ◽

Extensive Collection ◽

First Time

AbstractThe Steiner tree problem in graphs (SPG) is one of the most studied problems in combinatorial optimization. In the past 10 years, there have been significant advances concerning approximation and complexity of the SPG. However, the state of the art in (practical) exact solution of the SPG has remained largely unchallenged for almost 20 years. While the DIMACS Challenge 2014 and the PACE Challenge 2018 brought renewed interest into Steiner tree problems, even the best new SPG solvers cannot match the state of the art on the vast majority of benchmark instances. The following article seeks to advance exact SPG solution once again. The article is based on a combination of three concepts: Implications, conflicts, and reductions. As a result, various new SPG techniques are conceived. Notably, several of the resulting techniques are (provably) stronger than well-known methods from the literature that are used in exact SPG algorithms. Finally, by integrating the new methods into a branch-and-cut framework, we obtain an exact SPG solver that is not only competitive with, but even outperforms the current state of the art on an extensive collection of benchmark sets. Furthermore, we can solve several instances for the first time to optimality.

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Behavioral Genetics: Concepts for Research and Practice in Language Development and Disorders

Journal of Speech Language and Hearing Research ◽

10.1044/jshr.3805.1126 ◽

1995 ◽

Vol 38 (5) ◽

pp. 1126-1142 ◽

Cited By ~ 14

Author(s):

Jeffrey W. Gilger

Keyword(s):

Language Development ◽

Behavioral Genetics ◽

State Of The Art ◽

Genetic Research ◽

Great Promise ◽

Behavioral Genetic ◽

Fine Grained ◽

Future Goals ◽

Current State ◽

Research Designs

This paper is an introduction to behavioral genetics for researchers and practioners in language development and disorders. The specific aims are to illustrate some essential concepts and to show how behavioral genetic research can be applied to the language sciences. Past genetic research on language-related traits has tended to focus on simple etiology (i.e., the heritability or familiality of language skills). The current state of the art, however, suggests that great promise lies in addressing more complex questions through behavioral genetic paradigms. In terms of future goals it is suggested that: (a) more behavioral genetic work of all types should be done—including replications and expansions of preliminary studies already in print; (b) work should focus on fine-grained, theory-based phenotypes with research designs that can address complex questions in language development; and (c) work in this area should utilize a variety of samples and methods (e.g., twin and family samples, heritability and segregation analyses, linkage and association tests, etc.).

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