Miracle-dz/UniFAR-FTUs huggingface dataset:
Limits and potential of targeted sequencing analysis of liquid biopsy in patients with lung and colon carcinoma

The circulating free tumor DNA (ctDNA) represents an alternative, minimally invasive source of tumor DNA for molecular profiling. Targeted sequencing with next generation sequencing (NGS) can assess hundred mutations starting from a low DNA input. We performed NGS analysis of ctDNA from 44 patients with metastatic non-small-cell lung carcinoma (NSCLC) and 35 patients with metastatic colorectal carcinoma (CRC). NGS detected EGFR mutations in 17/22 plasma samples from EGFR-mutant NSCLC patients (sensitivity 77.3%). The concordance rate between tissue and plasma in NSCLC was much lower for other mutations such as KRAS that, based on the allelic frequency and the fraction of neoplastic cells, were likely to be sub-clonal. NGS also identified EGFR mutations in plasma samples from two patients with EGFR wild type tumor tissue. Both mutations were confirmed by droplet digital PCR (ddPCR) in both plasma and tissue samples. In CRC, the sensitivity of the NGS plasma analysis for RAS mutations was 100% (6/6) in patients that had not resection of the primary tumor before blood drawing, and 46.2% (6/13) in patients with primary tumor resected before enrollment. Our study showed that NGS is a suitable method for plasma testing. However, its clinical sensitivity is significantly affected by the presence of the primary tumor and by the heterogeneity of driver mutations.
A pediatric twin study of brain morphometry.

BACKGROUND Longitudinal pediatric neuroimaging studies have demonstrated increasing volumes of white matter and regionally-specific inverted U shaped developmental trajectories of gray matter volumes during childhood and adolescence. Studies of monozygotic and dyzygotic twins during this developmental period allow exploration of genetic and non-genetic influences on these developmental trajectories. METHOD Magnetic resonance imaging brain scans were acquired on a pediatric sample of 90 monozygotic twin pairs, 38 same-sex dyzygotic twin pairs, and 158 unrelated typically developing singletons. Structural equation modeling was used to estimate the additive genetic, common environment, and unique environment effects, as well as age by heritability interactions, on measures of brain volumes from these images. RESULTS Consistent with previous adult studies, additive genetic effects accounted for a substantial portion of variability in nearly all brain regions with the notable exception of the cerebellum. Significant age by heritability interactions were observed with gray matter volumes showing a reduction in heritability with increasing age, while white matter volume heritability increased with greater age. CONCLUSION Understanding the relative contributions of genetic and nongenetic factors on developmental brain trajectories may have implications for better understanding brain-based disorders and typical cognitive development.
Responses Cyclophosphamide Treatment on Antitumor Immune Expression and Oncolysis in Combination with Low-Dose Effect of Adenovirus-Mediated Heat Shock Protein

Heat shock proteins such as gp96 have the ability to chaperone peptides and activate antigen-presenting cells. In this study, we tested whether adenovirus-mediated overexpression of secreted or membrane-associated forms of gp96 in tumor cells would stimulate an antitumor immune response. Studies were carried out in C57Bl/6 mice bearing aggressively growing s.c. tumors derived from syngeneic TC-1 cells, a cell line that expresses HPV16 E6 and E7 proteins. We found that secreted gp96 can induce protective and therapeutic antitumor immune responses. Our data also indicate that the antitumor effect of sgp96 expression seems to be limited by the induction of suppressive regulatory T cells (Treg). TC-1 tumor transplantation increased the number of splenic and tumor-infiltrating Tregs. Importantly, treatment of mice with low-dose cyclophosphamide decreased the number of Tregs and enhanced the immunostimulatory effect of sgp96 expression. We also tested whether an oncolytic vector (Ad.IR-E1A/TRAIL), that is able to induce tumor cell apoptosis and, potentially, release cryptic tumor epitopes in immunogenic form, could stimulate antitumor immune responses. Although tumor cells infected ex vivo with Ad.IRE1A/TRAIL had no antitumor effect when used as a vaccine alone, the additional treatment with low-dose cyclophosphamide resulted in the elimination of pre-established tumors. This study gives a rationale for testing approaches that suppress Tregs in combination with oncolytic or immunostimulatory vectors. (Cancer Res 2006; 66(2): 960-9)
Taxes and Charitable Giving

This article reviews the basic mechanisms of federal tax incentives, the current level, sources and recipients of charitable donations, and the estimated magnitude of the response to tax incentives. In addition, we discuss the possible effects of recent tax proposals on charitable giving. These proposals include changing the marginal rate structure, allowing taxpayers using the standard deduction to reduce taxable income by the amount of their contributions, and repealing the estate tax.
Enteric Glia Cells Attenuate Cytomix-Induced Intestinal Epithelial Barrier Breakdown

Background Intestinal barrier failure may lead to systemic inflammation and distant organ injury in patients following severe injury. Enteric glia cells (EGCs) have been shown to play an important role in maintaining gut barrier integrity through secretion of S-Nitrosoglutathione (GSNO). We have recently shown than Vagal Nerve Stimulation (VNS) increases EGC activation, which was associated with improved gut barrier integrity. Thus, we sought to further study the mechanism by which EGCs prevent intestinal barrier breakdown utilizing an in vitro model. We postulated that EGCs, through the secretion of GSNO, would improve intestinal barrier function through improved expression and localization of intestinal tight junction proteins. Methods Epithelial cells were co-cultured with EGCs or incubated with GSNO and exposed to Cytomix (TNF-α, INF-γ, IL-1β) for 24 hours. Barrier function was assessed by permeability to 4kDa FITC-Dextran. Changes in tight junction proteins ZO-1, occludin, and phospho-MLC (P-MLC) were assessed by immunohistochemistry and immunoblot. Key Results Co-culture of Cytomix-stimulated epithelial monolayers with EGCs prevented increases in permeability and improved expression and localization of occludin, ZO-1, and P-MLC. Further, treatment of epithelial monolayers with GSNO also prevented Cytomix-induced increases in permeability and exhibited a similar improvement in expression and localization of occludin, ZO-1, and P-MLC. Conclusions & Inferences The addition of EGCs, or their secreted mediator GSNO, prevents epithelial barrier failure after injury and improved expression of tight junction proteins. Thus, therapies that increase EGC activation, such as VNS, may be a novel strategy to limit barrier failure in patients following severe injury.
RMDP: an FEC-based reliable multicast protocol for wireless environments

In this paper we present a Reliable Multicast data Distribution Protocols (RMDP), and discuss its performance. The protocol is based on the use of FEC techniques to drastically reduce the impact of independent losses for different receivers, which make ARQ-based protocols perform very poorly as the number of receivers grows. The protocol is well-suited to the use with mobile equipment because of its simplicity, robustness to losses, moderate demand for feedback, and scalability.
The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae)

The phylogenetic placement of the monotypic crab plover Dromasardeola (Aves, Charadriiformes) remains controversial. Phylogenetic analysis of anatomical and behavioral traits using phenetic and cladistic methods of tree inference have resulted in conflicting tree topologies, suggesting a close association of Dromas to members of different suborders and lineages within Charadriiformes. Here, we revisited the issue by applying Bayesian and parsimony methods of tree inference to 2,012 anatomical and 5,183 molecular characters to a set of 22 shorebird genera (including Turnix). Our results suggest that Bayesian analysis of anatomical characters does not resolve the phylogenetic relationship of shorebirds with strong statistical support. In contrast, Bayesian and parsimony tree inference from molecular data provided much stronger support for the phylogenetic relationships within shorebirds, and support a sister relationship of Dromas to Glareolidae (pratincoles and coursers), in agreement with previously published DNA-DNA hybridization studies.
Characteristics of resist films produced by spinning

A model is presented for the description of thin films prepared from solution by spinning. Using only the centrifugal force, linear shear forces, and uniform evaporation of the solvent, the thickness of the film and the time of drying can be calculated as functions of the various processing parameters. The model is compared with experimental results obtained on positive photoresists and excellent agreement is obtained. When adequate care are is taken, the liquid forms a level surface during spinning, and the film thickness becomes uniform and independent of the size of the substrate. The film thickness h shows the following dependence on spin speed f, initial viscosity ν0, and evaporation rate e:h∝f−2/3νo1/3e1/3, and e is proportional to f1/2.
Family, Class and Gender ‘Strategies’ in Mothers’ Employment and Childcare

Both women and men strive to achieve a work and family balance, but does this imply more or less equality? Does the persistence of gender and class inequalities refute the notion that lives are becoming more individualised? Leading international authorities document how gender inequalities are changing and how many inequalities of earlier eras are being eradicated. However, this book shows there are new barriers and constraints that are slowing progress in attaining a more egalitarian society. Taking the new global economy into account, the expert contributors to this book examine the conflicts between different types of feminisms, revise old debates about ‘equality’ and ‘difference’ in the gendered nature of work and care, and propose new and innovative policy solutions.
Redesigning production through teamworking: Case studies from the Volvo Truck Corporation

There has long been a debate concerning whether the technical division of labour should be structured around the individual or the group. With the developing of lean production and other forms of work organization under advanced manufacturing, teamworking has emerged as a central focus of redesigning production. However, considerable conceptual confusion remains, as well as sharply opposed models drawing on Japanese and Northern European traditions. Provides a framework for understanding the potentially different configurations of teamworking by distinguishing between technical, governance and normative dimensions. Explores these in the context of evidence from case studies of Volvo truck plants in Sweden. The variations observed in different production environments emphasize the point that there is no authentic, linear tradition, or undifferentiated package in theory or in practice.
Exchange Sponsored Analyst Coverage

This study examines the effects and consequences of an exchange-sponsored analyst coverage scheme to evaluate the effectiveness of stock exchanges promoting research coverage for firms. The context of this study is the Research Incentive Scheme pioneered by the Singapore Stock Exchange, under which the exchange acts as a ‘clearing house’ for matching up firms and analysts electing into the Scheme and partially funds the analyst’s research coverage. The empirical evidence reveals that forecasts issued under the scheme have similar bias to those issued by analysts voluntarily following a firm, but are less accurate. The market reactions to revisions are also qualitatively similar across these forecasts. Further, after controlling for self-selection, we document a variety of benefits to a firm from joining the scheme, including: (i) a decline in market surprises at earnings announcements, consistent with analysts improving market’s earnings expectations (ii) a quicker reflection of earnings and non-earnings information in stock prices (iii) an increase in stock price synchronicity, consistent with analyst helping incorporate more industry-wide information, and (iv) an increase in media visibility. We find little evidence that analyst coverage through the scheme improves liquidity or price efficiency.
The Composition Effect of Macroeconomic Factors on Foreign Direct Investment in Selected SAARC Countries

The objective of the study is to investigate the most promising economic variables i.e., foreign direct investment (FDI), exports and financial development on economic growth in selected South Asian Association of Regional Co-corporation (SAARC) countries. In addition, this study argued that whether FDI, Exports and financial development fosters or hinder economic growth in SAARC countries, for this purpose, panel data set of selected five SAARC countries namely, Bangladesh, India, Nepal, Pakistan and Srilanka considered for empirical consideration over a period of 1975 to 2011. By using two-stage least square (2SLSL) technique, empirical evidence on the effects of FDI, exports and financial development on economic growth is mix in terms of apriori expectations. In case of Bangladesh, exports and broad money supply (M2) is the positive and significant contributor to increase economic growth, whereas, M2 increases India’s GDP. FDI is the only significant contributor to increase Pakistan’s economic growth. In case of Nepal and Srilanka, broad money supply increases economic growth, whereas, due to high dependency on imports, exports could not considerably increases economic growth in those regions.
Effects of Institutional Structures on Accounts Manipulation: An International Study

This paper identifies, and then examines, whether institutional structures can be used to explain the occurrence of accounts manipulation. Specifically, it investigates whether legal origin, level of corruption, the extent of press freedom, State’s ownership of enterprises, and the State’s attempts at investor protection are (not) likely to affect the occurrence of accounts manipulation. Archival data cover the period January 2000-August 2008, inclusive. They are analysed using multivariate data analysis techniques, paired samples tests, and chi-square tests.We document evidence suggesting that legal origins can be associated with the occurrence of accounts manipulation. We also find that the State’s ownership of enterprises and its at-tempts at investor protection is likely to affect the occurrence of accounts manipulation by encouraging the act manipulation. There is evidence suggesting that these institutional structures explain more than 66% of the variation in occurrence of accounts manipulation after controlling for national cultural values and countries’ level of wealth. The result holds irrespective of whether we control for the influence of national cultures and managers’ economic status via the level of wealth of the country in which they operate.
What a Difference Ten Years Can Make: Research Possibilities for the Future of Media Literacy Education

The National Association for Media Literacy Education’s Journal of Media Literacy Education 3:1 (2011) 11 13 Media Literacy Education: On the Move Margaret Carmody Hagood Department of Teacher Education, College of Charleston, Charleston, SC, USA In 2005, several colleagues and I were awarded a five-year grant to create the Center of Excellence for the Advancement of New Literacies in Middle Grades at the College of Charleston. From 2006-2011, we have worked collaboratively with over 200 middle school teachers in underperforming local schools to assist them in stimulating their content area instruction with media literacy, and specifically with new literacies practices that include three components: (1) a broadened definition of reading and of text, which includes both print and non-print sources, and is built upon developing literacies that address reading, writing, listening, speaking, viewing, and designing, (2) a sociocultural perspective of literacy that builds upon connections between learners’ interests, identities, and texts they choose, and (3) uses of pop culture and digital technologies salient to learners’ lives. In this essay, I take a brief retrospective analysis of where we’ve been over the past several years and where we are heading for the future of media literacy education in schools.
Dependencies of Field Effect Mobility on Regioregularity and Side Chain Length in Poly(Alkylthiophene)Films

SUMMARY Carrier mobilities in poly(3-alkylthiphene) cast films have been studied by means of fabricating a field effect transistor (FET) at the field range of (0.4–1.6)×104 V/cm. It is found that the regioregurality is markedly effective to the mobilities than the side chain length. The FET mobilility of the regioregular poly(3-hexylthiophene), PHT is approximately 3×10 −3 cm 2 /Vs which is larger than that of regiorandom PHT by 3 orders of magnitude. The mobility of regioregular poly(3dodecylthiophene), PDDT is 8×10 −4 cm 2 /Vs and is also 3 orders of magnitude larger than that of regiorandom PDDT. The mobilities of regioregular ones decrease, however, those of regiorandom ones increase at higher fields. The FET mobilities are nearly same to the mobilities estimated by the time of flight method. These results have been discussed taking the regularity of the main chain and the length of side chain into consideration.
A gender-balanced approach to the study of peer victimization and aggression subtypes in early childhood

Abstract A short-term longitudinal study during early childhood (N = 301; 155 girls; M = 44.76 months old, SD = 8.20) investigated the prospective associations between peer victimization and aggression subtypes. Specifically, observations of relational and physical victimization as well as teacher reports of the forms (i.e., relational and physical) and functions (i.e., proactive and reactive) of aggression were collected at two time points during an academic year. Within- and between-group gender differences were examined as part of the preliminary analyses. In order to address key study questions, both directions of effect between peer victimization and aggression subtypes were examined. We found that teacher-reported proactive relational aggression predicted decreases in observed relational victimization over time, whereas reactive relational aggression predicted increases in observed relational victimization over time. Ways in which these and other findings extend the literature are discussed.
Covariation of Branch Lengths in Phylogenies of Functionally Related Genes

Recent studies have shown evidence for the coevolution of functionally-related genes. This coevolution is a result of constraints to maintain functional relationships between interacting proteins. The studies have focused on the correlation in gene tree branch lengths of proteins that are directly interacting with each other. We here hypothesize that the correlation in branch lengths is not limited only to proteins that directly interact, but also to proteins that operate within the same pathway. Using generalized linear models as a basis of identifying correlation, we attempted to predict the gene ontology (GO) terms of a gene based on its gene tree branch lengths. We applied our method to a dataset consisting of proteins from ten prokaryotic species. We found that the degree of accuracy to which we could predict the function of the proteins from their gene tree varied substantially with different GO terms. In particular, our model could accurately predict genes involved in translation and certain ribosomal activities with the area of the receiver-operator curve of up to 92%. Further analysis showed that the similarity between the trees of genes labeled with similar GO terms was not limited to genes that physically interacted, but also extended to genes functioning within the same pathway. We discuss the relevance of our findings as it relates to the use of phylogenetic methods in comparative genomics.
4 Classification of Pre-Filtered Multichannel Remote Sensing Images

Multichannel remote sensing (RS) has gained popularity and has been successfully applied for solving numerous practical tasks as forestry, agriculture, hydrology, meteorology, ecology, urban area and pollution control, etc. (Chang, 2007). Using the term “multichannel”, we mean a wide set of imaging approaches and RS systems (complexes) including multifrequency and dual/multi polarization radar (Oliver & Quegan, 2004), multiand hyperspectral optical and infrared sensors. While for such radars the number of formed images is a few, the number of channels (components or sub-bands) in images can be tens, hundreds and even more than one thousand for optical/infrared imagers. TerraSAR-X is a good example of modern multichannel radar system; AVIRIS, HYDICE, HYPERION and others can serve as examples of modern hyperspectral imagers, both airborne and spaceborne (Landgrebe, 2002; Schowengerdt, 2007).
Customized MFM probes with high lateral resolution

Magnetic force microscopy (MFM) is a widely used technique for magnetic imaging. Besides its advantages such as the high spatial resolution and the easy use in the characterization of relevant applied materials, the main handicaps of the technique are the lack of control over the tip stray field and poor lateral resolution when working under standard conditions. In this work, we present a convenient route to prepare high-performance MFM probes with sub-10 nm (sub-25 nm) topographic (magnetic) lateral resolution by following an easy and quick low-cost approach. This allows one to not only customize the tip stray field, avoiding tip-induced changes in the sample magnetization, but also to optimize MFM imaging in vacuum (or liquid media) by choosing tips mounted on hard (or soft) cantilevers, a technology that is currently not available on the market.
Microporous Titanium through Metal Injection Moulding of Coarse Powder and Surface Modification by Plasma Oxidation

Titanium is one of the most attractive materials for biomedical applications due to having excellent biocompatibility accompanied by good corrosion resistance. One popular processing technique for Ti is Metal Injection Moulding (MIM). However, there are several issues associated with the use of this technique, such as the high cost of the fine powder used, the high level of contamination and consequent alteration to material properties, as well as the large volume shrinkage that occurs during sintering. In this study, the use of a relatively coarse Ti powder with a mean particle size of 75 μm to process Ti parts with the potential for biomedical applications by MIM will be examined, compared to a commercial Ti feedstock, and subsequently coated using Plasma Electrolytic Oxidation (PEO). The results show that samples produced with the coarse powder shrink 35% less and have a relative density 14% less with an average pore size three-times larger than that of the commercial feedstock. This helps increase the potential competitiveness of MIM in the production of biomedical parts, as it reduces cost, shrinkage and results in more intentionally-induced micropores, such as are desired for biomedical implants. PEO treatment of the samples yields a thick rough coating comprised of a mixture of rutile and anatase with interconnected microporous channels and openings resembling the mouth of a volcanic crater.