Miracle-dz/UniFAR-FTUs huggingface dataset:
ApcMin/+ mouse model of colon cancer: Gene expression profiling in tumors

The ApcMin/+ mouse is a popular animal model for studies of human colon cancer, but the molecular changes associated with neoplasia in this system have only been partially characterized. Our aim was to identify novel genes involved in tumorigenesis in this model. RNA from intestinal adenomas and from pre‐neoplastic small intestine were prepared from six ApcMin/+ mice. The tumor transcriptomes were analyzed with high‐density oligonucleotide microarrays representing ∼12,000 probe sets; we compared their profiles with those of matched pre‐neoplastic intestine. Stringent analysis revealed reproducible changes for 98 probe sets representing 90 genes, including novel observations regarding 50 genes whose involvement in this mouse model has never been reported. In addition to the expected changes in growth regulatory genes, the altered gene products could be assigned to four functional groupings that should enhance tumorigenesis: metabolic changes that would result in a high rate of glycolysis, alterations in enzymes involved in reactive oxygen species or carcinogen metabolism, cytoskeletal elements, and proteins involved in tumor invasion or angiogenesis. A fifth group consisted of expression changes that might restrict tumor progression, suggesting that the adenomatous state reflects a balance of pro‐ and anti‐tumorigenic factors. Since many of the altered genes had not previously been reported to be involved in any tumorigenic processes, our observations provide a host of new candidates for potential modulation to prevent or treat intestinal neoplasia. Supplementary material for this article can be found at http://www.mrw. interscience.wiley. com/suppmat/0730‐2312/suppmat/v93.html. © 2004 Wiley‐Liss, Inc.
Fabrication of porous scaffolds by three‐dimensional plotting of a pasty calcium phosphate bone cement under mild conditions

The major advantage of hydroxyapatite (HA)‐forming calcium phosphate cements (CPCs) used as bone replacement materials is their setting under physiological conditions without the necessity for thermal treatment that allows the incorporation of biological factors. In the present study, we have combined the biocompatible consolidation of CPCs with the potential of rapid prototyping (RP) techniques to generate calcium phosphate‐based scaffolds with defined inner and outer morphology. We demonstrate the application of the RP technique three‐dimensional (3D) plotting for the fabrication of HA cement scaffolds. This was realized by utilizing a paste‐like CPC (P‐CPC) which is stable as a malleable paste and whose setting reaction is initiated only after contact with aqueous solutions. The P‐CPC showed good processability in the 3D plotting process and allowed the fabrication of stable 3D structures of different geometries with adequate mechanical stability and compressive strength. The cytocompatibility of the plotted P‐CPC scaffolds was demonstrated in a cell culture experiment with human mesenchymal stem cells. The mild conditions during 3D plotting and post‐processing and the realization of the whole procedure under sterile conditions make this approach highly attractive for fabrication of individualized implants with respect to patient‐specific requirements by simultaneous plotting of biological components. Copyright © 2012 John Wiley & Sons, Ltd.
Physical activity and risk of cardiovascular disease: what does the new epidemiological evidence show?

Purpose of review Abundant evidence has documented inverse associations of physical activity and the risk of cardiovascular disease (CVD). However, the effects of different types of physical activity (e.g., leisure time and occupational physical activity) are still poorly understood. Recent findings Drawing on recommended and established guidelines for study selection, we identified and included 23 prospective epidemiological studies published during the last 2 years. These studies included a total of more than 790 000 adults at baseline with some 22 000 incident cases occurring during follow-up. Our findings suggest that moderate and high levels of leisure time physical activity are associated with a moderately reduced risk of CVD. In contrast, moderate and high levels of occupational physical activity showed weak positive associations, that is, a slightly increased risk of CVD. Summary This updated meta-analysis supports the notion of primary prevention of CVD through engagement in leisure time physical activity. The role of occupational physical activity in CVD prevention is questionable.
18F-FDG uptake in squamous cell carcinoma of the cervix is correlated with glucose transporter 1 expression.

UNLABELLED This prospective study investigates the relationship between glucose transporter-1 (Glut-1) expression and PET images using (18)F-FDG and its uptake and compares them with the tumor status (primary vs. recurrent or persistent), initial grade of histologic differentiation, and International Federation of Gynecologic Obstetrics (FIGO) staging for cervical cancer patients. METHODS A dual-phase (18)F-FDG PET scan was performed on 51 participants within the 2 wk before surgery or biopsy. (18)F-FDG uptake was quantified by calculating standardized uptake values (SUVs). After (18)F-FDG PET scanning, 51 histologically proven squamous cell carcinoma specimens were examined to determine their degree of differentiation, using hematoxylin and eosin staining, and the expression of Glut-1 by an immunohistochemical stain. Twenty normal cervical and 20 cervical intraepithelial neoplasia (CIN) sets of tissue were also used to compare the results of Glut-1 expression in these tissues. The expression of Glut-1 was the product of (the intensity [with grades 0-3, defined qualitatively]) with (percentages of the lesion area that were positive). The results of Glut-1 expression were analyzed in combination with the SUVs (SUV1 was that at 40 min and SUV2 was that at 3 h), tumor status, initial cell differentiation, and FIGO staging. RESULTS Significant overexpression of Glut-1 was noted in 48 of the 51 (94.1%) cancer specimens. None or only minimal expression of Glut-1 was observed in basal layers of normal and CIN tissues. Significant positive correlation was observed between Glut-1 expression and the SUVs in cervical cancer specimens (r = 0.74, P < 0.000 for SUV1 and r = 0.65, P < 0.000 for SUV2). In recurrent or persistent tumor, tumor size was significantly associated with both Glut-1 expression (r = 0.508, P = 0.011) and SUV1 (r = 0. 456, P = 0.025). For recurrent or persistent tumor, only SUV1 reached statistical significance when compared with lymph node metastasis (P = 0.0226). CONCLUSION Glut-1 expression was related to (18)F-FDG uptake in cervical cancer patients. Recurrent or persistent cervical cancer tumor had significantly higher Glut-1 expression than metastatic lymph nodes. The values of SUV and the expression of Glut-1 did not correlate with the initial grade of histologic differentiation and FIGO staging.
The Impact of Individual Motivations on Idea Submission and Future Motivation to Participate in an Organization's Virtual Idea Campaign

We used time&#8208;lagged survey data to investigate the effects of various types of motivation on idea submission and future motivation to participate in a virtual idea campaign (VIC). We also used qualitative data to illuminate context and enrich explanations. Applying forms of motivation from self&#8208;determination theory&#8212;intrinsic motivation and external motivation&#8212;and the additional composite form of identified&#8208;prosocial motivation, our study offers insight into their effects on idea submission and future motivation to participate in idea campaigns. We found that intrinsic motivation led to idea submission and future motivation to participate, while external motivation negatively related to idea submission. Identified&#8208;prosocial motivation positively related to participants' motivation to participate in future idea campaigns, but surprisingly, its interaction with intrinsic motivation did not lead to idea submission. We provide managers and innovation researchers with useful lessons for the effective management of idea campaigns in organizations, and our results highlight the value of autonomous forms of motivation, especially intrinsic motivation.
Proposal of a Model Supporting Decision-Making on Information Security Risk Treatment

— Management is required to understand all information security risks within an organization, and to make decisions on which information security risks should be treated in what level by allocating how much amount of cost. However, such decision-making is not usually easy, because various measures for risk treatment must be selected with the suitable application levels. In addition, some measures may have objectives conflicting with each other. It also makes the selection difficult. Therefore, this paper provides a model which supports the selection of measures by applying multi-objective analysis to find an optimal solution. Additionally, a list of measures is also provided to make the selection easier and more effective without any leakage of measures.
Update on two-year performance of 120 kWp concentrator PV systems using multi-junction III–V solar cells and parabolic dish reflective optics

Multi-junction III–V solar cells have been in operation for the last two years in several 500X dish concentrator PV systems using reflective optics. The performance monitoring of these CPV systems on a 15-second basis has accumulated a very large amount of data and allowed for analysis of the influence of atmospheric parameters to the system efficiency. Dense array modules are assembled into large receivers of approximately a quarter of square meter in size and with a typical efficiency of 31.7% and power output of 36.5kWp under Standard Operating Conditions (SOC, 1000W/m2, AM1.5D, low AOD and 21°C cell temperature). At Normal Operating Cell Temperature (NOCT 53°C), the receiver efficiency and power output become 30% and 35.4kW. The DC efficiency of the dish unit is 24.5% at SOC. More interestingly, the specific Energy Production Rate (EPR) of each dish, being the ratio of the daily energy output and the daily incident direct-beam energy (DNR), was measured. In average, over a two-year period and over four dishes, the EPR was 27.5 m2, corresponding to the equivalent aperture of a 100%-efficient solar energy converter. The annualised efficiency of these CPV systems is 21.1%. A new generation of dense array modules have demonstrated efficiency of 36.1% at 50W/cm2 and 21°C. Also, a new redesigned optics has recently been implemented on one of the dishes and has demonstrated a significant boost in efficiency, bringing the SOC efficiency to 26.2% and an expected EPR of 30 m2. We expect that combining the 2nd generation modules with the redesigned optics would improve the DC efficiency to 28% at SOC.
A hybrid modeling strategy for GMM-SVM speaker recognition with adaptive relevance factor

In Gaussian mixture model (GMM) approach to speaker recognition, it has been found that the maximum a posteriori (MAP) estimation is greatly affected by undesired variability due to varying duration of utterance as well as other hidden factors related to recording devices, session environment, and phonetic contents. We propose an adaptive relevance factor (RF) to compensate for this variability. In the other side, in realistic application, it is likely that the different channel corresponds to its different training and test conditions in terms of quantity and quality of the speech signals. In this connection, we develop a hybrid model that combines multiple complementary systems, each of which focuses on speciﬁc condition(s). We show the effectiveness of the proposed method on the core task of the National Institute of Standards and Technology (NIST) speaker recognition evaluation (SRE) 2008.
Actual and counterfactual growth incidence and delta Lorenz curves: Estimation and inference

Different economic growth episodes display very different distributional characteristics, both across countries and over time. Growth is sometimes accompanied by rising and sometimes by falling inequality. Applied economists have come to rely on the growth incidence curve, which gives the quantile‐specific rate of income growth over a certain period, to describe these differences. This paper introduces a mean‐independent analogue, the delta Lorenz curve, which gives the cumulative change in income share up to each quantile. We also develop estimation and inference procedures for both functions of quantiles. We establish the limiting null distribution of the test statistics of interest for those functions, and propose resampling methods to implement inference in practice. The proposed methods are used to compare the growth processes in the USA and Brazil during 1995–2007. Although growth in the average real wages was disappointing in both countries, the distribution of that growth was markedly different. In the USA, wage growth was mediocre for the bottom 80% of the sample, but much more rapid for the top 20%. In Brazil, conversely, wage growth was rapid below the median, and negative at the top. Wage shares fell in the USA up to the 83rd percentile, and rose in Brazil up to the 65th percentile.
Industry Gender Imprinting and New Venture Creation: The Liabilities of Women’s Leagues in the Sports Industry

This paper examines how industry gender imprinting—the persistence of cultural values, beliefs, norms, and orientations associated with masculinity or femininity—influences new ventures. Our investigation of women’s leagues in the male-dominated sports industry reveals how gender imprinting negatively affects new ventures’ endeavors through three liabilities: identity, conformity, and differentiation. Our findings shed light on the challenges new ventures not aligned with the industry imprint encounter to obtaining material and symbolic support. We contribute to theory by advancing knowledge on how industry-specific sociocultural attributes influence entrepreneurial efforts, and to practice by suggesting how to overcome cultural roadblocks in gendered industries.
A simple and rapid method for extracting bacterial DNA from intestinal microflora for ERIC-PCR detection.

AIM To develop a simple and convenient method for extracting genomic DNA from intestinal microflora for enterobacterial repetitive intergenic consensus (ERIC)-PCR detection. METHODS Five methods of extracting bacterial DNA, including Tris-EDTA buffer, chelex-100, ultrapure water, 2% sodium dodecyl sulfate and 10% Triton-100 with and without sonication, were compared with the commercial fecal DNA extraction kit method, which is considered as the gold standard for DNA extraction. The comparison was based on the yield and purity of DNA and the indexes of the structure and property of micro-organisms that were reflected by ERIC-PCR. RESULTS The yield and purity of DNA obtained by the chelex method was similar to that obtained with the fecal DNA kit. The ERIC-PCR results obtained for the DNA extracted by the chelex method and those obtained for DNA extracted with the fecal DNA kit were basically the same. CONCLUSION The chelex method is recommended for ERIC-PCR experiments in view of its simplicity and cost-effectiveness; and it is suitable for extracting total DNA from intestinal micro-organisms, particularly for handling a large number of samples.
Breast Ultrasound Technology and Performance Evaluation of Ultrasound Equipment: B-Mode

Ultrasound (US) has become increasingly important in imaging and image-guided interventional procedures. In order to ensure that the imaging equipment performs to the highest level achievable and thus provides reliable clinical results, a number of quality control (QC) methods have been developed. Such QC is increasingly required by accrediting agencies and professional organizations; however, these requirements typically do not include detailed procedures for how the tests should be performed. In this paper, a detailed overview of QC methods for general and breast US imaging using computer-based objective methods is described. The application of QC is then discussed within the context of a common clinical application (US-guided needle biopsy) as well as for research applications, where QC may not be mandated, and thus is rarely discussed. The implementation of these methods will help in finding early stage equipment faults and in optimizing image quality, which could lead to better detection and classification of suspicious findings in clinical applications, as well as improving the robustness of research studies.
An Epidemic Model of Information Dissemination in Mobile Social Networks

In this paper, we propose a new model for information dissemination in mobile social networks. The dynamic equation of information dissemination is modified. Moreover, we investigate numerically the behavior of the model on a real scale-free social site with the exponent γ =1.08. We find that initial spreaders with big out-degree of can accelerate information dissemination, and the nodes with large in-degree would be easier to be a spreader or to become to stiflers.
A Phase I Trial of the Anti-KIR Antibody IPH2101 and Lenalidomide in Patients with Relapsed/Refractory Multiple Myeloma

Purpose: Natural killer (NK) cells may play an important role in the immune response to multiple myeloma; however, multiple myeloma cells express killer immunoglobulin-like receptor (KIR) ligands to prevent NK cell cytotoxicity. Lenalidomide can expand and activate NK cells in parallel with its direct effects against multiple myeloma; however, dexamethasone may impair these favorable immunomodulatory properties. IPH2101, a first-in-class antiinhibitory KIR antibody, has acceptable safety and tolerability in multiple myeloma as a single agent. The present work sought to characterize lenalidomide and IPH2101 as a novel, steroid-sparing, dual immune therapy for multiple myeloma. Experimental Design: A phase I trial enrolled 15 patients in three cohorts. Lenalidomide was administered per os at 10 mg on cohort 1 and 25 mg on cohorts 2 and 3 days 1 to 21 on a 28-day cycle with IPH2101 given intravenously on day 1 of each cycle at 0.2 mg/kg in cohort 1, 1 mg/kg in cohort 2, and 2 mg/kg in cohort 3. No corticosteroids were utilized. The primary endpoint was safety, and secondary endpoints included clinical activity, pharmacokinetics (PK), and pharmacodynamics (PD). Results: The biologic endpoint of full KIR occupancy was achieved across the IPH2101 dosing interval. PD and PK of IPH2101 with lenalidomide were similar to data from a prior single-agent IPH2101 trial. Five serious adverse events (SAE) were reported. Five objective responses occurred. No autoimmunity was seen. Conclusions: These findings suggest that lenalidomide in combination with antiinhibitory KIR therapy warrants further investigation in multiple myeloma as a steroid-sparing, dual immune therapy. This trial was registered at www.clinicaltrials. gov (reference: NCT01217203). Clin Cancer Res; 21(18); 4055–61. ©2015 AACR.
ddradseqtools: a software package for in silico simulation and testing of double‐digest RADseq experiments

Double‐digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particular features of the genome of the focal species, possible modifications to the library construction protocol, coverage needed to minimize missing data, and the potential sources of error that may impact upon the coverage. We present ddradseqtools, a software package to help ddRADseq experimental design by (i) the generation of in silico double‐digested fragments; (ii) the construction of modified ddRADseq libraries using adapters with either one or two indexes and degenerate base regions (DBRs) to quantify PCR duplicates; and (iii) the initial steps of the bioinformatics preprocessing of reads. ddradseqtools generates single‐end (SE) or paired‐end (PE) reads that may bear SNPs and/or indels. The effect of allele dropout and PCR duplicates on coverage is also simulated. The resulting output files can be submitted to pipelines of alignment and variant calling, to allow the fine‐tuning of parameters. The software was validated with specific tests for the correct operability of the program. The correspondence between in silico settings and parameters from ddRADseq in vitro experiments was assessed to provide guidelines for the reliable performance of the software. ddradseqtools is cost‐efficient in terms of execution time, and can be run on computers with standard CPU and RAM configuration.
Loop-Mediated Isothermal Amplification Method for Rapid Detection of the Periodontopathic Bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola

ABSTRACT Loop-mediated isothermal amplification (LAMP), a novel nucleic acid amplification method, was developed for the rapid detection of the major periodontal pathogens Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. The LAMP method amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand displacement activity. In this study, we initially designed the primers for LAMP assays to detect these bacteria and evaluated the specificity and sensitivity of these assays. The specificities of the primers for these bacteria were examined using various oral bacteria and various reaction times. The lower detection limits of the 60-min LAMP reaction without loop primers were 1 μg/tube for P. gingivalis, 10 fg/tube for T. forsythia, and 1 ng/tube for T. denticola. Addition of the loop primers for each bacterium improved the detection specificities and sensitivities by several magnitudes. Furthermore, LAMP assays were applied to the rapid detection of these periodontal pathogens in clinical specimens, and the results were compared with those of conventional PCR detection. The results of the LAMP assays corresponded to those of conventional PCR assays. These results indicate that the LAMP assay is an extremely rapid, highly sensitive, specific method. This method is very useful for the rapid detection of periodontopathic bacteria and the diagnosis of periodontal disease.
Factors affecting government-funded research quality

ABSTRACT As the number of research grants distributed to academic research in science has been continuously increasing, it is necessary to examine various factors that affect research quality. While there have been a large number of studies on factors that affect research productivity or performance, their empirical results have been quite inconclusive and conflicting. We argue that one of the reasons for mixed results involves the measurement of research performance. To tackle the problem, we measure the quality of government-funded research through journal impact factors as well as journal rankings, considering the specific features of academic disciplines. We find that the magnitude and degree of factors vary depending on how research quality is measured. More interestingly, several variables including researchers’ ages, the number of authors, and international collaboration show completely different results according to the level of journal ranking. Based on the empirical results, we suggest policy interventions that can improve the quality of government-supported research.