Literature Citations Research Articles

Abstract A05: The Mouse Tumor Biology (MTB) Database: An electronic tool for identifying and evaluating mouse and PDX models of human cancer

Abstract The increasing number and diversity of available mouse models of human cancer and their growing importance in scientific research have resulted in an enormous increase in the amount and types of data generated from these models. These models represent powerful tools for studying biological and genetic mechanisms of cancer and for translation into potential clinical therapeutics. However, the amount of available data makes it challenging to identify and evaluate specific models and data important for an individual laboratory's research. Placing these data in their proper genetic context is crucial to understanding the biochemical and molecular mechanisms of initiation, progression, and metastasis of different cancers. In addition, the ability of the immunodeficient NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mouse strain to host patient derived xenograft (PDX) models only increases the number of available models and the data produced from them. The Mouse Tumor Biology (MTB) Database provides access to data from mouse and PDX models of human tumors and the tools to analyze these data, facilitating the discovery and evaluation of novel mouse and PDX models of human cancers (http://tumor.informatics.jax.org). MTB includes data on endogenously arising tumors (both spontaneous and induced) in genetically defined mice (inbred, hybrid, mutant, and genetically engineered mice) and information from PDX models of human tumors and provides freely available web access to these data. MTB integrates data from peer-reviewed literature, laboratories studying mouse models of human cancer, production mouse colonies at The Jackson Laboratory (JAX), colonies of aging mice from the Jackson Aging Center, and PDX data from the Jackson Laboratory Patient-derived xenograft resource. MTB also incorporates data from PathBase, and mouse gene expression data sets from NCBI's Gene Expression Omnibus (GEO) and the Array Express Database. Data include tumor classification, incidence and latency, tumor associated quantitative trait loci (QTL), pathology reports, images and genetic changes in tumors (somatic) and background strain (germline). Data type specific query forms (tumor, genetic etc.) allow detailed searches. MTB also can be searched using human gene symbols for orthologous mouse genes and associated data. Pathology images are submitted by the scientific community, from primary literature (with publisher permission), and from JAX colonies. MTB also includes immunohistochemistry data on over 500 antibodies with accompanying images of positive control samples and links to the respective vendors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and has developed a web-based system to facilitate submission of data. Standard nomenclature, controlled vocabularies and literature citations facilitate data integration and robust searches. MTB is integrated with the Mouse Genome Informatics resource (MGI, http://www.informatics.jax.org) and provides links to other related online resources such as the Mouse Phenome Database (MPD), the Biology of the Mammary Gland Web Site, and the NCI Mouse Repository. MTB is supported by NCI grant CA089713. Citation Format: Dale A. Begley, Debra M. Krupke, Steven B. Neuhauser, Joel E. Richardson, John P. Sundberg, Carol J. Bult, Janan T. Eppig. The Mouse Tumor Biology (MTB) Database: An electronic tool for identifying and evaluating mouse and PDX models of human cancer. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr A05.

β-lactam/β-lactamase inhibitor combinations: from then to now.

To review the available evidence regarding the utility of the currently available β-lactam/β-lactamase inhibitor combinations (BLICs) as well as the emerging body of data for the novel agents in the pipeline. A MEDLINE literature search (1960-August 2014) was performed using the search terms β-lactamase, β-lactamase inhibitor, clavulanate, sulbactam, tazobactam, avibactam, NXL104, MK-7655, and RPX7009. Current studies focusing on new agents were obtained from clinicaltrials.gov. Additional references were identified from a review of literature citations and meeting abstracts. All English-language studies pertaining to BLICs were evaluated. Historical clinical and in vitro data focusing on the characteristics of the conventional BLICs are reviewed. Avibactam, relebactam (formerly MK-7655), and RPX7009 are new β-lactamase inhibitors that are being studied in combination with β-lactams. Clinical and in vitro data that provide support for their use for multidrug-resistant organisms are reviewed. β-Lactam antibiotics are a mainstay for the treatment of many infections. The addition of β-lactamase inhibitors enhances their activity against organisms that produce β-lactamases; however, organisms that produce extended-spectrum β-lactamases, AmpC β-lactamases, and carbapenemases are proliferating. The BLICs (amoxicillin/clavulanate, ticarcillin/clavulanate, ampicillin/sulbactam, and piperacillin/tazobactam) lack activity against some of these enzymes, presenting a critical need for new antibiotics. The historical BLICs are useful for many infections; however, evolving resistance limits their use. The new BLICs (combinations with avibactam, relebactam, and RPX7009) may be valuable options for patients infected with multidrug-resistant organisms.

Gender prejudice in the research world: female researchers in a conflict zone, Kashmir

Purpose– The research world is full of women who have explored the scientific world and given their best to humanity. Kashmir, known for its conflict rather than its beauty now, has also given birth to a number of women researchers who have excelled in their respective fields. The study attempts to explore the contributions to the scientific world of women from the University of Kashmir, one of the leading institutions of Kashmir. The research contributions of women from a conflict zone, Kashmir, have been taken into account in the study.Methodology– The data related to the women researchers of Kashmir were extracted from the largest citation and abstract database of peer-reviewed literature, Elsevier’s Scopus, which features smart tools that track, analyse and visualise research from varied dimensions.Findings– The study reveals the effect of conflict on women in the scientific world. The findings show that there are significant differences by gender in terms of research productivity in a conflict region. Furthermore, in the present context, a changing trend is seen as women researchers also show involvement in the scientific world which, if taken seriously, can help in developing a better and more promising feminist research world.Practical Implications– The study can help in laying down the real picture and status of women researchers in a conflict zone. The study urges that governments in conflict zones should take steps to popularise investment in women’s education and research programmes to better equip and motivate women researchers.Originality/value– Further research can be carried out to discover the problems faced by women researchers in a conflict zone.

Analysis of German nutrition brochures for pregnant women with evidence-based patient information criteria

ObjectiveTo evaluate nutrition brochures for pregnant women in Germany based on evidence-based patient information (EBPI) criteria. MethodsNutrition brochures for pregnant women in Germany were collected. Brochures addressing the risk of salmonellosis, toxoplasmosis or listeriosis were analyzed by two researchers independently. ResultsFifty brochures reporting any information on the risk of infection were analyzed. Most brochures did not include literature citations and only few brochures gave a risk description, predominantly verbally, which usually leads to an overestimation of the actual risk. Advertisement was present in 22% of the brochures. ConclusionGerman nutrition brochures for pregnant women should be adapted to comply with evidence-based patient information (EBPI) criteria for achieving a better quality of the disseminated information. Practice implicationsThe findings highlight the need of high quality nutrition brochures for pregnant women, which are relevant not only for pregnant women, but also to those responsible for creating brochures, and to physicians in charge of patient information.

Bibliographic citation in information service

This paper gives the history of the origin of citations in scientific literature and reveals the causes of the origin of different referencing styles. Modern methods for working with references in scientific technical literature are described. The role of network technologies in preparing scientific publications is pointed out.

Recent developments in drug therapy for aplastic anemia.

This article reviews recent developments in immunosuppressive therapy (IST) for aplastic anemia (AA) patients who are not candidates for stem cell transplant (SCT); including, front-line, salvage, and novel treatment options with a focus on response rates (RRs) and overall survival (OS). A PubMed literature search was performed from 1977 to June 2014 using the search terms aplastic anemia, horse antithymocyte globulin (hATG), rabbit ATG (rATG), thymoglobulin, and cyclosporine (CSA). Additional references were identified from a review of literature citations. All English-language studies investigating IST for treatment of AA in non-SCT candidates were evaluated. Studies indicate addition of CSA and corticosteroids to hATG for treatment of AA improves RRs, decreases relapse rates, and improves 5-year OS. hATG improved RRs, relapse rates, and OS compared to rATG in the front-line setting. Studies support the use of rATG when front-line IST with hATG fails or when hATG is unavailable. Front-line daclizumab can be considered for nonsevere AA (NAA); however, data is limited. Alemtuzumab or eltrombopag are options for relapsed AA in select patients. hATG with methylprednisolone and CSA is recommended for front-line treatment of AA, whereas rATG is reserved for salvage therapy. Front-line use of daclizumab has been studied in NAA patients, but additional prospective trials are needed before this is adopted into clinical practice. Alemtuzumab and eltrombopag have been studied for treatment of AA; recruiting is ongoing in clinical trials to assess the appropriate dosing strategy and place in therapy.

Prader-Willi syndrome and hyperphagia: an update

Purpose – Prader-Willi syndrome (PWS) is a genetic disorder characterised by excessive appetite and progressive obesity. The causes of hyperphagia are unknown and this has implications on treatment limiting the options available. The purpose of this paper is to systematically synthesise the latest evidence regarding all causes as well as management of hyperphagia in people with PWS. Design/methodology/approach – A computer-based literature search, citation tracking and related articles search was undertaken. Primary research studies using genetically confirmed Prader-Willi participants specifically focused on the causes and treatment of overeating was included. Studies were described, critically analysed, presented and discussed in the review. Findings – In total, 18 relevant studies were identified. Nine studies were included in the causes of hyperphagia and focused largely on the roles of secretory hormones, and reward-related areas of the brain. Nine studies were included in the management of hyperphagia and related to physical exercise and food control, antidiabetic agents and weight loss surgery. Originality/value – The causes and the management of hyperphagia are still to be determined despite promising findings. The small number and heterogeneity of the included studies and participants limits conclusions. There is the need for future research to use larger systematic studies to validate findings so far.

Efficacy of electronic cigarettes for smoking cessation.

To review data demonstrating effective smoking cessation with electronic cigarettes (e-cigarettes). A literature search of MEDLINE/PubMed (1946-March 2014) was performed using the search terms e-cigarettes, electronic cigarettes, and smoking cessation. Additional references were identified from a review of literature citations. All English-language clinical studies assessing efficacy of e-cigarettes compared with baseline, placebo, or other pharmacological methods to aid in withdrawal symptoms, smoking reduction, or cessation were evaluated. A total of 6 clinical studies were included in the review. In small studies, e-cigarettes significantly decreased desire to smoke, number of cigarettes smoked per day, and exhaled carbon monoxide levels. Symptoms of nicotine withdrawal and adverse effects were variable. The most common adverse effects were nausea, headache, cough, and mouth/throat irritation. Compared with nicotine patches, e-cigarettes were associated with fewer adverse effects and higher adherence. Most studies showed a significant decrease in cigarette use acutely; however, long-term cessation was not sustained at 6 months. There is limited evidence for the effectiveness of e-cigarettes in smoking cessation; however, there may be a place in therapy to help modify smoking habits or reduce the number of cigarettes smoked. Studies available provided different administration patterns such as use while smoking, instead of smoking, or as needed. Short-term studies reviewed were small and did not necessarily evaluate cessation with a focus on parameters associated with cessation withdrawal symptoms. Though long-term safety is unknown, concerns regarding increased poisoning exposures among adults in comparison with cigarettes are alarming.

Warfarin monitoring in antiphospholipid syndrome and lupus anticoagulant.

To review the available literature on international normalized ratio (INR) and chromogenic factor X (CFX) monitoring in patients with antiphospholipid syndrome (APS), specifically lupus anticoagulant (LA), and furthermore, to identify benefits of one monitoring test compared with the other in the presence of LA. A literature search was conducted through MEDLINE (1946-May 2014) utilizing the following MeSH terms chromogenic compounds, anticoagulants, and factor X. Further articles were identified from original literature citations. All English-language studies were included that involved INR and/or CFX monitoring in APS patients that focused on a therapeutic anticoagulation level with warfarin therapy. A total of 55 articles were identified, of which nine are referenced because of their relevance for this review: three articles focus on the efficacy of utilizing INR monitoring in patients with APS, five focus on CFX compared with INR for therapeutic warfarin dosing, and one compares different thromboplastins utilizing both INR and CFX monitoring. INR monitoring in patients with APS, specifically LA, was not found to be reliable because thromboplastin reagents are sensitive to LA. Furthermore, when INR was compared to CFX, patients with LA had supratherapeutic INRs despite having CFX within goal range. In a subgroup of APS patients, INR monitoring may not be safe for determining the dose of warfarin because their INR values can be falsely elevated. Although CFX monitoring is more accurate, it too comes with its own downsides. Managing warfarin therapy in the APS population needs to be individualized.

Varenicline in the treatment of alcohol use disorders.

To summarize the efficacy and safety data for the use of varenicline in the treatment of alcohol use disorders. A literature search was conducted in PubMed, International Pharmaceutical Abstracts, and Cochrane Library (through May 2014). Key search terms included varenicline, alcohol, alcohol dependence, alcoholism, ethanol, and nicotinic acetylcholine receptor. Additional references were identified from literature citations. Results were limited to clinical trials and case reports that discussed either the use of varenicline in alcohol drinking patients or adverse effects experienced with its use. Only English language studies in humans were reviewed. In all, 7 randomized, placebo-controlled clinical trials and 1 open-label study were identified that evaluated the impact of varenicline on various drinking-related end points. The studies were conducted in patients dependent on alcohol (n=4), non-alcohol-dependent patients (n=3), and patients with a history of alcohol dependence but who had been abstinent for at least 6 months (n=1). The majority of the studies classified their participants as heavy drinkers; however, this definition varied across studies. Most studies included smokers, but 2 trials included both smokers and nonsmokers. Evidence supports the use of varenicline for the reduction of alcohol craving as well as for the reduction of overall alcohol consumption in patients with alcohol use disorders. However, it is not likely to improve abstinence rates. Although most of the data were derived from patients with concurrent nicotine dependence, the effects of varenicline appear to occur independent of baseline smoking status.

The prevention of contrast-induced nephropathy.

Contrast-induced nephropathy (CIN) is a complication which may develop after exposure to iodinated contrast media. The resulting acute kidney injury (AKI) is associated with an increase in both short- and long-term morbidity and mortality, increased hospital length of stay, and greater health care costs. The pathophysiological mechanism associated with the development of CIN remains unknown. This narrative review summarizes the pathophysiology, risk factors, and current evidence for the prevention of CIN. A MEDLINE literature search (2004-May 2014) was performed using search terms contrast-induced nephropathy and prevention. Additional references were identified from literature citations, review articles, and meta-analyses. Abstracts of English-language human clinical trials that examined therapies for the prevention of CIN were evaluated. Studies that did not investigate a preventative intervention for CIN were excluded. Emphasis was placed on recent publications. A multitude of therapies focused on the prevention of CIN have been investigated. Unfortunately, many of these studies have produced negative and/or inconsistent results. There is a paucity of adequately designed clinical studies evaluating strategies for the prevention of CIN. However, the best data supports use of preprocedural hydration with isotonic solution as the standard of care for prophylaxis. Given the poor prognosis associated with CIN, there is need for improved methods to prevent it. At present, the best tools to protect patients from unnecessary risk for CIN are careful assessment of renal function, judicious use of procedures that utilize contrast media, and adequate hydration with isotonic solution.

Point-of-care platforms.

Point-of-care applications are gaining increasing interest in clinical diagnostics and emergency applications. Biosensors are used to monitor the biomolecular interaction process between a disease biomarker and a recognition element such as a reagent. Essential are the quality and selectivity of the recognition elements and assay types used to improve sensitivity and to avoid nonspecific interactions. In addition, quality measures are influenced by the detection principle and the evaluation strategies. For these reasons, this review provides a survey and validation of recognition elements, assays, and various types of detection methods for point-of-care testing (POCT) platforms. Common applications of clinical parameters are discussed and considered. In this ever-changing field, a snapshot of current applications is needed. We provide such a snapshot by way of a table including literature citations and also discuss these applications in more detail throughout.

Reflection of the Information Literacy Literature: A Webometric Study

Webometrics is the research network-based communication using informetric or other quantitative measures. The primary objective of this study is to examine the nature and pattern of citations in the recent information literacy literature. For the study, 84 articles published in 29 e-journals of LIS collection of Emerald Group available through UGC-Infonet digital library consortium of the last five years have been analyzed. This study concentrates on classification of web citations by author, year, country, and pattern of citations has also been calculated. The study reveals that current trend in citing is moving towards web citations.

Scientific retraction: a synonym for pseudoscience?

The phenomenon of scientific retraction is a shameful act for the scientific community, but a necessity to maintain the purity of science. The two main causes for retractions include plagiarism and research misconduct. The post retraction citation of articles is again a repetition of inappropriateness. Hence the editorial, peer review policies should be revised and the retractions should be publicized more to avoid the citation of the invalid literature. Also, the scientific readership has a responsibility to evaluate the scientific validity of published studies.

Validity Analysis of Finger Vein Application in Identity Authentication

Finger vein authentication is a novel biometrics technology for personal identification. In this paper, universality, collectability, acceptability, circumvention, uniqueness, permanency and performance of finger vein distribution pattern are analyzed. Thereinto, universality, collectability, acceptability and circumvention of finger vein pattern are described simply through the citation of relational literature, and uniqueness, permanency, performance of finger vein pattern are particularly studied by experimental means. The experimental result shows that there are favorable general performance for finger vein pattern in biometrics, finger vein can be applied effectively in personal identity authentication, finger vein identification technology have a well applying prospect and developmental potential.

Thinking Beyond the Thomson Reuters “Impact Factor”

Thinking Beyond the Thomson Reuters “Impact Factor”

Bad Science, Sloppy Reporting, and Retracted Publications: Should Peer Review be the Scapegoat?

There seems to be no study too fragmented, no hypothesis too trivial, no literature citation too biased or too egotistical, no design too warped, no methodology too bungled, no presentation of results too inaccurate, too obscure and too contradictory, no analysis too self-serving, no argument too circular, no conclusions too trifling or too unjustified, and no grammar and syntax too offensive for a paper to end up in print. (Rennie, 1986, pp. 2391–2392)

Integrating COPD care in Italy.

Doctors are not short of advice about how to manage their patients. In the case of COPD (Chronic Obstructive Pulmonary Disease) there are a wealth of guidelines, strategies and position papers synthesising an increasing body of data from observational studies and clinical trials into schemes that should help the doctor care for their COPD patients more effectively. In recent years particular attention has been paid to the views of the joint ERS/ATS COPD guidelines [1] and the regularly updated recommendations of the Global initiative for chronic Obstructive Lung Disease (GOLD) [2]. Now a new Italian document has been developed representing the combined efforts of three key Italian respiratory societies AIMAR, AIPO, SIMeR and the society of General Practice, SIMG, whose combined expertise covers almost all those who offer care to the COPD patient. So what does this new guidance tell us and does it add to what we have heard already? Appropriately this new document takes a very wide view of the problems of COPD. It emphasises the need for early accurate diagnosis supported when needed but supplementary physiological investigations such as the measurement of lung volumes and airway responsiveness. It points out the limitations of relying on a fixed FEV1/FVC ratio of 70% or less to support the diagnosis of COPD and suggest instead that the lower limit of normal (LLN) for this ratio is a more reliable guide. There might have been a little more advice for the busy clinician on the best way of accessing appropriate LLN data and perhaps a little more caution on the usefulness of bronchodilator testing in patient evaluation [3]. However there are some excellent figures to guide diagnosis and management as well as useful tabular summaries of what tests should be undertaken by which clinicians and how to approach smoking cessation. The authors have avoided some of the controversy and uncertainty surrounding the new GOLD severity assessment scheme [4], instead focussing on patient sub-groups that correspond to those seen in clinical practice and in clinical trials. Their treatment recommendations are not formally evidence based but closely follow those in guidelines where more extensive evidence evaluations have been conducted [5]. The authors offer clear practical guidance with support from selected but relevant literature citations which help the clinician understand why particular treatment choices have been made. There is an appropriate and pragmatic section emphasising the value of pulmonary rehabilitation together with a particularly helpful review of the role of telemedicine in COPD care, a topic scarcely touched on in other guidelines. This new approach to COPD care is needed in Italy now. As the authors point out, COPD remains a major health problem despite much good work to increase smoking cessation rates and improve air quality. International guidelines offer an overview of COPD care in all settings but there is still a need to develop management strategies which work locally and reflect the needs and perceptions of local physicians and patients. This new initiative has achieved both of these goals admirably.

Marsupiales (Didelphimorphia: Didelphidae) de Iquitos y sus alrededores (Loreto, Perú)

Introduction: Amazonia has a high diversity of marsupials, and while Emmons and Feer (1990) have cited 14 species for the area, 18 years later this number was increased to 28 by Gardner (2008a), a difference related to descriptions and revalidation of several species in recent years. Northeastern Peru is one of the areas with high biodiversity, a “hotspot”. The high diversity of small mammals can be explained by several factors: latitudinal gradient, size of the area, and lack of seasonal precipitations, among others. In this contribution 19 species are cited for the region of Iquitos, 14 collected through field trips and five recorded from the literature. These results confirm the presence of a species that was not known for the country ( Marmosops neblina), and two species (Marmosa regina and Marmosops bishopi) with new records for the area. The results show that the study area is one of the most diverse in South America with respect to marsupials. Material and methods: The specimens were collected between December 2002 and December 2005, at 41 collecting sites along the Iquitos-Nauta Highway. The study was carried out in undisturbed primary and secondary forests, and other rural areas. In total, 18,081 Sherman trap-nights, 19,271 Tomahawk trapnights, and 591 pitfall trap-nights were recorded. External and cranial morphometric data, body mass, sex, and reproductive condition were recorded for all specimens. A key to species is provided including the confirmed and probable species of the area. Species accumulation curves were calculated and plotted using EstimateS 8.2.0. Results: Three hundred and seventy three records were obtained belonging to 14 out of 27 species cited for the area; eight species were collected outside the Iquitos area. Most specimens were collected in primary and secondary forests (123 and 199 specimens respectively), only 49 were captured in other areas. Pitfall traps were the most successful (1.69% capture success), followed by Tomahawk traps (1.29%), and Sherman traps (0.55%). Arboreal traps were more successful than the ground traps, with 4.18% and 0.89% capture success respectively. The species accumulation curve did not reach stability and the estimates calculated are greater than the recorded species. Discussion: During three years of sampling, 14 species were collected, a number that rises to 19 when literature citations for the specific area of Iquitos are considered (and increases to 27 if the area is extended to a 200 km radius around Iquitos). Some species were very abundant (P. opossum, M. nudicaudatus, D. marsupialis, and M. regina), while others were documented by only 1 or 2 records (G. venusta, M. adusta, and P. olrogi). It is evident that the Peruvian Amazon is one of the areas with the highest diversity of marsupials, but further surveys and studies are necessary in order to determine with greater precision the distribution of many species, and to acquire a better understanding of their natural history. More extensive studies of the fauna of the region are required to obtain informational bases that will provide a strong management policy, in order to preserve the species in such a highly fragmented region.

J.G.C. Lehmann's 'Botanical Observations' of 1818 on Coldenia, Colsmannia, Cynoglossum, and Omphalodes (commented translation).

An annotated English translation of a German early 19th century text including Latin diagnoses is presented with a high-quality scan of the original publication and direct links to the cited pages with taxon and literature citations (including TL-2 entries).