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  This is an Open Access Journal Open Access journal
     ISSN (Online) 2046-1402
     Published by Faculty of 1000 Homepage  [1 journal]
  • Case Report: A case of hypertrophic lupus erythematosus with negative
           CD123 staining and absence of transepidermal elimination of elastin
           [v2; indexed,]

    • Authors: Matthew Hughes, Jerad M. Gardner, Ling Gao
      Abstract: We report the case of a 49-year-old male with clinical and histological findings consistent with hypertrophic lupus erythematosus (HLE). HLE must be clinically and histologically differentiated from keratoacanthoma, hypertrophic lichen planus, squamous cell carcinoma and plaque type psoriasis. CD123 positivity and transepidermal elimination of elastin have recently been reported as tools to distinguish HLE. Interestingly, in this case, biopsies of two separate lesions failed to reveal these two features. The etiology of this discrepancy is unknown and further studies are needed to clarify the utility of CD123 positivity and transepidermal elimination of elastin in the diagnosis of hypertrophic lupus erythematosus.
      PubDate: 2014-06-04
      DOI: 10.12688/f1000research.4723
      Issue No: Vol. 3 (2014)
  • Factors that contribute to social media influence within an Internal
           Medicine Twitter learning community [v1; indexed,]

    • Authors: Tejas Desai, Manish Patwardhan, Hunter Coore
      Abstract: Medical societies, faculty, and trainees use Twitter to learn from and educate other social media users. These social media communities bring together individuals with various levels of experience. It is not known if experienced individuals are also the most influential members. We hypothesize that participants with the greatest experience would be the most influential members of a Twitter community. We analyzed the 2013 Association of Program Directors in Internal Medicine Twitter community. We measured the number of tweets authored by each participant and the number of amplified tweets (re-tweets). We developed a multivariate linear regression model to identify any relationship to social media influence, measured by the PageRank. Faculty (from academic institutions) comprised 19% of the 132 participants in the learning community (p < 0.0001). Faculty authored 49% of all 867 tweets (p < 0.0001). Their tweets were the most likely to be amplified (52%, p < 0.01). Faculty had the greatest influence amongst all participants (mean 1.99, p < 0.0001). Being a faculty member had no predictive effect on influence (β = 0.068, p = 0.6). The only factors that predicted influence (higher PageRank) were the number of tweets authored (p < 0.0001) and number of tweets amplified (p < 0.0001) The status of “faculty member” did not confer a greater influence. Any participant who was able to author the greatest number of tweets or have more of his/her tweets amplified could wield a greater influence on the participants, regardless of his/her authority.
      PubDate: 2014-05-29
      DOI: 10.12688/f1000research.4585
      Issue No: Vol. 3 (2014)
  • Visual record of intertidal disturbance caused by drift ice in the spring
           on the Atlantic coast of Nova Scotia [v1; indexed,]

    • Authors: Willy Petzold, Maike T. Willers, Ricardo A. Scrosati
      Abstract: In the early spring of 2014, an unusually large amount of sea ice drifted from the Gulf of St. Lawrence, where it had been produced, towards the open Atlantic Ocean through the Cabot Strait, between Nova Scotia and Newfoundland, Canada. In early April, significant amounts of drift ice reached the Atlantic coast of mainland Nova Scotia. The ice floes persisted in those coastal waters for up to 16 days, depending on the location. During that time, the ice fragments caused extensive physical disturbance in rocky intertidal communities, removing high quantities of seaweeds and invertebrates. For example, at a location where the ice stayed for 9 days, the loss of macroalgal and invertebrate biomass was almost total. At a location where the ice stayed for 4 days, losses were lower, albeit still high overall. Such a magnitude of disturbance is not common on this coast, as sea ice had not reached the surveyed locations in the previous 4–5 years. We suggest that the frequency of ice scour events may help to predict intertidal community structure. This notion could be tested through multiannual surveys of ice conditions and biological communities along the Atlantic coast of Nova Scotia.
      PubDate: 2014-05-16
      DOI: 10.12688/f1000research.4439
      Issue No: Vol. 3 (2014)
  • Case report: Heterotopic intrarenally located adrenocortical oncocytoma
           [v2; indexed,]

    • Authors: Konstantin Godin, Nicole Bang, Yuri Tolkach
      Abstract: The clinical case of a 65-year-old woman with an incidentally detected left-sided mass in the upper renal pole is presented. A functional adrenal tumor was excluded. The mass was removed retroperitoneoscopically. The perioperative period was uneventful. The histopathological examination revealed a heterotopic intrarenal adrenocortical oncocytoma. Adrenal oncocytic neoplasms are very rare, with, to the authors’ knowledge, only 159 described cases so far. Most cases are non-functioning adenomas that can reach a considerable size. Only 10 heterotopic adrenal oncocytomas have been described (three retroperitoneal and seven intraspinal cases). Although the intrarenal adrenal rest is the most frequently appearing variant of adrenal heterotopia, to the best of our knowledge, this report is the first description of an intrarenally growing adrenocortical oncocytic adenoma. In addition to retroperitoneally located oncocytomas, this case could be interesting for urological practice because there are no diagnostic features which could provide a secure preoperative diagnosis of an adrenal oncocytic neoplasm and its malignant variant. Generally accepted indications for surgery of adrenal masses have to be respected. The definitive pathologic diagnosis is in most cases surprising because of its rarity. Benign adrenal oncocytic neoplasms do not require any adjuvant treatment. The oncocytic variant of adrenocortical carcinoma generally has a poor prognosis.
      PubDate: 2014-05-12
      DOI: 10.12688/f1000research.4467
      Issue No: Vol. 3 (2014)
  • Transient acid treatment cannot induce neonatal somatic cells to become
           pluripotent stem cells [v1; indexed,]

    • Authors: Mei Kuen Tang, Lok Man Lo, Wen Ting Shi, Yao Yao, Henry Siu Sum Lee, Kenneth Ka Ho Lee
      Abstract: Currently, there are genetic- and chemical-based methods for producing pluripotent stem cells from somatic cells, but all of them are extremely inefficient.  However, a simple and efficient technique has recently been reported by Obokata et al (2014a, b) that creates pluripotent stem cells through acid-based treatment of somatic cells.  These cells were named stimulus-triggered acquisition of pluripotency (STAP) stem cells. This would be a major game changer in regenerative medicine if the results could be independently replicated. Hence, we isolated CD45+ splenocytes from five-day-old Oct4-GFP mice and treated the cells with acidified (pH 5.7) Hank’s Balanced Salt Solution (HBSS) for 25 min, using the methods described by Obokata et al 2014c. However, we found that this method did not induce the splenocytes to express the stem cell marker Oct4-GFP when observed under a confocal microscope three to six days after acid treatment. qPCR analysis also confirmed that acid treatment did not induce the splenocytes to express the stemness markers Oct4, Sox2 and Nanog.  In addition, we obtained similar results from acid-treated Oct4-GFP lung fibroblasts. In summary, we have not been able to produce STAP stem cells from neonatal splenocytes or lung fibroblasts using the acid-based treatment reported by Obokata et al (2014a, b, c).
      PubDate: 2014-05-08
      DOI: 10.12688/f1000research.4382
      Issue No: Vol. 3 (2014)
  • Computational science: shifting the focus from tools to models [v1;

    • Authors: Konrad Hinsen
      Abstract: Computational techniques have revolutionized many aspects of scientific research over the last few decades. Experimentalists use computation for data analysis, processing ever bigger data sets. Theoreticians compute predictions from ever more complex models. However, traditional articles do not permit the publication of big data sets or complex models. As a consequence, these crucial pieces of information have disappeared from the scientific record. Moreover, they have become prisoners of scientific software: many models exist only as software implementations, and the data are often stored in proprietary formats defined by the software. In this article, I argue that this emphasis on software tools over models and data is detrimental to science in the long term, and I propose a means by which this can be reversed.
      PubDate: 2014-05-07
      DOI: 10.12688/f1000research.4263
      Issue No: Vol. 3 (2014)
  • shRNA-seq data analysis with edgeR [v1; indexed,]

    • Authors: Zhiyin Dai, Julie M. Sheridan, Linden J. Gearing, Darcy L. Moore, Shian Su, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
      Abstract: Pooled short hairpin RNA sequencing (shRNA-seq) screens are becoming increasingly popular in functional genomics research, and there is a need to establish optimal analysis tools to handle such data. Our open-source shRNA processing pipeline in edgeR provides a complete analysis solution for shRNA-seq screen data, that begins with the raw sequence reads and ends with a ranked lists of candidate shRNAs for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, hairpins in the rows) with options for allowing mismatches and small shifts in hairpin position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or a generalized linear modelling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from
      PubDate: 2014-04-24
      DOI: 10.12688/f1000research.4204
      Issue No: Vol. 3 (2014)
  • Evidence from molecular dynamics simulations of conformational
           preorganization in the ribonuclease H active site [v1; indexed,

    • Authors: Kate A. Stafford, Arthur G. Palmer III
      Abstract: Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold.
      PubDate: 2014-03-07
      DOI: 10.12688/f1000research.3859
      Issue No: Vol. 3 (2014)
  • Lentigo maligna mimicking invasive melanoma in Mohs surgery: a case report
           [v1; indexed,]

    • Authors: Teresa Tsakok, Nisith Sheth, Alistair Robson, Catherine Gleeson, Raj Mallipeddi
      Abstract: Lentigo maligna is a lentiginous proliferation of atypical melanocytes confined to the epidermis, typically on chronically sun-damaged skin. Following biopsy and exclusion of invasive disease, therapy may involve Mohs surgery, topical treatment or radiotherapy. However, lentigo maligna often involves adnexal structures, creating histological difficulty in distinguishing these foci from invasive melanoma. We present a case in which, during Mohs excision, a nodule of severely atypical melanocytes appeared to lie within the dermis, potentially altering treatment and prognosis. The use of laminin-5 provided a means of resolving this diagnostic dilemma, facilitating continuation of Mohs surgery until tumour clearance was achieved.
      PubDate: 2014-01-24
      DOI: 10.12688/f1000research.3-25.v1
      Issue No: Vol. 3 (2014)
  • Detection and quantification of tumor cells in peripheral blood and
           ascitic fluid from a metastatic esophageal cancer patient using the
           CellSearch® technology [v1; indexed,]

    • Authors: Qian Tu, Marcelo De Carvalho Bittencourt, Huili Cai, Claire Bastien, Camille Lemarie-Delaunay, Marie C Bene, Gilbert C Faure
      Abstract: Analysis of ascitic fluid should help to identify and characterize malignant cells in gastrointestinal cancer. However, despite a high specificity, the sensitivity of traditional ascitic fluid cytology remains insufficient, at around 60%. Since 2004 the CellSearch® technology has shown its advantages in the detection of circulating tumor cells (CTCs) in peripheral blood, which can perform an accurate diagnosis and molecular analysis at the same time. To our knowledge, no previous study has explored the potential utility of this technology for the detection and quantification of tumor cells in ascitic fluid samples. Herein we report a case of metastatic esophageal adenocarcinoma in a 70-year-old man presenting with dysphagia and a large amount of fluid in the peritoneal cavity. Analysis of a peripheral blood sample and ascites sample with the CellSearch® technology both revealed the presence of putative tumor cells that were positive for epithelial cell adhesion molecule (EpCAM) and cytokeratin (CK) expression. This study confirmed the hematogenous dissemination of esophageal cancer by the detection of circulating tumor cells in the peripheral blood, and is the first to demonstrate that tumor cells can be identified in ascitic fluid by using CellSearch® technology.
      PubDate: 2014-01-15
      DOI: 10.12688/f1000research.3-12.v1
      Issue No: Vol. 3 (2014)
  • Implementation of a worksite educational program focused on promoting
           healthy eating habits [v2; indexed,]

    • Authors: Dimitra Tanagra, Dimitris Panidis, Yannis Tountas, Elina Remoudaki, Evangelos C. Alexopoulos
      Abstract: Objective: To estimate the effectiveness of a short-term educational-counseling worksite program focused on lipid intake, by monitoring the possible change on nutrition knowledge and eating habits. Methods: an 8-week educational program based on the Health Belief Model was implemented in a honey packaging and sales company in Greece. 20 out of the 29 employees initially enrolled completed the program. Knowledge level and eating habits were evaluated prior and after the intervention by the “Nutrition Knowledge Questionnaire” and the “Food Habits Questionnaire”. ANOVA, Spearman rho test and paired Wilcoxon test were employed in statistical analysis. Results: Non smokers and those with higher educational level had healthier eating habits. Knowledge following the intervention was significantly improved concerning recommendations and basic food ingredients but as far as eating habits were concerned, scores were not improved significantly, while intake of fried food was increased. Conclusions and Implications: Short-term interventions may produce substantial improvement in knowledge but not necessarily modifications in unhealthy eating habits.
      PubDate: 2014-03-07
      DOI: 10.12688/f1000research.2-201.v2
      Issue No: Vol. 2 (2014)
  • Accumulation of oocytes and/or embryos by vitrification: a new strategy
           for managing poor responder patients undergoing pre implantation diagnosis
           [v2; indexed,]

    • Authors: Alexia Chatziparasidou, Martine Nijs, Martha Moisidou, Oraiopoulou Chara, Christina Ioakeimidou, Christos Pappas, Nicos Christoforidis
      Abstract: Background: Low (or poor) responder patients are women who require large doses of stimulation medications and produce less than an optimal number of oocytes during IVF cycles. Low responder patients produce few oocytes and embryos, which significantly reduces their chances for success in a preimplantation genetic diagnosis (PGD) cycle. Accumulation of vitrified oocytes or embryos before the actual PGD cycle is a possible strategy that might increase patient’s chances for a healthy pregnancy. Aim of the study: This retrospective study evaluates the efficacy of a PGD program in low responder patients after repeated ovarian stimulation cycles with cumulative vitrification of oocytes and embryos. Methods: Over a period of 30 months, 13 patients entering the PGD program were identified as poor responders after their first ovarian stimulation. These patients started a PGD cycle for one of the following indications: history of recurrent implantation failure (n=1), cystic fibrosis (n=1), X-linked microtubular myopathy (n=1), recurrent miscarriages (n=5), Duchene muscular dystrophy (n=1), chromosomal translocation (n=1) and high sperm aneuploidy (n=1).  After multiple ovarian hormonal stimulations patients had either all mature oocytes (Group A; 3 patients) or all of their day 2 embryos vitrified (group B; 10 patients). Mean total number of oocyte collections per patient was 2.3 (range: 2 - 5 cycles). Results: In the actual PGD cycle, all vitrified oocytes from group A patients were warmed and underwent intra cytoplasmic sperm injection (ICSI) followed by culture up to day 3. For group B patients all vitrified day 2 embryos were warmed and cultured overnight. On day 3 of culture, all embryos from Group A and B had blastomere biopsy followed by genetic analysis. In group A, 20 embryos were found suitable for biopsy and genetic analysis; at least one healthy embryo was available for transfer for each patient.  For group B, 72 embryos in total were available for biopsy and PGD.  All patients, except one, had at least one healthy day 5 embryo for transfer (mean number of 2.1 embryos per transfer). Nine patients had a clinical pregnancy; 7 patients delivered a healthy baby. Conclusion: Low responder patients entering a PGD program might increase their chances for a healthy pregnancy by repeat ovarian stimulation in combination with cumulative oocyte or embryo vitrification.
      PubDate: 2014-03-03
      DOI: 10.12688/f1000research.2-240.v2
      Issue No: Vol. 2 (2014)
  • Learning intrinsic excitability in medium spiny neurons [v2; indexed,

    • Authors: Gabriele Scheler
      Abstract: We present an unsupervised, local activation-dependent learning rule for intrinsic plasticity (IP) which affects the composition of ion channel conductances for single neurons in a use-dependent way. We use a single-compartment conductance-based model for medium spiny striatal neurons in order to show the effects of parameterization of individual ion channels on the neuronal membrane potential-curent relationship (activation function). We show that parameter changes within the physiological ranges are sufficient to create an ensemble of neurons with significantly different activation functions. We emphasize that the effects of intrinsic neuronal modulation on spiking behavior require a distributed mode of synaptic input and can be eliminated by strongly correlated input. We show how modulation and adaptivity in ion channel conductances can be utilized to store patterns without an additional contribution by synaptic plasticity (SP). The adaptation of the spike response may result in either "positive" or "negative" pattern learning. However, read-out of stored information depends on a distributed pattern of synaptic activity to let intrinsic modulation determine spike response. We briefly discuss the implications of this conditional memory on learning and addiction.
      PubDate: 2014-02-26
      DOI: 10.12688/f1000research.2-88.v2
      Issue No: Vol. 2 (2014)
  • Endovascular treatment of chronic mesenteric ischemia in an adolescent
           male: case report [v1; indexed,]

    • Authors: Sadiq Muhammed Al-Hammash, Abd El-Salam Dawood Al-Ethawi, Kasim Abbas Ismail
      Abstract: Chronic mesenteric ischemia (CMI) is a condition characterized by inadequate blood flow to the bowel resulting from stenosis of one or more of the three mesenteric arteries. Fibromuscular dysplasia is the most common cause in children and young adults; whereas atherosclerosis is the most common cause in the elderly. Treatment is mandatory in symptomatic patients, because it may lead to malnutrition, bowel infarction or even death.Herein, we present the case of a 14-year old male, diagnosed with CMI who underwent percutaneous balloon angioplasty (PTA) followed by stent placement with immediate positive results.
      PubDate: 2013-12-17
      DOI: 10.12688/f1000research.2-277.v1
      Issue No: Vol. 2 (2013)
  • Self-organization of signal transduction [v1; indexed,

    • Authors: Gabriele Scheler
      Abstract: We propose a model of parameter learning for signal transduction, where the objective function is defined by signal transmission efficiency. We apply this to learn kinetic rates as a form of evolutionary learning, and look for parameters which satisfy the objective. This is a novel approach compared to the usual technique of adjusting parameters only on the basis of experimental data. The resulting model is self-organizing, i.e. perturbations in protein concentrations or changes in extracellular signaling will automatically lead to adaptation. We systematically perturb protein concentrations and observe the response of the system. We find compensatory or co-regulation of protein expression levels. In a novel experiment, we alter the distribution of extracellular signaling, and observe adaptation based on optimizing signal transmission. We also discuss the relationship between signaling with and without transients. Signaling by transients may involve maximization of signal transmission efficiency for the peak response, but a minimization in steady-state responses. With an appropriate objective function, this can also be achieved by concentration adjustment. Self-organizing systems may be predictive of unwanted drug interference effects, since they aim to mimic complex cellular adaptation in a unified way.
      PubDate: 2013-04-23
      DOI: 10.12688/f1000research.2-116.v1
      Issue No: Vol. 2 (2013)
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
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