Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymerization of hemoglobins in Arctic fish: Lycodes reticulatus and Gadus morhua

In vitro, and possibly in vivo, hemoglobin polymerization and red blood cell sickling appear to be widespread in codfish. In this article, we show that the hemoglobins of the two Arctic fish Lycodes reticulatus and Gadus morhua also have the tendency to polymerize, as monitored by dynamic light scattering experiments. The elucidation of the primary structure of the single hemoglobin of the zoarcid L. reticulatus shows the presence of a large number of cysteyl residues in α and β chains. Their role in eliciting the ability to produce polymers was also addressed by MALDI‐TOF and TOF‐TOF mass spectrometry. The G.morhua globins are also rich in Cys, but unlike in L. reticulatus, polymerization does not seem to be disulfide driven. The widespread occurrence of the polymerization phenomenon displayed by hemoglobins of Arctic fish supports the hypothesis that this feature may bea response to stressful environmental conditions. © 2011 IUBMB IUBMB Life, 63(5): 346–354, 2011
Refining image annotation using contextual relations between words

In this paper, we present a probabilistic approach to refine image annotations by incorporating semantic relations between annotation words. Our approach firstly predicts a candidate set of annotation words with confidence scores. This is achieved by the relevance vector machine (RVM), which is a kernel based probabilistic classifier in order to cope with nonlinear classification. Given the candidate annotations, we model semantic relationships between words using a conditional random field (CRF) model where each vertex indicates the final decision (true / false) on a candidate annotation word. The refined annotation is given by inferring the most likely states of these vertexes. In the CRF model, we consider the confidence scores given by the RVM classifiers as local evidences. In addition, we utilise Normalized Google distances (NGD's) between two words as their contextual potential. NGD is a distance function between two words obtained by searching a pair of words using the Google search engine. It has a simple mathematical formulation with a foundation in Kolmogorov theory. We also propose a learning algorithm to tune the weight parameters in the CRF model. These weight parameters control the balance between the local evidence of a single word and the contextual relation between words. Our experiments on the Corel images demonstrate the effect of our approach.
Testing Physical Systems

We present a formal theory of model-based testing, an algorithm for test generation based on it, and outline how testing is implemented by a diagnostic engine. The key to making the complex task of test generation feasible for systems with continuous domains is the use of model abstraction. Tests can be generated using manageable finite models and then mapped back to a detailed level. We state conditions for the correctness of this approach and discuss the preconditions and scope of applicability of the theory.
Performance Analysis of Fast Handover Schemes for Proxy Mobile IPv6

As wireless technologies have grown, many people want to use wireless networks during movements. Accordingly, Mobile IPv6 was developed by the Internet Engineering Task Force to support the mobility service. However, Mobile IPv6 cannot satisfy requirements of real-time applications such as video streaming service and VoIP service due to its high handover latency. To address this problem, Proxy Mobile IPv6 has been introduced by the Internet Engineering Task Force. Then, optimization issues including Fast Handover are under the proposal phase. In this paper, we analyze and compare the existing Fast Handover schemes for Proxy Mobile IPv6 in terms of handover latency and required packet buffering size
Improvements in Phrase-Based Statistical Machine Translation

In statistical machine translation, the currently best performing systems are based in some way on phrases or word groups. We describe the baseline phrase-based translation system and various refinements. We describe a highly efficient monotone search algorithm with a complexity linear in the input sentence length. We present translation results for three tasks: Verbmobil, Xerox and the Canadian Hansards. For the Xerox task, it takes less than 7 seconds to translate the whole test set consisting of more than 10K words. The translation results for the Xerox and Canadian Hansards task are very promising. The system even outperforms the alignment template system.
Fluoroscopy radiation safety for spine interventional pain procedures in university teaching hospitals.

BACKGROUND Fluoroscopic guidance is frequently utilized in performing various types of interventional techniques. The major purpose of fluoroscopy is accurate needle placement to ensure target specificity and accurate delivery of the injected drug. However, radiation exposure may be associated with risks to physician, patient, and personnel. Multiple studies have evaluated the risk of radiation exposure and techniques to reduce the risk in private practice settings. However, the literature is scant in evaluating the risk of radiation exposure in teaching hospitals in university settings. OBJECTIVE To evaluate safety and duration of radiation exposure for fluoroscopy guided interventional pain procedures in university pain clinics. STUDY DESIGN Retrospective, case study. METHODS The data was reviewed from the fluoroscopy machines from March 2004 to April 2004 at two university pain clinics. Mean fluoroscopy time (FT), mean radiation dose per procedure, and utilization of pulsed fluoroscopy were analyzed. RESULTS Data of a total of 165 cases of spine injection procedures were collected. The mean fluoroscopy time for lumbar epidural steroid injection, facet joint block, sympathetic nerve block, sacroiliac joint injection, and discography were 46.6 +/- 4.2; 81.5 +/- 12.8; 64.4 +/- 11; 50.6 +/- 41.9 and 146.8 + 25.1 seconds respectively. There were significant differences in fluoroscopy exposure times and radiation dosage for epidural steroid injection among different teaching physicians. Pulsed fluoroscopy was used in less than 10% of cases. CONCLUSION The results of this study show that the fluoroscopy exposure time for various interventional procedures performed in the university settings are significantly higher than the radiation exposure periods in private practice settings. This study also showed significant differences among physicians in the same university setting.
Repression and Derepression of Minus-Strand Synthesis in a Plus-Strand RNA Virus Replicon

ABSTRACT Plus-strand viral RNAs contain sequences and structural elements that allow cognate RNA-dependent RNA polymerases (RdRp) to correctly initiate and transcribe asymmetric levels of plus and minus strands during RNA replication. cis-acting sequences involved in minus-strand synthesis, including promoters, enhancers, and, recently, transcriptional repressors (J. Pogany, M. R. Fabian, K. A. White, and P. D. Nagy, EMBO J. 22:5602-5611, 2003), have been identified for many viruses. A second example of a transcriptional repressor has been discovered in satC, a replicon associated with turnip crinkle virus. satC hairpin 5 (H5), located proximal to the core hairpin promoter, contains a large symmetrical internal loop (LSL) with sequence complementary to 3′-terminal bases. Deletion of satC 3′-terminal bases or alteration of the putative interacting bases enhanced transcription in vitro, while compensatory exchanges between the LSL and 3′ end restored near-normal transcription. Solution structure analysis indicated that substantial alteration of the satC H5 region occurs when the three 3′-terminal cytidylates are deleted. These results indicate that H5 functions to suppress synthesis of minus strands by sequestering the 3′ terminus from the RdRp. Alteration of a second sequence strongly repressed transcription in vitro and accumulation in vivo, suggesting that this sequence may function as a derepressor to free the 3′ end from interaction with H5. Hairpins with similar sequence and/or structural features that contain sequence complementary to 3′-terminal bases, as well as sequences that could function as derepressors, are located in similar regions in other carmoviruses, suggesting a general mechanism for controlling minus-strand synthesis in the genus.
Photometric Catalogue of Quasars and Other Point Sources in the Sloan Digital Sky Survey

We present a catalogue of about six million unresolved photometric detections in the Sloan Digital Sky Survey (SDSS) Seventh Data Release, classifying them into stars, galaxies and quasars. We use a machine learning classifier trained on a subset of spectroscopically confirmed objects from 14th to 22nd magnitude in the SDSS i band. Our catalogue consists of 2 430 625 quasars, 3 544 036 stars and 63 586 unresolved galaxies from 14th to 24th magnitude in the SDSS i band. Our algorithm recovers 99.96 per cent of spectroscopically confirmed quasars and 99.51 per cent of stars to i ∼ 21.3 in the colour window that we study. The level of contamination due to data artefacts for objects beyond i = 21.3 is highly uncertain and all mention of completeness and contamination in the paper are valid only for objects brighter than this magnitude. However, a comparison of the predicted number of quasars with the theoretical number counts shows reasonable agreement.
B7-H1 Expression Is Associated with Poor Prognosis in Colorectal Carcinoma and Regulates the Proliferation and Invasion of HCT116 Colorectal Cancer Cells

Background And Objective The investigation concerning the B7-H1 expression in colorectal cancer cells is at an early stage. It is unclear whether B7-H1 expression may have diagnostic or prognostic value in colorectal carcinoma. Additionally, how B7-H1 is associated with the clinical features of colorectal carcinoma is not known. In order to investigate the relationship between B7-H1 and colorectal cancer, we analyzed B7-H1 expression and its effect in clinical specimens and HCT116 cells. Methods Paraffin-embedded specimens from 143 eligible patients were used to investigate the expression of CD274 by immunohistochemistry. We also examined whether B7-H1 itself may be related to cell proliferation, apoptosis, migration and invasion in colon cancer HCT116 cells. Results Our results show that B7-H1 was highly expressed in colorectal carcinoma and was significantly associated with cell differentiation status and TNM (Tumor Node Metastasis) stage. Patients with positive B7-H1 expression showed a trend of shorter survival time. Using multivariate analysis, we demonstrate that positive B7-H1 expression is an independent predictor of colorectal carcinoma prognosis. Our results indicate that B7-H1 silencing with siRNA inhibits cell proliferation, migration and invasion. Furthermore, cell apoptosis was also increased by B7-H1 inhibition. Conclusions Positive B7-H1 expression is an independent predictor for colorectal carcinoma prognosis. Moreover, knockdown of B7-H1 can inhibit cell proliferation, migration and invasion.
The role of movement in the development of joints and related structures: the head and neck in the chick embryo.

Skeletal muscle contractions are necessary during embryonic life for the normal development of joints. The general features of joint development in immobile limbs were first studied with the techniques of grafting and organ culture. (Murray, 1926; Murray & Selby, 1930; Fell, 1925; Fell & Canti, 1934; Hamburger & Waugh, 1940; Lelkes, 1958). However, these methods of necessity entail a drastic alteration in the environment of the developing articulations, which may result in gross distortions of the skeletal structures themselves. More recently, neuromuscular blocking agents have been used to produce paralysis of chick embryos in ovo. When administered intravenously, these pharmacological substances produce profound paralysis, which may be continued for prolonged periods during embryonic development (Drachman & Coulombre, 1962a, b). Drachman & Sokoloff (1966) have analyzed the primary development of the knee, ankle and toe joints of the chick embryo by the use of these methods.
Internet Exchanges for Used Goods: An Empirical Analysis of Trade Patterns and Adverse Selection

In the past few years, we have witnessed the increasing ubiquity of user-generated content on seller reputation and product condition in Internet-based used-good markets. Recent theoretical models of trading and sorting in used-good markets provide testable predictions to use to examine the presence of adverse selection and trade patterns in such dynamic markets. A key aspect of such empirical analyses is to distinguish between product-level uncertainty and seller-level uncertainty, an aspect the extant literature has largely ignored. Based on a unique, 5-month panel data set of user-generated content on used good quality and seller reputation feedback collected from Amazon, this paper examines trade patterns in online used-good markets across four product categories (PDAs, digital cameras, audio players, and laptops). Drawing on two different empirical tests and using content analysis to mine the textual feedback of seller reputations, the paper provides evidence that adverse selection continues to exist in online markets. First, it is shown that after controlling for price and other product, and for seller-related factors, higher quality goods take a longer time to sell compared to lower quality goods. Second, this result also holds when the relationship between sellers' reputation scores and time to sell is examined. Third, it is shown that price declines are larger for more unreliable products, and that products with higher levels of intrinsic unreliability exhibit a more negative relationship between price decline and volume of used good trade. Together, our findings suggest that despite the presence of signaling mechanisms such as reputation feedback and product condition disclosures, the information asymmetry problem between buyers and sellers persists in online markets due to both product-based and seller-based information uncertainty. No consistent evidence of substitution or complementarity effects between product-based and seller-level uncertainty are found. Implications for research and practice are discussed.
A New Class of Asset Pricing Models with Lévy Processes : Theory and Applications

We develop a new class of discrete-time asset pricing models with Lévy processes and use a¢ ne GARCH dynamics to drive the models time variation. These models are easy to implement and can capture three important stylized facts of asset returns, which are non-normality, time-varying return volatility, and the leverage e¤ect. In addition, this framework yields asset return dynamics that have an a¢ ne structure in their conditional transform, which leads to simple valuation of various derivatives including zero-coupon bonds and European options. We apply this newly proposed framework to various two-factor models consisting of a normal and a pure jump Lévy component. The results from joint estimation of options and returns on the market index reveal the important economic role of jumps. Models without jumps cannot reconcile the di¤erence between market-realized returns and investorsex-ante expectations of returns with an economically justi able equity premium level. We nd that investors demand 3 to 5% in annual excess return for bearing the market jump risk. JEL Classi cation: G10; G12; G13; C51. Keywords: Lévy process; time change; discrete-time; GARCH; a¢ ne transform; option valuation; ltering; risk premia. I would like to thank my co-supervisors Peter Christo¤ersen and Kris Jacobs for encouragement and support. This paper has bene ted from the comments by David Bates, Darrell Du¢ e, Louis Ederington, Olaf Korn, and seminar participants at the Georgia Institute of Technology, HEC Montreal, University of Saskatchewan, Bank of Canada, Oxford-Man Conference, and the 2008 FMA meeting. I would like to acknowledge CIREQ and the J.W. McConnell foundation for nancial support. Any remaining inadequacies are mine alone. Correspondence to: Chayawat Ornthanalai, Desautels Faculty of Management, McGill University, 1001 Sherbrooke Street West, Montreal, Canada H3A 1G5; Tel: (514) 398-4000 ext 00996; Fax: (514) 398-3876; E-mail: chayawat.ornthanalai@mail.mcgill. ca; Website: www.ornthanalai. com.
Polymorphisms in the Estrogen Receptor 1 and Vitamin C and Matrix Metalloproteinase Gene Families Are Associated with Susceptibility to Lymphoma

Background Non-Hodgkin lymphoma (NHL) is the fifth most common cancer in the U.S. and few causes have been identified. Genetic association studies may help identify environmental risk factors and enhance our understanding of disease mechanisms. Methodology/Principal Findings 768 coding and haplotype tagging SNPs in 146 genes were examined using Illumina GoldenGate technology in a large population-based case-control study of NHL in the San Francisco Bay Area (1,292 cases 1,375 controls are included here). Statistical analyses were restricted to HIV- participants of white non-Hispanic origin. Genes involved in steroidogenesis, immune function, cell signaling, sunlight exposure, xenobiotic metabolism/oxidative stress, energy balance, and uptake and metabolism of cholesterol, folate and vitamin C were investigated. Sixteen SNPs in eight pathways and nine haplotypes were associated with NHL after correction for multiple testing at the adjusted q<0.10 level. Eight SNPs were tested in an independent case-control study of lymphoma in Germany (494 NHL cases and 494 matched controls). Novel associations with common variants in estrogen receptor 1 (ESR1) and in the vitamin C receptor and matrix metalloproteinase gene families were observed. Four ESR1 SNPs were associated with follicular lymphoma (FL) in the U.S. study, with rs3020314 remaining associated with reduced risk of FL after multiple testing adjustments [odds ratio (OR) = 0.42, 95% confidence interval (CI) = 0.23–0.77) and replication in the German study (OR = 0.24, 95% CI = 0.06–0.94). Several SNPs and haplotypes in the matrix metalloproteinase-3 (MMP3) and MMP9 genes and in the vitamin C receptor genes, solute carrier family 23 member 1 (SLC23A1) and SLC23A2, showed associations with NHL risk. Conclusions/Significance Our findings suggest a role for estrogen, vitamin C and matrix metalloproteinases in the pathogenesis of NHL that will require further validation.
A new approach for 3D cloud‐resolving simulations of large‐scale atmospheric circulation

We present a computationally efficient new method for simulating the interactions of large‐scale atmospheric circulations with deep convection in a 3D cloud‐resolving model. This is accomplished by reducing the scale difference between the large‐scale and convective circulations. Our method, Diabatic Acceleration and REscaling (DARE), consists of accelerating all diabatic processes, reducing the planetary radius and increasing its rotation rate. A second useful interpretation of this rescaling, Reduced Acceleration in the VErtical (RAVE) is also presented briefly. The DARE/RAVE approach is expected to be useful for a wide range of problems involving interactions between large‐scale circulation, deep convection, and associated cloud and radiation processes, whose investigation has long been plagued by deficiencies in cumulus/cloud parameterizations. Initial results from a near‐global scale equatorial β‐plane simulation using the DARE approach are briefly presented.
Comparison of the early response of human embryonic stem cells and human induced pluripotent stem cells to ionizing radiation

Despite the well-demonstrated efficacy of stem cell (SC) therapy, this approach has a number of key drawbacks. One important concern is the response of pluripotent SCs to treatment with ionizing radiation (IR), given that SCs used in regenerative medicine will eventually be exposed to IR for diagnostic or treatment-associated purposes. Therefore, the aim of the present study was to examine and compare early IR-induced responses of pluripotent SCs to assess their radioresistance and radiosensitivity. In the present study, 3 cell lines; human embryonic SCs (hESCs), human induced pluripotent SCs (hiPSCs) and primary human dermal fibroblasts (PHDFs); were exposed to IR at doses ranging from 0 to 15 gray (Gy). Double strand breaks (DSBs), and the gene expression of the following DNA repair genes were analyzed: P53; RAD51; BRCA2; PRKDC; and XRCC4. hiPSCs demonstrated greater radioresistance, as fewer DSBs were identified, compared with hESCs. Both pluripotent SC lines exhibited distinct gene expression profiles in the most common DNA repair genes that are involved in homologous recombination, non-homologous end-joining and enhanced DNA damage response following IR exposure. Although hESCs and hiPSCs are equivalent in terms of capacity for pluripotency and differentiation into 3 germ layers, the results of the present study indicate that these 2 types of SCs differ in gene expression following exposure to IR. Consequently, further research is required to determine whether hiPSCs and hESCs are equally safe for application in clinical practice. The present study contributes to a greater understanding of DNA damage response (DDR) mechanisms activated in pluripotent SCs and may aid in the future development of safe SC-based clinical protocols.
Detection of Cardiac Allograft Rejection and Response to Immunosuppressive Therapy With Peripheral Blood Gene Expression

Background—Assessment of gene expression in peripheral blood may provide a noninvasive screening test for allograft rejection. We hypothesized that changes in peripheral blood expression profiles would correlate with biopsy-proven rejection and would resolve after treatment of rejection episodes. Methods and Results—We performed a case-control study nested within a cohort of 189 cardiac transplant patients who had blood samples obtained during endomyocardial biopsy (EMB). Using Affymetrix HU133A microarrays, we analyzed whole-blood expression profiles from 3 groups: (1) control samples with negative EMB (n=7); (2) samples obtained during rejection (at least International Society for Heart and Lung Transplantation grade 3A; n=7); and (3) samples obtained after rejection, after treatment and normalization of the EMB (n=7). We identified 91 transcripts differentially expressed in rejection compared with control (false discovery rate <0.10). In postrejection samples, 98% of transcripts returned toward control levels, displaying an intermediate expression profile for patients with treated rejection (P<0.0001). Cluster analysis of the 40 transcripts with >25% change in expression levels during rejection demonstrated good discrimination between control and rejection samples and verified the intermediate expression profile of postrejection samples. Quantitative real-time polymerase chain reaction confirmed significant differential expression for the predictive markers CFLAR and SOD2 (UniGene ID No. 355724 and No. 384944). Conclusions—These data demonstrate that peripheral blood expression profiles correlate with biopsy-proven allograft rejection. Intermediate expression profiles of treated rejection suggest persistent immune activation despite normalization of the EMB. If validated in larger studies, expression profiling may prove to be a more sensitive screening test for allograft rejection than EMB.