Ethnic identity and Chicano literature: How ethnicity affects reading and reading affects ethnic consciousness

This article interrogates the impact of readers’ ethnicity (Latino and non-Latino) on meanings crafted from Chicano literature. This article addresses the effect of Chicano literature on ethnic identity and worldview formation. The data source is participant observation and interviews with eighteen students in a college-level Chicano literature seminar in the United States. Latino students found that the literature spoke to their experience as Latinos, inciting a sense of membership in a community that merits inclusion in a college course. This connection with the literature transmuted into ethnic validation for nearly all Latino students. Non-Latinos, hindered from relating to the course content on an ethnic level, discovered alternate entryways into the texts that allowed for identification on other particular levels. Non-Latinos ascertained how ethnic distinctions partially shape human experience and that this understanding is critical to cross-cultural appreciation and empathy. Non-Latinos additionally perceived that a common humanity tunnels beneath ethnic difference.     

TogoDoc server/client system: smart recommendation and efficient management of life science literature

In this paper, we describe a server/client literature management system specialized for the life science domain, the TogoDoc system (Togo, pronounced Toe-Go, is a romanization of a Japanese word for integration). The server and the client program cooperate closely over the Internet to provide life scientists with an effective literature recommendation service and efficient literature management. The content-based and personalized literature recommendation helps researchers to isolate interesting papers from the "tsunami" of literature, in which, on average, more than one biomedical paper is added to MEDLINE every minute. Because researchers these days need to cover updates of much wider topics to generate hypotheses using massive datasets obtained from public databases or omics experiments, the importance of having an effective literature recommendation service is rising. The automatic recommendation is based on the content of personal literature libraries of electronic PDF papers. The client program automatically analyzes these files, which are sometimes deeply buried in storage disks of researchers' personal computers. Just saving PDF papers to the designated folders makes the client program automatically analyze and retrieve metadata, rename file names, synchronize the data to the server, and receive the recommendation lists of newly published papers, thus accomplishing effortless literature management. In addition, the tag suggestion and associative search functions are provided for easy classification of and access to past papers (researchers who read many papers sometimes only vaguely remember or completely forget what they read in the past). The TogoDoc system is available for both Windows and Mac OS X and is free. The TogoDoc Client software is available at http://tdc.cb.k.u-tokyo.ac.jp/, and the TogoDoc server is available at https://docman.dbcls.jp/pubmed_recom.     

Neighbours,strangers, and the asymmetric war of attrition

The literature showing that territorial residents generally respond more intensely to an intrusion by a stranger than by a known neighbour is reviewed. The functional basis of this discrimination has not been seriously considered in this extensive literature, and it is shown here how the asymmetric war of attrition can explain why neighbours settle with relatively little aggression. In the asymmetric war-of-attrition model the degree of escalation observed in a territorial contest depends on the familiarity of the contestants with each other. Predictions of this model about neighbour-stranger contests are supported by data in the literature.     

数据挖掘在生物信息学中的应用——文献计量学视角

基因组和蛋白质结构与功能方面已积累了海量数据。如何从海量数据中获取有效信息成为生物信息学迫切要解决的问题。本文以相关主题词检索文献,分析了该领域历年文章数量、发文最多的机构和作者、被引用频次居前论文、期刊载文量,并对关键词和被引用频次居前论文的作者进行共现分析。我们发现,生物信息学中运用数据挖掘方法的文献逐年增多,该领域30.1%的文献发表在十个期刊上,分类、聚类、特征选择和支持向量机等数据挖掘方法使用较多。本研究描绘了生物信息学与数据挖掘这一交叉领域的研究概况,为后续数据挖掘方法与生物信息学研究相结合提供帮助。     

Gynaecological cancers and their cell lines

Cell lines are widely used for various research purposes including cancer and drug research. Recently, there have been studies that pointed to discrepancies in the literature and usage of cell lines. That is why we have prepared a comprehensive overview of the most common gynaecological cancer cell lines, their literature, a list of currently available cell lines, and new findings compared with the original studies. A literature review was conducted via MEDLINE, PubMed and ScienceDirect for reviews in the last 5 years to identify research and other studies related to gynaecological cancer cell lines. We present an overview of the current literature with reference to the original studies and pointed to certain inconsistencies in the literature. The adherence to culturing rulesets and the international guidelines helps in minimizing replication failure between institutions. Evidence from the latest research suggests that despite certain drawbacks, variations of cancer cell lines can also be useful in regard to a more diverse genomic landscape.     

The next generation of literature analysis: integration of genomic analysis into text mining

Text-mining systems are indispensable tools to reduce the increasing flux of information in scientific literature to topics pertinent to a particular interest in focus. Most of the scientific literature is published as unstructured free text, complicating the development of data processing tools, which rely on structured information. To overcome the problems of free text analysis, structured, hand-curated information derived from literature is integrated in text-mining systems to improve precision and recall. In this paper several text-mining approaches are reviewed and the next step in development of text-mining systems, which is based on a concept of multiple lines of evidence, is described: results from literature analysis are combined with evidence from experiments and genome analysis to improve the accuracy of results and to generate additional knowledge beyond what is known solely from literature.     

Systematic reviews: a primer for plastic surgery research

Clinicians rely on review articles to keep current with the rapid accumulation of medical and surgical literature. Traditional expert reviews, however, often suffer from inherent personal biases and may not reflect a true synthesis of the existing literature on a particular subject. Systematic reviews are structured, scientific articles that address the shortcomings of traditional reviews by adhering to strict, reproducible methods and recommended guidelines. The methods are designed to eliminate possible sources of bias, ensure as complete a review of the existing literature as possible, and present the results in a way that is useful for its intended audience. Systematic reviews may at times include a quantitative synthesis of the available data in the form of a meta-analysis. Meta-analysis is a statistical tool for combining the numerical results of separate studies to obtain a summary outcome with increased precision due to the larger, combined number of patients. Meta-analyses may be particularly helpful when individual study results are conflicting and the existing literature is inconclusive. The validity of meta-analysis, however, is highly dependent on the quality of data available in the literature. In its strictest form, meta-analysis is used to combine data from only randomized controlled clinical trials. Because randomized controlled clinical trials are infrequently performed in plastic surgery research, this article will focus on systematic reviews to provide the readers with a useful guide in performing this field of study.     

Electrochemical biofilm control: a review

One of the methods of controlling biofilms that has widely been discussed in the literature is to apply a potential or electrical current to a metal surface on which the biofilm is growing. Although electrochemical biofilm control has been studied for decades, the literature is often conflicting, as is detailed in this review. The goals of this review are: (1) to present the current status of knowledge regarding electrochemical biofilm control; (2) to establish a basis for a fundamental definition of electrochemical biofilm control and requirements for studying it; (3) to discuss current proposed mechanisms; and (4) to introduce future directions in the field. It is expected that the review will provide researchers with guidelines on comparing datasets across the literature and generating comparable datasets. The authors believe that, with the correct design, electrochemical biofilm control has great potential for industrial use.     

Systematic review: External carbon source for biological denitrification for wastewater

Nitrogen mitigation is serious environmental issue around the globe. Several methods for wastewater treatment have been introduced, but biological denitrification has been recommended, particularly with addition of the best external carbon source. The key sites of denitrification are wetlands; it can be carried out with different methods. To highlight the aforementioned technology, this paper deals to review the literature to evaluate biological denitrification and to demonstrate cost effective external carbon sources. The results of systematic review disclose the denitrification process and addition of different external carbon sources. The online literature exploration was accomplished using the most well-known databases, that is, science direct and the web of science database, resulting 625 review articles and 3084 research articles, published in peer-reviewed journals between 2015 and 2021 were identified in first process. After doing an in-depth literature survey and exclusion criteria, we started to shape the review from selected review and research articles. A number of studies confirmed that both nitrification and denitrification are significant for biological treatment of wastewater. The studies proved that the carbon source is the main contributor and is a booster for the denitrification. Based on the literature reviewed it is concluded that biological denitrification with addition of external carbon source is cost effective and best option in nitrogen mitigation in a changing world. Our study recommends textile waste for recovery of carbon source.     

Children and Youth in Aboriginal Australia: An Overview of the Literature

The following overview of the existing literature relating to Aboriginal childhood and adolescence across Australia is intended to support the development of this potentially strong interdisciplinary research field. It presents a select number of works in historical context, concluding with critical comments and supplemented by additional references presented according to type of study. No claim is made to have covered the literature exhaustively.     

Biological effects of exposure to magnetic resonance imaging: an overview

The literature on biological effects of magnetic and electromagnetic fields commonly utilized in magnetic resonance imaging systems is surveyed here. After an introduction on the basic principles of magnetic resonance imaging and the electric and magnetic properties of biological tissues, the basic phenomena to understand the bio-effects are described in classical terms. Values of field strengths and frequencies commonly utilized in these diagnostic systems are reported in order to allow the integration of the specific literature on the bio-effects produced by magnetic resonance systems with the vast literature concerning the bio-effects produced by electromagnetic fields. This work gives an overview of the findings about the safety concerns of exposure to static magnetic fields, radio-frequency fields, and time varying magnetic field gradients, focusing primarily on the physics of the interactions between these electromagnetic fields and biological matter. The scientific literature is summarized, integrated, and critically analyzed with the help of authoritative reviews by recognized experts, international safety guidelines are also cited.     

PATTERNS IN TREE BALANCE AMONG CLADISTIC,PHENETIC, AND RANDOMLY GENERATED PHYLOGENETIC TREES

I examine patterns in tree balance for a sample of 208 cladograms and phenograms from the recent literature. I provide an expression for expected imbalance under a simple, uniform-rate random speciation model, and I estimate variances by simulation for the same model. Imbalance decreases with tree size (number of included taxa) in both theoretical and literature trees. In contrast to previous suggestions, I find cladistic trees to be no more imbalanced than phenetic trees when confounding variables are appropriately controlled. The degree of imbalance found in literature trees is inconsistent with the uniform-rate speciation model; this is most likely a result of variability in speciation and extinction rates among real lineages. The existence of such variation is a necessary (but not sufficient) condition for the operation of the macroevolutionary processes of species sorting and species selection.     

Discovering patterns to extract protein-protein interactions from full texts

MOTIVATION: Although there are several databases storing protein-protein interactions, most such data still exist only in the scientific literature. They are scattered in scientific literature written in natural languages, defying data mining efforts. Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a robust and powerful methodology to mine protein-protein interactions from biomedical texts. RESULTS: We present a novel and robust approach for extracting protein-protein interactions from literature. Our method uses a dynamic programming algorithm to compute distinguishing patterns by aligning relevant sentences and key verbs that describe protein interactions. A matching algorithm is designed to extract the interactions between proteins. Equipped only with a dictionary of protein names, our system achieves a recall rate of 80.0% and precision rate of 80.5%. AVAILABILITY: The program is available on request from the authors.     

Discovering implicit protein–protein interactions in the <Emphasis Type="Italic">Cell Cycle</Emphasis> using bioinformatics approaches

The cell division control protein (Cdc2) kinase is a catalytic subunit of a protein kinase complex, called the M phase promoting factor, which induces entry into mitosis and is universal among eukaryotes. This protein is believed to play a major role in cell division and control. The lives of biological cells are controlled by proteins interacting in metabolic and signaling pathways, in complexes that replicate genes and regulate gene activity, and in the assembly of the cytoskeletal infrastructure. Our knowledge of protein–protein (P–P) interactions has been accumulated from biochemical and genetic experiments, including the widely used yeast two-hybrid test. In this paper we examine if P–P interactions in regenerating tissues and cells of the anuran Xenopus laevis can be discovered from biomedical literature using computational and literature mining techniques. Using literature mining techniques, we have identified a set of implicitly interacting proteins in regenerating tissues and cells of Xenopus laevis that may interact with Cdc2 to control cell division. Genome sequence based bioinformatics tools were then applied to validate a set of proteins that appear to interact with the Cdc2 protein. Pathway analysis of these proteins suggests that Myc proteins function as the regulator of M phase initiation by controlling expression of the Akt1 molecule that ultimately inhibits the Cdc2-cyclin B complex in cells. P–P interactions that are implicitly appearing in literature can be effectively discovered using literature mining techniques. By applying evolutionary principles on the P–P interacting pairs, it is possible to quantitatively analyze the significance of the associations with biological relevance. The developed BioMap system allows discovering implicit P–P interactions from large quantity of biomedical literature data. The unique similarities and differences observed within the interacting proteins can lead to the development of the new hypotheses that can be used to design further laboratory experiments.     

A Systematic Review Concerning the Relation between the Sympathetic Nervous System and Heart Failure with Preserved Left Ventricular Ejection Fraction

BackgroundHeart failure with preserved left ventricular ejection fraction (HFPEF) affects about half of all patients diagnosed with heart failure. The pathophysiological aspect of this complex disease state has been extensively explored, yet it is still not fully understood. Since the sympathetic nervous system is related to the development of systolic HF, we hypothesized that an increased sympathetic nerve activation (SNA) is also related to the development of HFPEF. This review summarizes the available literature regarding the relation between HFPEF and SNA.ConclusionCurrent literature confirms a relation between increased SNA and HFPEF. However, current literature is not able to distinguish whether enhanced SNA results in HFPEF, or HFPEF results in enhanced SNA. The most likely setting is a vicious circle in which HFPEF and SNA sustain each other.     

An adult patient with a distal interstitial 14q deletion: clinical report and literature review

We report a patient with an interstitial 14q32.1-->q32.3 deletion and review the literature. The adult patient presented with moderate mental retardation, a friendly behavior and a non-specific phenotype. The deletion seemed to be terminal but with FISH probes appeared to be interstitial. Comparison with other 14q terminal and interstitial deletion patients reported in literature and those with a ring 14 chromosome is given.     

Automated extraction of information in molecular biology

We review data mining techniques in molecular biology, specifically those that extract information from the scientific literature itself. As more of the biological literature is published electronically, there is an opportunity, and even a need, to automatically summarize the literature in a customized way, for example by associating keywords to a topic. These keywords can be extracted from relevant publications. The process of keyword extraction can be automated and optimized to keep literature pointers automatically up-to-date or to filter relevant information from the literature. To illustrate these points, OMIM (Online Mendelian Inheritance in Man), a database of human inherited diseases, was linked to the literature and keywords were derived that covered distinct aspects such as genetic information on the one hand and disease-specific protein and phenotypic information on the other. They were used to extract information that is helpful for keeping entries about disease up-to-date.     

Comparison of the serum selenium content of healthy adults living in the Antwerp region (Belgium) with recent literature data.

Graphite furnace atomic absorption spectrometry, after improved matrix modification and using Zeeman background correction, was used to measure the serum selenium content of healthy adults living in the Antwerp region (Belgium). The mean serum concentration of 13 men and 13 women, sampled once a month during 1 year, was 84.3 +/- 9.4ng/ml with a broad range of 51.4-121.7 ng/ml. The intra-individual variation was remarkably high. Recent literature on selenium concentrations is reviewed and values are tabulated, with limitation to healthy adults and European countries. The mean serum selenium concentration measured corresponded well to older literature data for Belgium. The obtained values were found to be in the medium range compared with the literature data for other European countries.     

How to Build a Standardized Country-Specific Environmental Food Database for Nutritional Epidemiology Studies

There is a lack of standardized country-specific environmental data to combine with nutritional and dietary data for assessing the environmental impact of individual diets in epidemiology surveys, which are consequently reliant on environmental food datasets based on values retrieved from a heterogeneous literature. The aim of this study was to compare and assess the relative strengths and limits of a database of food greenhouse gas emissions (GHGE) values estimated with a hybrid method combining input/output and LCA approaches, with a dataset of GHGE values retrieved from the literature. France is the geographical perimeter considered in this study, but the methodology could be applied to other countries. The GHGE of 402 foodstuffs, representative of French diet, were estimated using the hybrid method. In parallel, the GHGE of individual foods were collected from existing literature. Median per-food-category GHGE values from the hybrid method and the reviewed literature were found to correlate strongly (Spearman correlation was 0.83), showing similar rankings of food categories. Median values were significantly different for only 5 (out of 29) food categories, including the ruminant meats category for which the hybrid method gave lower estimates than those from existing literature. Analysis also revealed that literature values came from heterogeneous studies that were not always sourced and that were conducted under different LCA modeling hypotheses. In contrast, the hybrid method helps build reliably-sourced, representative national standards for product-based datasets. We anticipate this hybrid method to be a starting point for better environmental impact assessments of diets.     

Trunk muscle activation in low-back pain patients, an analysis of the literature.

This paper provides an analysis of the literature on trunk muscle recruitment in low-back pain patients. Two models proposed in the literature, the pain-spasm-pain model and the pain adaptation model, yield conflicting predictions on how low- back pain would affect trunk muscle recruitment in various activities. The two models are outlined and evidence for the two from neurophsysiological studies is reviewed. Subsequently, specific predictions with respect to changes in activation of the lumbar extensor musculature are derived from both models. These predictions are compared to the results from 30 clinical studies and three induced pain studies retrieved in a comprehensive literature search. Neither of the two models is unequivocally supported by the literature. These data and further data on timing of muscle activity and load sharing between muscles suggest an alternative model to explain the alterations of trunk muscle recruitment due to low-back pain. It is proposed that motor control changes in patients are functional in that they enhance spinal stability.