Miracle-dz/UniFAR-FTUs huggingface dataset:
From the SelectedWorks of Kevin Jones November , 2013 Zebrafish : Modeling for Herpes Simplex Virus Infections

For many years, zebrafish have been the prototypical model for studies in developmental biology. In recent years, zebrafish has emerged as a powerful model system to study infectious diseases, including viral infections. Experiments conducted with herpes simplex virus type-1 in adult zebrafish or in embryo models are encouraging as they establish proof of concept with viral-host tropism and possible screening of antiviral compounds. In addition, the presence of human homologs of viral entry receptors in zebrafish such as 3-O sulfated heparan sulfate, nectins, and tumor necrosis factor receptor superfamily member 14-like receptor bring strong rationale for virologists to test their in vivo significance in viral entry in a zebrafish model and compare the structure–function basis of virus zebrafish receptor interaction for viral entry. On the other end, a zebrafish model is already being used for studying inflammation and angiogenesis, with or without genetic manipulations, and therefore can be exploited to study viral infection-associated pathologies. The major advantage with zebrafish is low cost, easy breeding and maintenance, rapid lifecycle, and a transparent nature, which allows visualizing dissemination of fluorescently labeled virus infection in real time either at a localized region or the whole body. Further, the availability of multiple transgenic lines that express fluorescently tagged immune cells for in vivo imaging of virus infected animals is extremely attractive. In addition, a fully developed immune system and potential for receptor-specific knockouts further advocate the use of zebrafish as a new tool to study viral infections. In this review, we focus on expanding the potential of zebrafish model system in understanding human infectious diseases and future benefits.
Prolonged breastfeeding as a birth spacing method.

The majority of mothers in developing countries start nursing their babies after birth and continue for one to two years.1 One reason that nursing in developing countries is common and prolonged is the widespread belief that it is effective in postponing the next conception (Association Algerienne, 1971; Jelliffe, 1967; Marzouk, 1972; Niehoff and Meister, 1972; Wyon and Gordon, 1971; and Yaukey, 1961). This paper summarizes findings of recent investigations on the fertility reducing effect of breastfeeding. These studies fall into two groups: those that determine the effect of lactation on pregnancy and birth intervals; and those that focus on the impact of lactation on the resumption of ovulation and menstruation.
Deep Convolutional Neural Networks for Image Resolution Detection

In this paper, we present a novel approach based on convolutional neural networks (CNNs) to estimate the paper format (pixels per inch) of digitized document images. This format information is often required by commercial document analysis software. A correct estimation of format helps high-level tasks such as OCR and layout analysis. The contribution of this work is two-fold: First, it presents an algorithm for the estimation of paper formats. Second, it is the first publicly available collection of documents (aggregated from public datasets) useful as research benchmark. The collection is a mixture of modern and historical documents with a Pixel Per Inch (PPI) value range from 177 up to 711. The task is modeled as a regression task, leading to more flexible results than in a classification task (one class per format, e.g., A3, A4). For example, if an unknown format is presented to the network, it returns a useful output. Furthermore, more categories can be easily learned by curriculum learning without modifying the network structure itself. On the proposed dataset, the network is able to estimate the PPI values with only an average deviation (from the ground truth) of 14.8 PPI. On a private dataset, stemming from health insurance companies, an average deviation of 6.8 PPI points has been calculated.
Deformation of Wrinkled Graphene

The deformation of monolayer graphene, produced by chemical vapor deposition (CVD), on a polyester film substrate has been investigated through the use of Raman spectroscopy. It has been found that the microstructure of the CVD graphene consists of a hexagonal array of islands of flat monolayer graphene separated by wrinkled material. During deformation, it was found that the rate of shift of the Raman 2D band wavenumber per unit strain was less than 25% of that of flat flakes of mechanically exfoliated graphene, whereas the rate of band broadening per unit strain was about 75% of that of the exfoliated material. This unusual deformation behavior has been modeled in terms of mechanically isolated graphene islands separated by the graphene wrinkles, with the strain distribution in each graphene island determined using shear lag analysis. The effect of the size and position of the Raman laser beam spot has also been incorporated in the model. The predictions fit well with the behavior observed experimentally for the Raman band shifts and broadening of the wrinkled CVD graphene. The effect of wrinkles upon the efficiency of graphene to reinforce nanocomposites is also discussed.
A Novel Germline Mutation in BRCA1 Causes Exon 20 Skipping in a Korean Family with a History of Breast Cancer

Germline mutations in the BRCA1 and BRCA2 genes are strong genetic factors for predispositions to breast, ovarian, and other related cancers. This report describes a family with a history of breast and ovarian cancers that harbored a novel BRCA1 germline mutation. A single nucleotide deletion in intron 20, namely c.5332+4delA, was detected in a 43-year-old patient with breast cancer. This mutation led to the skipping of exon 20, which in turn resulted in the production of a truncated BRCA1 protein that was 1773 amino acids in length. The mother of the proband had died due to ovarian cancer and had harbored the same germline mutation. Ectopically expressed mutant BRCA1 protein interacted with the BARD1 protein, but showed a reduced transcriptional function, as demonstrated by the expression of cyclin B1. This novel germline mutation in the BRCA1 gene caused familial breast and ovarian cancers.
Down-regulation of MDR1 by epigenetic alteration in human epithelial ovarian cancer cells.

e16556 Background: Ovarian cancer is one of the most lethal malignancies in women. Despite recent studies of many oncogenes and tumor-suppressor genes concerning about its progression, the details of ovarian cancer biology still remains to be unclear. P-glycoprotein (P-gp) encoded by the MDR1 gene is a membrane protein that can export many kinds of antineoplastic agents from cells, and overexpression of P-gp has been reported to be implicated in treatment failure in cancer. DNA methylation, a major epigenetic process, can affect every step in carcinogenesis as well as genetic alterations. The contribution of such epigenetic alteration to the expression of MDR1 remains largely unexplored in human ovarian cancer. METHODS In this study, we evaluated the DNA methylation status of the MDR1 gene by methylation-specific PCR. Then, the expression of MDR-1 mRNA and protein in primary epithelial ovarian cancer specimens were evaluated by real-time RT-PCR and immunohistochemistry using anti-mouse P-gp F4 monoclonal antibody, respectively. The correlation between these results and clinicopathological features was examined. RESULTS MDR1 was hypermethylated in 12 of 12 (100%) ovarian cancer cell lines, and 5 of 13 (38%) primary ovarian cancers by methylation-specific PCR analysis. MDR1 mRNA expression was subsequently found to be lost in ovarian cancer cell lines with methylation by both real-time RT-PCR and immunohistochemistry. Thus, MDR1expression was associated with the DNA methylation status of the MDR1 gene. CONCLUSIONS In conclusion, MDR1 was frequently hypermethylated in human ovarian cancers. Our results suggest that epigenetic regulation might play a role in the expression of MDR1 and clinical treatment outcomes in human ovarian cancer. No significant financial relationships to disclose.
Serological evaluation of Escherichia coli-expressed human T-cell leukemia virus type I env, gag p24, and tax proteins

Three proteins (env, gag, and tax) encoded by the human T-cell leukemia virus type I (HTLV-I) genome were cloned and expressed in Escherichia coli. The env protein contained a substantial part of the gp46 domain and a majority of the p21e domain. The gag protein contained all of p24 and portions of p19 and p15. In addition to these two structural proteins, a full-length tax (p40X) construct was obtained. All three recombinant proteins were purified to near homogeneity. When used in an immunoblot assay, the three recombinant proteins detected antibodies in more HTLV-I antibody-positive patient sera than did the corresponding native proteins. Antibodies to at least two of these three different gene products were detected in 98.4% of adult T-cell leukemia patients, 100% of HTLV-I-associated myelopathy patients, 97.4% of asymptomatic carriers, and 94% of uncharacterized HTLV-I-positive patients. Antibody to recombinant tax was found in 4.9% of adult T-cell leukemia patients, whereas antibody to recombinant env could not be detected. These recombinant proteins from three different gene products may be useful in detecting or confirming the presence of antibodies to HTLV-I.
Mesenchymal stem cell therapy of intestinal disease: are their effects systemic or localized?

Purpose of review Stem cell therapy for intestinal diseases is an emerging area in clinical gastroenterology. We will review recent literature regarding mesenchymal stem cells, which have been utilized in preclinical models and are now headed for clinical trials in several gastrointestinal diseases including inflammatory bowel disease. Recent findings Important studies over the last 2 years have made significant inroads into understanding the mechanisms of action of these cell types. The two major competing hypotheses are that mesenchymal stem cells home to areas of injury where they repair based on their stem cell activity or that mesenchymal stem cells act as a source of secreted factors that stimulate repair and inhibit inflammation. Summary Mesenchymal stem cells show promise for therapy in a number of intestinal diseases. Further understanding of their mechanism of action should improve our ability to use them therapeutically.
Health impact of pain in the hip region with and without radiographic evidence of osteoarthritis: a study of new attenders to primary care

OBJECTIVES To assess the health impact of hip pain at the time of first presentation to primary care, and the influence on this of radiographic evidence of osteoarthritis. SUBJECTS AND METHODS Cross sectional survey of 195 patients (63 male, 132 female), aged 40 years and over, presenting with a new episode of hip pain, recruited from 35 general practices across the UK. Health status at presentation was determined by a structured questionnaire on symptoms, healthcare use, and health related quality of life (SF-36). Pelvic radiographs were assessed blindly for hip osteoarthritis using standard scoring systems. RESULTS The overall impact on health was substantial. Before their first consultation, three quarters of patients needed analgesics, half used topical creams or ointments, and one in eight used a walking stick. Most of these impact measures were, however, unrelated to the degree of radiographic change, though use of a walking stick was increased in those with the most severe damage. Health status, as judged by the SF-36, was also impaired for measures of physical function and pain, but the impact on the “mental health”, “general health”, and “vitality” dimensions was small. There was a weak relation between the SF-36 scores and radiographic change, with many domains unrelated to the severity of radiographic damage. CONCLUSIONS This study is the first to show the therapeutic impact and pattern of impairment in health status resulting from hip pain at the time of first presentation to the healthcare services. Unlike many regional pain syndromes seen in primary care, such as back pain, hip pain does not impact on wider aspects of quality of life, such as general health status, mental health, or vitality. Furthermore, any impact of hip pain in this group is not markedly influenced by the degree of structural damage. Further follow up is required to determine whether such damage influences the persistence of any adverse impact.
Ridge Preservation Techniques in the Anterior Esthetic Zone

Purpose:Various techniques have been developed to limit resorption of the alveolar ridge after tooth extraction, and results from using them have been promising. The aim of this study was to evaluate the role and reliability of ridge preservation (RP) in the anterior esthetic zone, in anticipation of later implant placement. Materials and Methods:Using the MEDLINE and PubMed databases, searches were performed using combinations of different terms. Results:A total of 223 studies were identified, from which 55 articles were further examined. Of these, 11 studies were randomized clinical trials, controlled clinical trials, or prospective/retrospective studies with a minimum of 5 subjects and at least 3 months of follow-up. Only human studies of RP for single-rooted tooth or bicuspid sites were included. Selection criteria also excluded studies in which primary closure was obtained. Conclusion:Although a direct comparison of the 11 articles was difficult because of the different techniques, materials, and healing time, no single graft material seemed to be superior. However, all studies found less ridge contraction at grafted than nongrafted sites. Long-term data about the outcomes for implants placed in sites where RP was attempted are still needed.
Sentinel-2 Satellite Imagery based Population Estimation Strategies at FabSpace 2.0 Lab Darmstadt

This paper elaborates the Sentinel-2 image processing approaches used for the estimation of the population of an area of interest at Image CLEF Remote 2017 lab by the FabSpace 2.0 Darmstadt team. The task is introduced by Image CLEF Lab as a new pilot task in 2017 (Remote) which aims at exploring Copernicus Earth Observation data (i.e. Sentinel-2 satellite imagery) in order to estimate the population of an area of interest [2]. Therefore, the pilot task is focusing on mapping human settlement to estimate population using Sentinel-2 data for humanitarian activities and/or establishing communication infrastructure etc. Human societies and civilizations have been expanding with consequent impact throughout the decades. The expansion of human societies has wider implication in relation to the physical environment and other natural resources. Therefore, it could be a fundamental potential of technological innovation in supporting human activities and sufferings throughout mapping diverse human societies in the world. Although there exist a lot of previous studies used commercial and non-commercial high to moderate resolution satellite imagery for the estimation of the population, this study will investigate the potential of the new Sentinel-2 European satellites. They provide data with 10 m resolution imagery for free, thanks to the Copernicus open data policy for all imagery in five days interval. Thus the use of Sentinel-2 data to develop any new application i.e. population estimation can be cost effective and is reasonably accurate. Keyword: Sentinel-2, Population Estimation, Classification, Lusaka, Uganda
Performance of Baseband Digital Data Transmission in Nonlinear Channels with Memory

This paper considers the performance of digital data transmission in nonlinear channels with memory. The analysis is based on the application of a particular form of Volterra series representation for the nonlinear system describing the transmission channel. First, expressions are derived for the output mean and power spectral density under certain conditions. Next, the paper presents a computationally convenient expression for the error rate involved in such transmission.
Event detection and trending in multiple social networking sites

A continuous rise in popularity of social media motivates many people to express their opinions and news on the real-time basis. In this paper, the social networking sites such as Twitter and Facebook are considered as a platform for event detection. Since social information streams are sparse and continuous, the processing time and speed are vital while detecting events. We suggest a novel approach of discovering events from multiple social streams using widely used Euclidean realization of locality sensitive hashing (LSH) algorithm. In our proposed method, the LSH is used twice in event detection. Firstly, it is used to obtain the events independently from both social streams. The cross-over events between social networks are detected by applying the algorithm one more time. The detected events can be trended to show their activeness on different networks. We explore a theoretical approach on the design of event detection and trending in multiple social sites.
A RANSAC-based fast road line detection algorithm for high-speed wheeled vehicles

Real-time trajectory tracking and control is a well-known problem in robotics which has recently become very interesting also for automotive industry, due to the need for constantly improving car comfort and safety. While several solutions for vehicle trajectory control already exist, assuring fast, accurate and reliable tracking using low-cost devices is still a challenging problem. In this paper an effective road line detection system is described. The proposed technique relies on the so-called RANSAC algorithm applied to the images collected by a high frame rate video camera. The main advantage of the proposed solution is the low computational burden, which is compatible for real-time trajectory monitoring even when a vehicle is travelling at high speed.
Prevention of invasive fungal infections in liver transplant recipients: the role of prophylaxis with lipid formulations of amphotericin B in high-risk patients.

BACKGROUND Invasive fungal infections (IFI) are associated with high mortality in liver transplant recipients. Prevention remains an elusive goal, especially for IFI caused by moulds. PATIENTS AND METHODS From January 1998, patients who fulfilled four or more variables identified as risk factors for IFI received a cumulative dose of 1-1.5 g of lipid formulations of amphotericin B (L-AmpB; AmBisome or Abelcet). The development of IFI in these patients was compared with historical patients. RESULTS Two hundred and eighty liver transplant recipients were analysed over a period of 8 years. In the historical group, IFI were observed in 22 of 131 patients (17%) and invasive aspergillosis in 13 of them (10%). After January 1998, IFI were observed in nine of 149 (6%) (P < 0.01) and invasive aspergillosis in six patients (4%) (P = 0.08). In patients with four or more risk factors (high risk) for IFI, the administration of L-AmpB reduced the risk from 36% to 14% (P = 0.07), and the risk of aspergillosis from 23% to 5% (P = 0.08). Notably, prophylaxis reduced the risk of aspergillosis from 32% to 0% in dialysed patients (P = 0.03). Variables independently associated with IFI in high-risk patients were dialysis [odds ratio (OR) 3.9; 95% confidence interval (CI) 1-16.7] and surgical reintervention (OR 5.4; 95% CI 1.2-24.6), while L-AmpB was a protective factor in this multivariate analysis (OR 0.1; 95% CI 0.02-0.8). The analysis in these high-risk patients was not able to demonstrate an association between the administration of L-AmpB and higher survival. CONCLUSIONS Selected risk factors are good predictors of IFI in liver transplant recipients. The administration of L-AmpB in high-risk patients is independently associated with a reduction of IFI.
Optimal Tenuring and Major Collection times for a Generational Garbage Collector

It is an important problem to determine the tenuring collection time or major collection time to meet the pause time goal for a generational garbage collector. From such a viewpoint, this paper proposes two stochastic models based on the working schemes of a generational garbage collector: Garbage collections occur at a nonhomogeneous Poisson process. Minor collections are made when the garbage collector begins to work, tenuring collection is made at a planned time T or at the first collection time when surviving objects have exceeded K for the first model. Major collection is made at time T or at the Nth collection for the second model. Using the techniques of cumulative processes and reliability theory, expected cost rates are obtained, and optimal policies of tenuring and major collection times which minimize them are discussed analytically and computed numerically.
Hypertrophic Cardiomyopathy rogressive Left Ventricular emodeling in Patients With ypertrophic Cardiomyopathy and evere Left Ventricular Hypertrophy

OBJECTIVES The aim of this study was to determine the natural history of patients with hypertrophic cardiomyopathy (HCM) and severe left ventricular hypertrophy (LVH) (i.e., maximal left ventricular wall thickness [MLVWT] 30 mm) and whether changes in cardiac morphology influence the course of the disease. BACKGROUND Severe LVH is common in young and rare among elderly patients with HCM. This has been explained by a high incidence of sudden death. We hypothesized that this age-related difference might be explained by left ventricular wall thinning. METHODS A total of 106 (age 33 15 years; 71 males) consecutive patients with severe LVH underwent history taking, examination, electrocardiography, echocardiography, cardiopulmonary exercise testing, and Holter analysis. Survival data were collected at subsequent clinic visits or by communication with patients and their general practioners. In order to assess morphologic and functional changes, 71 (67.0%) patients (mean age 31 15 years; 47 males) followed at our institution underwent serial ( 1 year) assessment. RESULTS Of the 106 patients, the majority (78 [71.6%]) were 40 years of age. During follow-up (92 50 months [range 1 to 169]), 18 (17.0%) patients died or underwent heart transplantation (13 sudden cardiac deaths, 2 heart failure deaths, 1 heart transplantation, 1 stroke, 1 postoperative death). Five-year survival from sudden death was 90.1% (95% confidence interval [CI] 84.0% to 96.3%), and that from heart failure death or transplantation was 97.7% (95% CI 94.5 to 100). In patients serially evaluated over 85 51 months, there was an overall reduction in MLVWT of 0.6 mm/year (95% CI 0.31 to 0.81, p 0.00004). Wall thinning 5 mm was observed in 41 patients (57.7%; age 35 13 years; 28 males). On multivariate analysis, the follow-up duration only predicted wall thinning (0.6 mm/year, 95% CI 0.38 to 0.85, p 0.00001). CONCLUSIONS Left ventricular remodeling is common in patients with severe LVH and contributes to the low prevalence of severe LVH seen in middle age and beyond. (J Am Coll Cardiol 2004; 44:398–405) © 2004 by the American College of Cardiology Foundation