Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Characterization Reveals a Molecular Portrait of Nasopharyngeal Carcinoma Differentiation

Nasopharyngeal carcinoma (NPC) is categorized into three different differentiated subtypes by World Health Organization (WHO). Based on an earlier comparative proteomic database of the three histological subtypes, the study was to deepen our understanding of molecular mechanisms associated with NPC differentiation through bio-information mining. Among the three subtypes were 194 differentially expressed proteins (DEPs) of 725 identified proteins. Two DEPs, heat shock protein family B (small) member 1 (HSPB1) and keratin 5 (KRT5), were validated in a series of NPC tissue samples by using immunohistochemistry. Quantified protein families including keratins, S100 proteins (S100s) and heat shock proteins exhibited characteristic expression alterations. Comparisons of predicted bio-function activation states among different subtypes, including formation of cellular protrusion, metastasis, cell death, and viral infections, were conducted. Canonical pathway analysis inferred that Rho GTPases related signaling pathways regulated the motility and invasion of dedifferentiated NPC. In conclusion, the study explored the proteomic characteristics of NPC differentiation, which could deepen our knowledge of NPC tumorigenesis and allow the development of novel targets of therapeutic and prognostic value in NPC.
Creating and Capturing Value in Repeated Exchange Relationships: Managing a Second Paradox of Embeddedness

Prior empirical studies suggest repeated exchange develops increasing value in buyer-supplier relationships. A first order implication of this finding is that buyers will focus exchange to generate maximum value in relationships. However, buyers are equally concerned with value capture. By distributing rather than focusing exchange, buyers may position themselves to capture more of the value created, leaving buyers potentially conflicted concerning the choice. We label this dynamic the second paradox of embeddedness, distinguishing it from Uzzi’s (1997) paradox driven by technological uncertainty. By examining the procurement activities of a large, diversified manufacturing company, we then test for supplier and buyer behavior consistent with the conditions that enable and behaviors that result from this second paradox.
Low-energy spin excitations in the molecular magnetic cluster V15

We report an Inelastic Neutron Scattering (INS) study of the fully deuterated molecular compound K6[V15IVAs6O42] · 9D2O (V15). Due to geometrical frustration, the essential physics at low temperatures of the V15 cluster containing 15 coupled V4+ (S = 1/2) is determined by three weakly coupled spin-(1/2) on a triangle. The INS spectra at low energy allow us to directly determine the effective exchange coupling J0 = 0.211(2) meV within the triangle and the gap 2Δ = 0.035(2) meV between the two spin-(1/2) doublets of the ground state. Results are discussed in terms of deviations from trigonal symmetry and Dzyaloshinskii-Moriya (DM) interactions.
A major transmembrane protein of Golgi-derived COPI-coated vesicles involved in coatomer binding

Formation of non-clathrin-coated vesicles requires the recruitment of several cytosolic factors to the Golgi membrane. To identify membrane proteins involved in this budding process, a highly abundant type I transmembrane protein (p23) was isolated from mammalian Golgi-derived COPI-coated vesicles, and its cDNA was cloned and sequenced. It belongs to the p24 family of proteins involved in the budding of transport vesicles (Stamnes, M.A., M.W. Craighead, M.H. Hoe, N. Lampen, S. Geromanos, P. Tempst, and J.E. Rothman. 1995. Proc. Natl. Acad. Sci. USA. 92:8011-8015). p23 consists of a large NH2-terminal luminal domain and a short COOH-terminal cytoplasmic tail (-LRRFFKAKKLIE-CO2-) that shows similarity, but not identity, with the sequence motif-KKXX-CO2-, known as a signal for retrieval of escaped ER-resident membrane proteins (Jackson, M.R., T. Nilsson, and P.A. Peterson. 1990. EMBO (Eur. Mol. Biol. Organ.) J. 9:3153-3162; Nilsson, T. , M. Jackson, and P.A. Peterson. 1989. Cell. 58:707-718). The cytoplasmic tail of p23 binds to coatomer with similar efficiency as known KKXX motifs. However, the p23 tail differs from the KKXX motif in having an additional motif needed for binding of coatomer. p23 is localized to Golgi cisternae and, during vesicle formation, it concentrates into COPI-coated buds and vesicles. Biochemical analysis revealed that p23 is enriched in vesicles by a factor of approximately 20, as compared with the donor Golgi fraction, and is present in amounts stoichiometric to the small GTP-binding protein ADP-ribosylation factor (ARF) and coatomer. From these data we conclude that p23 represents a Golgi- specific receptor for coatomer involved in the formation of COPI-coated vesicles.
Geographic patterns of diversity in streams are predicted by a multivariate model of disturbance and productivity

1 Univariate explanations of biodiversity have often failed to account for broad‐scale patterns in species richness. As a result, increased attention has been paid to the development and testing of more synthetic multivariate hypotheses. One class of multivariate hypotheses, founded in successional diversity theory, predict that species richness is jointly influenced by periodic disturbances that create new niche opportunities in space or time, and the production of community biomass that speeds displacement of inferior by superior competitors. 2 While the joint response of diversity to disturbance and productivity has gained support from theoretical and small‐scale experimental studies, evidence that corresponding patterns of biodiversity occur broadly across natural systems is scarce. 3 Using a data set that employed standardized methods to sample 85 streams throughout the mid‐Atlantic United States of America, we show that biogeographical patterns of primary producer diversity in stream ecosystems are consistent with the predictions of a multivariate model that incorporates disturbance frequency and community biomass production as independent variables. Periphyton species richness is a concave‐down function of disturbance frequency (mean no. floods year−1) and of biomass production (µg of biomass accrual cm−2 day−1), and an increasing function of their interaction. 4 Changes in richness across the disturbance × productivity response surface can be related to several predicted life‐history traits of the dominant species. 5 Our findings complement prior studies by showing that multivariate models which consider interactive effects of community production and ecosystem disturbance are, in fact, candidate explanations of much broader patterns of richness in natural systems. Because multivariate models predict synergistic effects of ecological variables on species diversity, human activities – which are simultaneously altering both the disturbance regime and productivity of streams – could be influencing biodiversity more than previously anticipated.
SPANISH COMPANY FOREIGN MARKET ENTRY

The aim of this paper is to analyse the determinants of diversification mode (acquisition versus greenfield) through foreign direct investment considering various theories, such as those of mergers and acquisitions, transaction costs, the learning organisation, the institutional context of the company and the cultural environment of the host country, and to analyse the determinants of entry mode combining diversification mode with ownership structure decision (greenfield wholly-owned subsidiaries, greenfield joint ventures, full acquisition and partial acquisition) and proposing various research hypotheses. The methodology used estimates various binomial and multinomial logit models, over a sample of 141 Spanish manufacturing companies between 1998 and 2000, finding that entry mode into a foreign country through direct investment is mainly explained by related diversification, international and local experience, advertising intensity, cultural distance, company size and ownership structure. El proposito de este trabajo consiste en analizar, por un lado, los determinantesdel modo de diversificacion (adquisicion versus desarrollo interno) de la inversiondirecta en el exterior considerando diversas aproximaciones teoricas, como las defusiones y adquisiciones, costes de transaccion, del aprendizaje organizativo, asi comodel contexto institucional de la empresa y del entorno cultural del pais receptor. Por otrolado, se examinan los determinantes de la inversion directa exterior combinando elmodo de diversificacion con la estructura de la propiedad empresarial (adquisicion total,adquisicion parcial, filial de plena propiedad y filial de propiedad compartida)proponiendo diversas hipotesis de investigacion. La metodologia aplicada estimadiversos modelos logit, binomial y multinomial, sobre 141 empresas espanolasmanufactureras entre 1998 y 2000, detectando que el modo de entrada medianteinversion directa exterior viene explicada por la diversificacion relacionada, laexperiencia internacional y local de la empresa, la intensidad publicitaria, la distanciacultural, asi como por el tamano y estructura de la propiedad de la empresa.
Content based image retrieval with LIRe

LIRe (Lucene Image Retrieval) is an open source library for content based image retrieval. Besides providing multiple common and state of the art retrieval mechanisms it allows for easy use on multiple platforms. LIRe is actively used for research, teaching and commercial applications. Due to its modular nature it can be used on process level (e.g. index images and search) as well as on image feature level. Developers and researchers can easily extend and modify LIRe to adapt it to their needs.
Essays in Dynamic Corporate Finance

My dissertation aims at understanding the financing and investment decisions of firms. It contains two chapters. Chapter One studies the currency composition of debt for firms in emerging economies. Using a dataset of traded Mexican firms, I document two stylized facts about firms in the non-tradable sector: (i) they take on large amounts of dollar-denominated debt and (ii) their earnings are not sensitive to the exchange rate. I propose an explanation based on imperfect competition in the domestic goods market that reconciles these seemingly contradictory empirical facts. First I develop a stylized model of production and financing for firms in an open economy. I show that non-exporting firms are exposed to exchange rate risk because of the presence of exporters in the economy, and that they hedge their currency exposure using dollar debt. An extended model is used to quantify how much of the dollar debt in the data can be explained through this channel. A calibrated version of the model can account for all of the dollar debt observed in the data. Chapter Two investigates the relationship between the investment decisions of firms and their cost of financing. Recent empirical work using panel data documents that, while the correlation of investment and Tobin's Q is low, the correlation of investment and credit spreads is high. We propose an explanation for these empirical findings, based on time-varying risk, i.e. stochastic volatility. In our model, firms finance investments using defaultable debt as well as equity issuance, and they are subject to standard profitability shocks as well as shocks to volatility. An increase in volatility leads to an increase in the probability of default and hence the credit spread, while reducing investment and increasing equity value. This shock hence generates a negative correlation between investment and credit spreads, and between investment and Q, helping the model match the data. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Finance First Advisor Joao F. Gomes Second Advisor Urban J. Jermann Third Advisor Andrew B. Abel This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/151
Mild Cognitive Impairment Is Not “Mild” at All in Altered Activation of Episodic Memory Brain Networks: Evidence from ALE Meta-Analysis

The present study conducted a quantitative meta-analysis aiming at assessing consensus across the functional neuroimaging studies of episodic memory in individuals with amnestic mild cognitive impairment (aMCI) and elucidating consistent activation patterns. An activation likelihood estimation (ALE) was conducted on the functional neuroimaging studies of episodic encoding and retrieval in aMCI individuals published up to March 31, 2015. Analyses covered 24 studies, which yielded 770 distinct foci. Compared to healthy controls, aMCI individuals showed statistically significant consistent activation differences in a widespread episodic memory network, not only in the bilateral medial temporal lobe and prefrontal cortex, but also in the angular gyrus, precunes, posterior cingulate cortex, and even certain more basic structures. The present ALE meta-analysis revealed that the abnormal patterns of widespread episodic memory network indicated that individuals with aMCI may not be completely “mild” in nature.
Osteogenic differentiation of hypertrophic chondrocytes involves asymmetric cell divisions and apoptosis

We have investigated the early cellular events that take place during the change in lineage commitment from hypertrophic chondrocytes to osteoblast-like cells. We have induced this osteogenic differentiation by cutting through the hypertrophic cartilage of embryonic chick femurs and culturing the explants. Immunocytochemical characterization, [3H]thymidine pulse-chase labeling, in situ nick translation or end labeling of DNA breaks were combined with ultrastructural studies to characterize the changing pattern of differentiation. The first responses to the cutting, seen after 2 d, were upregulation of alkaline phosphatase activity, synthesis of type I collagen and single-stranded DNA breaks, probably indicating a metastable state. Associated with the change from chondrogenic to osteogenic commitment was an asymmetric cell division with diverging fates of the two daughter cells, where one daughter cell remained viable and the other one died. The available evidence suggests that the viable daughter cell then divided and generated osteogenic cells, while the other daughter cell died by apoptosis. The results suggest a new concept of how changes in lineage commitment of differentiated cells may occur. The concepts also reconcile previously opposing views of the fate of the hypertrophic chondrocyte.
Local adaptation and pronounced genetic differentiation in an extremophile fish, Poecilia mexicana, inhabiting a Mexican cave with toxic hydrogen sulphide

We investigated genetic differentiation and migration patterns in a small livebearing fish, Poecilia mexicana, inhabiting a sulfidic Mexican limestone cave (Cueva del Azufre). We examined fish from three different cave chambers, the sulfidic surface creek draining the cave (El Azufre) and a nearby surface creek without the toxic hydrogen sulphide (Arroyo Cristal). Using microsatellite analysis of 10 unlinked loci, we found pronounced genetic differentiation among the three major habitats: Arroyo Cristal, El Azufre and the cave. Genetic differentiation was also found within the cave between different pools. An estimation of first‐generation migrants suggests that (i) migration is unidirectional, out of the cave, and (ii) migration among different cave chambers occurs to some extent. We investigated if the pattern of genetic differentiation is also reflected in a morphological trait, eye size. Relatively large eyes were found in surface habitats, small eyes in the anterior cave chambers, and the smallest eyes were detected in the innermost cave chamber (XIII). This pattern shows some congruence with a previously proposed morphocline in eye size. However, our data do not support the proposed mechanism for this morphocline, namely that it would be maintained by migration from both directions into the middle cave chambers. This would have led to an increased variance in eye size in the middle cave chambers, which we did not find. Restricted gene flow between the cave and the surface can be explained by local adaptations to extreme environmental conditions, namely H2S and absence of light. Within the cave system, habitat properties are patchy, and genetic differentiation between cave chambers despite migration could indicate local adaptation at an even smaller scale.
Insights into Accounting Choice from the Adoption Timing of International Financial Reporting Standards

This paper collects survey evidence on the costs and benefits of adopting International Financial Reporting Standards (IFRS). It also examines the motivations for the timing of IFRS adoption. Significant differences exist between early and late adopters for three of nine benefits and for one of six cost measures. No significant differences exist in terms of firm size or the impact of IFRS on contracts. Early adopters perceive themselves as market leaders. They are more certain about the manageability of implementing IFRS and are more specific with regard to the impact of IFRS adoption. Late adoption decisions are motivated by adverse consequences and uncertainty.
Clinical Scores for Dyspnoea Severity in Children: A Prospective Validation Study

Background In acute dyspnoeic children, assessment of dyspnoea severity and treatment response is frequently based on clinical dyspnoea scores. Our study aim was to validate five commonly used paediatric dyspnoea scores. Methods Fifty children aged 0–8 years with acute dyspnoea were clinically assessed before and after bronchodilator treatment, a subset of 27 children were videotaped and assessed twice by nine observers. The observers scored clinical signs necessary to calculate the Asthma Score (AS), Asthma Severity Score (ASS), Clinical Asthma Evaluation Score 2 (CAES-2), Pediatric Respiratory Assessment Measure (PRAM) and respiratory rate, accessory muscle use, decreased breath sounds (RAD). Results A total of 1120 observations were used to assess fourteen measurement properties within domains of validity, reliability and utility. All five dyspnoea scores showed overall poor results, scoring insufficiently on more than half of the quality criteria for measurement properties. The AS and PRAM were the most valid with good values on six and moderate values on three properties. Poor results were mainly due to insufficient measurement properties in the validity and reliability domains whereas utility properties were moderate to good in all scores. Conclusion This study shows that commonly used dyspnoea scores show insufficient validity and reliability to allow for clinical use without caution.
Sensitivity Analysis of Vegetation Reflectance to Biochemical and Biophysical Variables at Leaf, Canopy, and Regional Scales

The objective of this paper is to investigate the sensitivity of reflectance to the variation in biochemical and biophysical variables at leaf, canopy, and regional scales using a modeling approach. The results show that, at the leaf scale, the variations in chlorophyll a+b content, the leaf structure parameter, and the water content dominate the reflectance variance in the visible light (VIS), near infrared (NIR), and short-wave infrared (SWIR) regions, respectively. At the canopy scale, the sensitivity of reflectance to variation in the leaf structure parameter is very slight. For sparse foliage cover (leaf area index ), LAI is the most important variable to the canopy reflectance. As LAI increases, the sensitivity of reflectance to variation in LAI is reduced to a very low value. Moreover, chlorophyll a+b, dry matter, and water content control the variation of canopy reflectance in the VIS, NIR, and SWIR regions, respectively. At the regional scale, the sensitivity of reflectance to variation in vegetation variables is highly influenced by the mixed pixels. Thirty-six vegetation indices (VIs) are chosen in this paper to illustrate the scale dependence of the estimation accuracy of vegetation variables. The results show that the relationships between the VIs and the variables highly depend on the observation scale. For chlorophyll a+b content estimation, transformed chlorophyll absorption in reflectance index (TCARI), Blue Green pigment Index, leaf chlorophyll index (LCI), modified Normalized Difference (mND705), and Plant Biochemical Index at the leaf scale and canopy scale of and TCARI at the canopy scale of are highly related. The correlation between the indices and chlorophyll content in the regional scale is, however, much lower. For water content estimation, disease water stress index (DSWI), leaf water vegetation index 2 (LWVI_2), moisture stress index (MSI), normalized difference infrared index (NDII), normalized difference water index (NDWI), hyperspectral perpendicular vegetation index (RVI), SWIR water stress index (SIWSI), SR water index (SRWI), and water index (WI) are good choices at the leaf scale and canopy scale of , while at the canopy scale of and the regional scale, the correlation between the indices and water content is very low. For LAI estimation, VIs, including the Greenness Index, simple ratio (SR), Normalized Difference VI, modified soil-adjusted vegetation index (MSAVI), modified triangular vegetation index 1 (MTVI1), modified triangular vegetation index 2 (MTVI2), optimized soil-adjusted vegetation index (OSAVI), modified chlorophyll absorption ratio index 1 (MCARI1), modified chlorophyll absorption ratio index 2 (MCARI2), Enhanced VI, LAI Determining Index, renormalized difference vegetation index (RDVI), Spectral Polygon VI, Wide Dynamic Range VI, and triangular vegetation index (TVI), have high correlation with LAI at the canopy scale of while a low correlation at the canopy scale of and the regional scale.
Essay on Monetary Policy and Economic Growth

The global economic crisis has led to the global reduction in credit activity, a fall of domestic product as well as the level of foreign direct investments, and has imposed the sources of economic growth as one of the key problems. Therefore, the objective of this paper is the monetary policy review and the task is to research the circumstances when it is possible for the money supply to become the source of economic growth without inflationary consequences. The paper analyzes the demand and supply functions for money, the quantity theory of money, velocity of circulation and instruments of monetary policy and strives to propose such a combination of measures of a new economic policy based on theoretical arguments that will stimulate economic growth. This aim requires a completely new approach to the mechanism of money creation and selection of monetary instruments, proposing the money supply connection to the growth of real GDP, the money supply control as the key instrument, and a low and stable long-term interest rate as the factor for maintaining stability of velocity. In such case, monetary policy will have a real impact on economic growth, even in the long run.