Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Valid Reference Genes for the Normalization of RT-qPCR Expression Studies in Human Breast Cancer Cell Lines Treated with and without Transient Transfection

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a powerful technique for examining gene expression changes during tumorigenesis. Target gene expression is generally normalized by a stably expressed endogenous reference gene; however, reference gene expression may differ among tissues under various circumstances. Because no valid reference genes have been documented for human breast cancer cell lines containing different cancer subtypes treated with transient transfection, we identified appropriate and reliable reference genes from thirteen candidates in a panel of 10 normal and cancerous human breast cell lines under experimental conditions with/without transfection treatments with two transfection reagents. Reference gene expression stability was calculated using four algorithms (geNorm, NormFinder, BestKeeper and comparative delta Ct), and the recommended comprehensive ranking was provided using geometric means of the ranking values using the RefFinder tool. GeNorm analysis revealed that two reference genes should be sufficient for all cases in this study. A stability analysis suggests that 18S rRNA-ACTB is the best reference gene combination across all cell lines; ACTB-GAPDH is best for basal breast cancer cell lines; and HSPCB-ACTB is best for ER+ breast cancer cells. After transfection, the stability ranking of the reference gene fluctuated, especially with Lipofectamine 2000 transfection reagent in two subtypes of basal and ER+ breast cell lines. Comparisons of relative target gene (HER2) expression revealed different expressional patterns depending on the reference genes used for normalization. We suggest that identifying the most stable and suitable reference genes is critical for studying specific cell lines under certain circumstances.
Adolescents’ identity experiments on the internet

The aim of this article is to investigate how often adolescents engage in internet-based identity experiments, with what motives they engage in such experiments and which self-presentational strategies they use while experimenting with their identity. Six hundred nine to 18-year-olds completed a questionnaire in their classroom. Of the adolescents who used the internet for chat or Instant Messaging, 50 percent indicated that they had engaged in internet-based identity experiments. The most important motive for such experiments was self-exploration (to investigate how others react), followed by social compensation (to overcome shyness) and social facilitation (to facilitate relationship formation). Age, gender and introversion were significant predictors of the frequency with which adolescents engaged in internet-based identity experiments, their motives for such experiments, and their self-presentational strategies.
Congenital heart diseases among patients with Down syndrome consulting cardiology unite in Alsader Teaching Hospital in Basrah

Aim of the study: This study is aimed to assess the types and the frequency of congenital heart disease among patients with Down syndrome (DS). Patients & methods: Sixty-five patients with DS collected from echocardiographic department in Basrah cardiology center at Alsader Teaching Hospital and a private clinic were evaluated by echocardiography from February 2009 to August 2013. Results: Their ages range from 6 months to 25 year. Of 65 patients with DS diagnosed clinically, 89% have CHD and 11% have normal heart. Most of the cases were isolated congenital heart disease (CHD). Ventricular septal defect (VSD), pulmonic stenosis (PS) and atrial septal defect (ASD) were the commonest isolated CHD respectively while tetralogy of Fallot (TOF) and single ventricle was the commonest complex CHD in DS. Conclusion: This study had concluded that CHD are common in DS and most of the cases are amenable for surgical corrections.
Strong Rules for Nonconvex Penalties and Their Implications for Efficient Algorithms in High-Dimensional Regression

We consider approaches for improving the efficiency of algorithms for fitting nonconvex penalized regression models such as smoothly clipped absolute deviation (SCAD) and the minimax concave penalty (MCP) in high dimensions. In particular, we develop rules for discarding variables during cyclic coordinate descent. This dimension reduction leads to an improvement in the speed of these algorithms for high-dimensional problems. The rules we propose here eliminate a substantial fraction of the variables from the coordinate descent algorithm. Violations are quite rare, especially in the locally convex region of the solution path, and furthermore, may be easily corrected by checking the Karush–Kuhn–Tucker conditions. We extend these rules to generalized linear models, as well as to other nonconvex penalties such as the ℓ2-stabilized Mnet penalty, group MCP, and group SCAD. We explore three variants of the coordinate decent algorithm that incorporate these rules and study the efficiency of these algorithms in fitting models to both simulated data and on real data from a genome-wide association study. Supplementary materials for this article are available online.
Sustainable Transportation: An Overview, Framework and Further Research Directions

In our study we have attempted to develop a theoretical framework for sustainable transportation based on synthesis of exhaustive review of extant literature. To test the framework statistically, a structured questionnaire was designed. Measures for the questionnaire were adopted from extant literature and to operationalise the constructs further, the questionnaire was to be pretested. Adding to this, the validity of the constructs was examined using confirmatory factor analysis followed by partial least square-structural equation modelling to test research hypotheses. The statistical analyses suggest that model exceed the threshold limit for goodness of fit test. Except government policy, all five research hypotheses are accepted. The present study is a unique contribution in terms of its theoretical implications and practical use. Finally, our research findings were concluded and further research directions were outlined.
A clinical evaluation of stumps in lower limb amputees

A study was carried out on 93 consecutive unilateral below-knee (BK) and 62 above-knee (AK) amputees. The dimensions of the amputation stumps were measured and the general condition and contralateral limb assessed at the time of prosthetic fitting. After one postoperative year, follow-up information for 124 (89%) of the surviving patients was obtained by personal contact. The observations were based on the standard formula for stump classification constructed by the International Society for Prosthetics and Orthotics. The 93 BK stumps had a mean length of 16.0 cm and the 62 AK stumps a mean length of 28.0 cm. The scar on the stump was adherent in 13% of BK and 2% of AK stumps. The scar was deeply wrinkled in 7% of BK stumps and 10% of AK stumps. The scar on the stump was most frequently adherent or deeply wrinkled in trauma patients (33%). The skin was undamaged in 93% of all the patients at the first visit and in 94% at the time of follow-up. The mobility of the stump in the proximal joint was limited at the time of prosthetic fitting in 15% of cases. Phantom pain was reported by 59% and stump pain by 5% of patients at this time. Although the phantom pain was mild in most cases, it was usually still present after one year, and 53% of the surviving patients suffered from phantom pain. At the first visit, 20% of patients had problems in their contralateral leg. During the first postoperative year, 6 contralateral BK amputations were performed in the BK group and one contralateral AK amputation in the AK group. Thus, along with examination of the stump, attention must be paid to the contralateral limb with a view to preserving it. The study supports the usefulness of the standard form and classification of amputation stumps.
A Prototype Intraoral Periapical Sensor with High Frame Rates for a 2.5D Periapical Radiography System

X-ray radiography is currently used in dentistry and can be divided into two categories: two-dimensional (2D) radiographic images (e.g., using periapical film, cephalometric film, and panoramic X-ray) and three-dimensional (3D) radiographic images (e.g., using dental cone-beam computed tomography (CBCT)). Among them, 2D periapical film images are most commonly used. However, 2D periapical film compresses 3D image information into a 2D image, which means that depth cannot be identified from the image. Such compressed images lose a considerable amount of information, reducing their clinical applicability. A 2.5D periapical radiography system prototype was developed by our research team. Our previous study indicated that this prototype could be used to capture images at different depths of an object. However, the prototype was limited by its commercially available intraoral periapical sensor, which had a low temporal resolution and could not capture multiple images in a short period of time. Therefore, the total time required for image capture was too long for practical clinical application. The present study developed a high-frame-rate intraoral periapical sensor with a sensor imaging speed of up to 15 Hz. The primary components of the developed intraoral periapical sensor include a scintillator, complementary metal oxide semiconductor chip, component circuit board, and video processing board. The external dimensions of the sensor are 41 × 26 × 6.6 mm3. The performance of the developed high-frame-rate intraoral periapical sensor was verified through qualified and quantified analyses using line pairs. The results showed that the resolution of the developed intraoral periapical sensor could reach 18 lp/mm. The sensor was further installed in our 2.5D periapical radiography system to conduct image capturing. The results indicated that the developed sensor could be used for high-frame-rate imaging to incorporate tomosynthesis to obtain reconstructed slice images of different depths. The developed sensor has the potential for clinical dentistry applications in the future.
Properties of wide‐separation lensed quasars by clusters of galaxies in the Sloan Digital Sky Survey

We use high-resolution N-body numerical simulations to study the number of predicted large-separation multiply imaged systems produced by clusters of galaxies in the Sloan Digital Sky Survey (SDSS) photometric and spectroscopic quasar samples. We incorporate the condensation of baryons at the centre of clusters by (artificially) adding a brightest cluster galaxy (BCG) as a truncated isothermal sphere. We make predictions in two flat cosmological models: a Lambda cold dark matter (Lambda CDM) model with a matter density Omega(m,0) = 0.3, sigma(8) = 0.9 (Lambda CDM 0) and a model favoured by the Wilkinson Microwave Anisotropy Probe (WMAP) three-year data with Omega(m,0) = 0.238 and sigma(8)= 0.74 (WMAP3). We found that the predicted multiply imaged quasars with separation > 10 arcsec is about 6.2 and 2.6 for the SDSS photometric (with an effective area of 8000 deg(2)) and spectroscopic (with an effective area of 5000 deg(2)) quasar samples, respectively, in the Lambda CDM0 model; the predicted numbers of large-separation lensed quasars agree well with the observations. These numbers are reduced by a factor of 7 or more in the WMAP3 model, and are consistent with the data at less than or similar to 8 per cent level. The predicted cluster lens redshift peaks around redshift 0.5, and 90 per cent are between 0.2 and 1. The ratio of systems with at least four image systems (N-img >= 4) and those with N-img >= 2 is about 1/3.5 for both the Lambda CDM0 and the WMAP3 models, and for both the photometric and the spectroscopic quasar samples. We find that the BCG creates a central circular region, comparable to the Einstein ring of the BCG, where the central image disappears in the usual three- and five-image configurations. If we include four image systems as an extreme case of five-image systems (with an infinitely demagnified central image), we find that 68 per cent of the central images are fainter by a factor of 100 than the brightest image and about 80 per cent are within 1.5 arcsec of the BCG.
Cytolytic effect of 6-hydroxydopamine on neuroblastoma cells.

Summary The effect of a dopamine analog, 6-hydroxydopamine, was investigated in tissue culture of a cell line of human neuroblastoma, mouse neuroblastoma C-1300, and cultures of HeLa cells and mouse sarcoma 37. Addition to the cultured medium of 6-hydroxydopamine results in degeneration of human and mouse neuroblastoma cells, while other neoplastic cells and fibroblasts do not appear to be affected. The hypothesis that this toxic effect might be due to selective uptake of this dopamine analog was tested by pulse labeling mouse and human neuroblastoma in vitro with catecholamine-3H. In both experimental series, neoplastic cells were heavily labeled. The action of 6-hydroxydopamine was also explored by injecting it into mice bearing transplants of C-1300 neuroblastoma. Marked tumor regression was noticeable in all cases in the first week of treatment. Histological examination performed at the end of this period shows large areas of necrosis and cell degeneration throughout the neoplastic tissue. A decrease in the effectiveness of the treatment became apparent in subsequent days, however, as the tumor increased in size.
Buying in: Analyzing the First Fan Adopters of a New National Collegiate Athletic Association (NCAA) Division I Football Program

Establishing a strong fan base within the inaugural year of a National Collegiate Athletic Association (NCAA) Division I Football Program presents many challenges. Tracking consumers and their behavior becomes imperative as sport marketers seek to better understand the first fan adopters of a new program. With new NCAA football programs being established every year, sport marketers of a new program are challenged to not only find a loyal fan-base who will continue to support the program despite win or lose, but find new and innovative ways to grow their fan base. The purpose of this study was to examine attendance demographics and consumer behavior for the inaugural football season at a NCAA Division 1 program. Data were collected (n = 914) from a relatively equal distribution of fan groups (students- 34.8%, alumni- 32.9%, and other- 32.3%) via an in-person survey completed on a tablet interface. Results demonstrate that the level of fandom (temporary, devoted, or fanatic) impacts certain consumer behaviors, including; overall support of the program, media consumption, and game day behaviors. Key words: First fan adopters, Division I football, consumer behavior.
Associations between Long-Term Exposure to Chemical Constituents of Fine Particulate Matter (PM2.5) and Mortality in Medicare Enrollees in the Eastern United States

Background: Several epidemiological studies have reported that long-term exposure to fine particulate matter (PM2.5) is associated with higher mortality. Evidence regarding contributions of PM2.5 constituents is inconclusive. Objectives: We assembled a data set of 12.5 million Medicare enrollees (≥ 65 years of age) to determine which PM2.5 constituents are a) associated with mortality controlling for previous-year PM2.5 total mass (main effect); and b) elevated in locations exhibiting stronger associations between previous-year PM2.5 and mortality (effect modification). Methods: For 518 PM2.5 monitoring locations (eastern United States, 2000–2006), we calculated monthly mortality rates, monthly long-term (previous 1-year average) PM2.5, and 7-year averages (2000–2006) of major PM2.5 constituents [elemental carbon (EC), organic carbon matter (OCM), sulfate (SO42–), silicon (Si), nitrate (NO3–), and sodium (Na)] and community-level variables. We applied a Bayesian hierarchical model to estimate location-specific mortality rates associated with previous-year PM2.5 (model level 1) and identify constituents that contributed to the spatial variability of mortality, and constituents that modified associations between previous-year PM2.5 and mortality (model level 2), controlling for community-level confounders. Results: One–standard deviation (SD) increases in 7-year average EC, Si, and NO3– concentrations were associated with 1.3% [95% posterior interval (PI): 0.3, 2.2], 1.4% (95% PI: 0.6, 2.4), and 1.2% (95% PI: 0.4, 2.1) increases in monthly mortality, controlling for previous-year PM2.5. Associations between previous-year PM2.5 and mortality were stronger in combination with 1-SD increases in SO42– and Na. Conclusions: Long-term exposures to PM2.5 and several constituents were associated with mortality in the elderly population of the eastern United States. Moreover, some constituents increased the association between long-term exposure to PM2.5 and mortality. These results provide new evidence that chemical composition can partly explain the differential toxicity of PM2.5. Citation: Chung Y, Dominici F, Wang Y, Coull BA, Bell ML. 2015. Associations between long-term exposure to chemical constituents of fine particulate matter (PM2.5) and mortality in Medicare enrollees in the eastern United States. Environ Health Perspect 123:467–474; http://dx.doi. org/10.1289/ehp.1307549
Involvement of miR-20a in Promoting Gastric Cancer Progression by Targeting Early Growth Response 2 (EGR2)

Gastric cancer (GC) is one of the most common cancers, with high incidences in East Asia. microRNAs (miRNAs) play essential roles in the carcinogenesis of GC. miR-20a was elevated in GC, while the potential function of miR-20a was poorly understood. miR-20a expression was examined in GC tissues and cell lines. The effects of miR-20a on the growth, migration, invasion, and chemoresistance of GC cells were examined. Luciferase reporter assay and Western blot were used to screen the target of miR-20a. miR-20a was increased in GC tissues and cell lines. miR-20a promoted the growth, migration and invasion of GC cells, enhanced the chemoresistance of GC cells to cisplatin and docetaxel. Luciferase activity and Western blot confirmed that miR-20a negatively regulated EGR2 expression. Overexpression of EGR2 significantly attenuated the oncogenic effect of miR-20a. miR-20a was involved in the carcinogenesis of GC through modulation of the EGR2 signaling pathway.
Rapid and long-term disappearance of CD 4 + T lymphocyte responses specific for Anaplasma marginale major surface protein-2 ( MSP 2 ) in MSP 2 vaccinates following challenge with live

long-term disappearance of CD4+ T lymphocyte responses specific for Anaplasma marginale major surface protein-2 (MSP2) in MSP2 vaccinates following challenge with live A. marginale' General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact openaccess@ed.ac. uk providing details, and we will remove access to the work immediately and investigate your claim.
Seasonal Variation of North American Form of Gigantolaelaps mattogrossensis (Acari: Laelapidae) on Marsh Rice Rat in Southern Coastal Texas

Abstract The ectoparasites of a small mammal community within an intertidal zone in the upper Gulf coast region of Texas were studied to assess the seasonal variation in abundances of the mite Gigantolaelaps mattogrossensis (Fonseca) (Acari: Laelapidae) on the marsh rice rat, Oryzomys palustris (Harlan). Further study into the ecology and dynamics of this parasite–host relationship was deemed to be necessary to expand the understanding of these potential participants in the ecology of Bayou Hantavirus, an important causative agent of Hantavirus pulmonary syndrome. The objective of this study was to determine the effects of five predictor variables on mite abundance: prevalences of hosts, relative humidity, precipitation, temperature, and length of daylight. Mite abundance was modeled as a function of the five variables with analyses of variance and multiple regressions; however, because the predictor variables pertain to the sampling period rather than to the individual rodent host, the effective sample size was small and thus the sums of squares and cross products matrix was singular. We therefore developed and used a new method for estimating regression coefficients based on the “noise-addition method” (random residual variation) combined with a bootstrap step converting the reduced rank data to full rank, providing realistic estimates of confidence intervals for the regression statistics. The population abundances of mites fluctuated significantly across collecting periods. Humidity and precipitation were the most influential variables in explaining the variation in abundances of mites. Model interpretation suggests that G. mattogrossensis is a nidicolous parasite. These results provide a baseline understanding of the seasonal interactions between parasite and host.
Compact complex manifolds with numerically effective tangent bundles

1. Basic properties of nef line bundles . p. 5 1.A. Nef line bundles . p. 5 1.B. Nef vector bundles . p. 11
Reaping the Rewards of Functional Diversity in Healthcare Teams: Why Team Processes Improve Performance

Functional diversity in healthcare teams—where members from different healthcare professions work together—is often advocated as the key to achieving quality patient outcomes. However, although functionally diverse teams promise much, they do not always deliver on that promise. Based on the informational diversity perspective, we argue that functional diversity increases role conflict and is an important factor that can help to explain why functional diversity does not always lead to effective team performance. We also argue that team processes play an important role in moderating the effect of functional diversity on role conflict and that depending on how functionally diverse healthcare teams are, certain team processes are more important than others for reducing role conflict thereby leading to improved team performance. We contrast two specific team processes (interpersonal conflict management and back up and helping) and argue for their relative importance depending on the level of functional diversity in healthcare teams. Data from 75 hospital teams support our differential predictions that interpersonal conflict management is a particularly important team process for reducing role conflict and improving team performance for teams with high functional diversity, whereas for teams with low functional diversity, back up and helping is a more important team process. These results have important implications for the management of functionally diverse healthcare teams. By identifying the relative importance of team processes, these results provide evidence for investing in team processes that enable healthcare teams to reap the rewards of functional diversity.