Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Statistic for Global Association Testing Based on Penalized Regression

Natural genetic structures like genes may contain multiple variants that work as a group to determine a biologic outcome. The effect of rare variants, mutations occurring in less than 5% of samples, is hypothesized to be explained best as groups collectively associated with a biologic function. Therefore, it is important to develop powerful association tests to identify a true association between an outcome of interest and a group of variants, in particular a group with many rare variants. In this article we first delineate a novel penalized regression‐based global test for the association between sets of variants and a disease phenotype. Next, we use Genetic Analysis Workshop 18 (GAW18) data to assess the power of the new global association test to capture a relationship between an aggregated group of variants and a simulated hypertension status. Rare variant only, common variant only, and combined variant groups are studied. The power values are compared to those obtained from eight well‐regarded global tests (Score, Sum, SSU, SSUw, UminP, aSPU, aSPUw, and sequence kernel association test (SKAT)) that do not use penalized regression and a set of tests using either the SSU or score statistics and least absolute shrinkage and selection operator penalty (LASSO) logistic regression. Association testing of rare variants with our method was the top performer when there was low linkage disequilibrium (LD) between and within causal variants. This was similarly true when simultaneously testing rare and common variants in low LD scenarios. Finally, our method was able to provide meaningful variant‐specific association information.
PCSK9: a convertase that coordinates LDL catabolism Published, JLR Papers in Press, November 19, 2008.

The identification and characterization of proprotein convertase subtilisin-like/kexin type 9 (PCSK9) have provided new insights into LDL metabolism and the causal role of LDL in coronary heart disease (CHD). PCSK9 is a secreted protease that mediates degradation of the LDL receptor by interacting with the extracellular domain and targeting the receptor for degradation. Individuals with loss-of-function mutations in PCSK9 have reduced plasma levels of LDL cholesterol and are protected from CHD; these observations have validated PCSK9 as a therapeutic target and suggested new approaches for the treatment and prevention of CHD.
Scientific Progress in Strategic Management: The Case of the Resource-Based View

Does the Resource-Based View (RBV) represent a case of scientific progress? And has it emerged as the dominant approach to the understanding of competitive advantage for this reason? Conventional criteria for scientific progress, notably those of the growth of knowledge literature, are not particularly helpful for understanding this. Instead, it is argued that in order to understand why the RBV is an instance of scientific progress, we should begin from the notion that reduction is at the heart of progress in science, and that many scientists implicitly or explicitly hold this view. The RBV is a case of scientific progress because it identified theoretical mechanisms at levels lower than those that were usually investigated in strategy research prior to the RBV. Unfortunately, the micro-emphasis of the RBV gave way during the 1990s to more aggregative modes of theorising (i.e., the capabilities approach). Thus, the RBV represents an 'unfinished revolution' as there is still considerable potential to dig deeper in the deep structure of competitive advantage.
Clinical, Immunophenotypic, and Genetic Analysis of Adult Lymphomas With Morphologic Features of Burkitt Lymphoma

A prompt distinction of Burkitt lymphoma (BL) versus diffuse large B cell lymphomas (DLBCL) has important clinical implications; however, this distinction can be difficult. We analyzed 74 adult gray zone and 10 reference pediatric BL using immunohistochemistry (Ki-67, CD10, bcl2, bcl6) and fluorescence in situ hybridization (FISH) for MYC, BCL2, and BCL6 breakpoints. Two algorithms for classification were followed: algorithm A used a two-step review by four hematopathologists and algorithm B a set of only biologic markers (Ki-67 ≥ 90%, CD10+, bcl6+, bcl2−, MYC breakpoint+, BCL2 and BCL6 breakpoint−). Both algorithms categorized all reference cases as BL. In the adult group, algorithm A resulted in 21 adult BL and 52 DLBCL and algorithm B in 23 BL and 51 “non-Burkitt” lymphomas (nBL); 9 cases (12%) contained two different translocations and were categorized as nBL in algorithm B. Fifteen cases (20%) fulfilled the BL criteria of both algorithms. Although not considered as BL according to both algorithms, many other lymphomas showed nonetheless a phenotypic and/or genetic shift to BL. BL according to algorithm B was more homogeneous with respect to clinical presentation (gender and localization) than BL defined by algorithm A. Our data suggest that only a few cases of these gray zone lymphomas represent true de novo BL. Immunohistochemistry for Ki-67, CD10, and bcl2 with analysis of MYC and preferably also BCL2 and BCL6 may be advised as a marker panel for this diagnostic dilemma.
Convolutional neural network training with artificial pattern for Bangla handwritten numeral recognition

Recognition of handwritten numerals has gained much interest in recent years due to its various application potentials. The progress of handwritten Bangla numeral is well behind Roman, Chinese and Arabic scripts although it is a major language in Indian subcontinent and is the first language of Bangladesh. Handwritten numeral classification is a high-dimensional complex task and existing methods use distinct feature extraction techniques and various classification tools in their recognition schemes. Recently, convolutional neural network (CNN) is found efficient for image classification with its distinct features. In this study, a CNN based method has been investigated for Bangla handwritten numeral recognition. A moderated pre-processing has been adopted to produce patterns from handwritten scan images. On the other hand, CNN has been trained with the patterns plus a number of artificial patterns. A simple rotation based approach is employed to generate artificial patterns. The proposed CNN with artificial pattern is shown to outperform other existing methods while tested on a popular Bangla benchmark handwritten dataset.
A Stochastic Volatility Forward Libor Model with a Term Structure of Volatility Smiles

Volatility smiles of European swaptions of various expiries and maturities typically have different slopes. This important feature of interest rate markets has not been incorporated in any of the practical interest rate models available to date. In this paper, we build a model that treats the swaption skew matrix as a market input and is calibrated to it. The model is constructed as an extension of a Stochastic Volatility Forward Libor model, with local volatility functions imposed upon forward Libor rates being time-dependent and Libor-rate specific. The focus of the paper is on deriving efficient European swaption approximation formulas that allow calibration of the model to all European swaptions across all expiries, maturities and strikes. The main conceptual contribution of the paper is its focus on recovering all available market volatility skew information across a full swaption grid within a consistent model. The model we develop has a potential to change the way skew calibration is approached, in the same way the introduction of the log-normal forward Libor model had changed the way volatility calibration is approached. The main technical contribution of the paper is a formula for the "effective" skew in a stochastic volatility model, a formula that relates a total amount of skew generated by the model over a given time period to the time-dependent slope of the instantaneous local volatility function. A new "effective" volatility approximation for stochastic volatility models with time-dependent volatility functions is also derived. The formulas we obtain are simple and intuitive; their applicability goes beyond interest rate modeling.
SHIFTING EXPORT SPECIALIZATION AND THE COMPETITIVENESS OF THE MALAYSIAN MANUFACTURING: Trends and Analysis

This study provides an in-depth analysis of shifting export specialization at the Standard International Trade Classification (SITC) three-digit product category level and links this analysis to Malaysian export potential. The research uses the revealed comparative advantage framework to analyze the extent of export competition between Malaysia and other Association of Southeast Asian Nations (ASEAN) economies. It argues that the degree of competition among ASEAN countries will intensify with the implementation of the ASEAN Free Trade Area (AFTA) and the emergence of other low-cost producers in the region. It aims to explore how AFTA will in uence Malaysian manufacturing. In the presence of growing trade liberalization, competitive pressures, and the changing structure of world demand, this study calls for a reassessment of the factors that in uence Malaysia's export competitiveness. * * * * *
Cultural Change and Marketing

ABSTRACT The results of this study suggest that marketing strategies need to be adjusted to changing cultures. Culture affects marketing decisions regarding product, price, promotion and place (the 4 Ps). Many marketing studies have been reported based on Hofstede's seminal work on national culture (1980). Marketing managers need to be cautious about assuming the validity of the Anglo cluster equating the cultures of the United States (U.S.) and Canada. We should recognize that national cultures are changing in the U.S., Canada and Mexico, as well as most other countries in the world. Our findings for a very recent sample of people attending executive and MBA programs would seem to apply to the upwardly-mobile business class. Contrary to the ubiquitous Hofstede data found in textbooks, we found no significant differences in Power Distance between the U.S., Mexico and Canada. Our findings regarding differences in Uncertainty Avoidance show that Mexico did not have a significantly higher mean than the U.S., but that the U.S. had a higher mean than Canada. The U.S. and Canada did not differ significantly on Individualism/Collectivism. Our results suggest that caution should be taken in automatically assuming cultural parity between the U.S. and Canada and that established cultural positions between the North American Free Trade Agreement (NAFTA) member nations may be changing.
Model predictive control of a large fleet of thermal loads and electric power generators, with an assessment for the Netherlands

In this paper we propose a novel control architecture to manage a large fleet of thermal loads and adjust traditional power plant generation setpoints for reference tracking and production costs minimization. The time scales considered are determined by sampling times of a few seconds and control horizons of a few minutes. The control architecture consists in a model predictive controller (MPC) combined with a block called index generator. The index generator receives aggregated control signals from the MPC and splits these among individual loads while satisfying temperature and switching constraints of the controlled appliances. It then computes an updated estimate of the aggregated controllability of the loads and provides this to the MPC for setpoint calculations. This control architecture facilitates handling very large numbers of single thermal appliances and tens of traditional generation units with very small computational efforts. We assess the added value of controlling thermal loads by implementing our control architecture within a simulation framework which accurately represents the Dutch power system.
Liberating the Intellectual Domain From the Practice: Public Relations, Activism, and the Role of the Scholar

Unlike practitioners, public relations scholars must consider unintended consequences of public relations practices at the societal and individual levels. By extending the domain in this way, logical paradoxes involving activism and nomothetic models of public relations may be resolved through the introduction of critical theory. Use of critical theory illuminates the role of invisible clients in setting the public relations research agenda and in truncating our intellectual vision. Critical theory suggests ways to study activism from a new perspective that would enhance practices and further the evolution of the intellectual domain.
Foreign exchange intervention and monetary policy in Japan, 2003–04

This article examines the rationale behind the massive increase in Japanese foreign exchange market intervention operations in 2003-04, and evaluates its effectiveness both in limiting yen exchange rate appreciation and influencing the direction of monetary policy. The two main questions addressed in this study are: Was the intervention effective in slowing exchange rate appreciation compared to a counterfactual case with no intervention? And, has intervention on such a large scale authorized by the Ministry of Finance been able to directly influence liquidity creation or indirectly influence the stance of Bank of Japan policy?
On-line signature verification by dynamic time-warping

In this paper, we discuss an on-line signature verification system based on dynamic time-warping (DTW). The DTW-algorithm originates from the field of speech recognition, and has been applied successfully in the signature verification area more than once. However, until now, few adaptations have been made in order to take the specific characteristics of signature verification into account. According to us, one of the most important differences is the availability of a rather large number of reference patterns, making it possible to determine which parts of a reference signature are important and which are not. By disconnecting the DTW-stage and the feature extraction process we are able to deal efficiently with this extra amount of information. We demonstrate the benefits of our approach by building and evaluating a complete system.
Nível de evidenciação × custo da dívida das empresas brasileiras

This study aims to investigate the relation between the voluntary disclosure level and the cost of capital of third parties. Increased disclosure by companies is expected to result in decreased information asymmetry, reducing the risk offered to the company's financial backers, as well as a rise in visibility and liquidity of its bonds and in the information quantity disseminated to its stakeholders in general. Before analyzing the regression with panel data, the multivariate Correspondence Analysis (ANACOR) technique was used for an exploratory analysis of the study variables. We examined 23 publicly-traded companies between 2000 and 2004, looking at the disclosure level (ND), and between 2001 and 2005 to look at the cost of capital of third parties (Kd) and the control variables, in accordance with the following equation: (Kdt) = ƒ(NDt-1, control variablest -1). The empirical results demonstrated that, based on the use of the pooling effect and the generalized least squares method, whose R2 was approximately 28.49%, the voluntary disclosure level is inversely related to the cost of capital of third parties, that is, the higher the disclosure level, the lower the cost of capital of third parties. Thus, the study hypothesis was not rejected.
CONSUMERS' WILLINGNESS TO PAY FOR FOOD SAFETY: A PATHOGEN SPECIFIC ANALYSIS

Estimates of the economic benefits of intervention strategies to make food safer from specific pathogens for different durations of protection are not available. We estimated consumers' willingness to pay for a hypothetical vaccine that would deliver a 1-year, 5- years, 10-years, or lifetime protection against Salmonella, E. coli, or Listeria. We used logit and Tobit models to estimate the economic benefits of food safety measures against these major foodborne pathogens. Based on FoodNet 2002 population survey data, consumers were willing to pay for protection against foodborne pathogens. They were willing to pay more for longer protection and for protection against E. coli compared to Salmonella or Listeria. However, they were less willing to pay if the protection was costly.
Genetic Structure and Colonization History of the Fruit Fly Bactrocera tau (Diptera: Tephritidae) in China and Southeast Asia

ABSTRACT Bactrocera tau (Walker), a major invasive pest worldwide, was first described in Fujian (China) in 1849 and has dispersed to tropical and subtropical Asia and the South Pacific region. Few data are available on its colonization history and expansion processes. This pilot study attempted to reconstruct the colonization history and pathways of this pest in China and neighboring Southeast Asian countries based on mitochondrial DNA. Results of the study showed six genetic groups corresponding to geographical characteristics, although the pattern was relatively weak. Homogeneous genetic patterns were observed within southern and central China, and northern Vietnam. Continuous colonization from the coast of southern China to inland regions of China and northern Vietnam was suggested. Strong genetic structure was observed in western China, Thailand, and Laos. The isolation of four of the six groups was most probably attributable to major topographical barriers of western China. Yunnan acted as a contact zone of B. tau in China and neighboring Southeast Asia. The absence of isolation by distance and the overall low phylogeographic structure of B. tau suggested that long distance dispersal events and human activities could play a major role in the colonization and expansion patterns of B. tau. By analyzing the genetic diversity, gene flow, haplotype phylogeny, and demographic history of 23 fly populations,wehypothesized that B. tau could have been introduced long ago in southern China, from which it further expanded or that southern China could correspond to the native range of this species.
Reassessment of the prevalence of heat-stable enterotoxin (NAG-ST) among environmental Vibrio cholerae non-O1 strains isolated from Calcutta, India, by using a NAG-ST DNA probe

A collection of 521 environmental isolates of Vibrio cholerae which were previously examined by the suckling mouse assay and found to be negative for the heat-stable enterotoxin NAG-ST were reassessed by a recently developed DNA probe for NAG-ST. A total of 12 (2.3%) of the isolates hybridized with the NAG-ST probe. By using a cholera toxin (CT) DNA probe, the CT gene was detected in six of the strains in the collection, although none of the isolates of V. cholerae non-O1 hybridized with both of the toxin probes. All of the NAG-ST and CT probe-positive strains were hemolysin positive. Thirty-fold-concentrated supernatants of the three representative NAG-ST DNA probe-positive V. cholerae non-O1 strains gave positive fluid accumulation ratios in the suckling mouse assay even after heating (100 degrees C for 5 min) and also inhibited the binding of a NAG-ST monoclonal antibody to the bound NAG-ST in a competitive enzyme-linked immunosorbent assay (ELISA). Likewise, all six CT probe-positive V. cholerae non-O1 strains produced in vitro CT when examined by the CT bead ELISA. HindIII digest patterns of chromosomal DNA from the representative NAG-ST gene-positive strains were visually indistinguishable. Between the groups of NAG-ST probe-positive strains examined, there was a variation in the hybridizable fragments, with one group of strains exhibiting a hybridizable fragment similar to that of the NRT 36 reference strain; a smaller HindIII fragment hybridized with the NAG-ST probe in the other group of strains. (ABSTRACT TRUNCATED AT 250 WORDS)
Path Analysis Modeling Indicates Free Transport Increases Ambulance Use for Minor Indications

Introduction. Clinically unnecessary ambulance transport is increasing, diverting limited resources from patients needing ambulance transport. It was anecdotally observed that inappropriate ambulance use increased after abolition of a direct patient cost for ambulance transport. Hypothesis. In July 2003, direct patient fees were abolished in favor of a universally applied ambulance levy, potentially leading to increased ambulance use by patients with low illness acuity andadmission rates. Methods. The influence of age, illness acuity, andneed for admission on ambulance use was assessed for 55,397 emergency department attendances in 2002 and2004. Ambulance users were compared with nonusers in both years andattendances for 2002 compared with 2004 using chi-square test for two groups. Logistic regression provided a multivariate model leading to ambulance use. Path analysis modeling to assess interrelationships between factors associated with ambulance use was developed. Results. Ambulance users in both years were older, had more acute illness, andhad greater need for admission compared with nonusers. The odds ratio (OR) of arrival by ambulance in 2004 compared with 2002 was 1.14 (95% confidence interval, [CI], 1.12 to 1.17). In 2002, ambulance users were older (OR, 1.42; 95% CI, 1.40 to 1.43), were more likely to need admission (OR, 2.28; 95% CI, 2.16 to 2.4) andhad higher illness acuity (OR, 2.02; 95% CI, 1.94 to 2.09). There was a negative correlation between 2004 andillness acuity. Conclusions. Ambulance use increased in 2004 after patient transport fees were abolished. Increased use was associated with decreased age, clinical acuity, andadmission need. Abolishing direct patient cost stimulates ambulance use, potentially including inappropriate transport. Path analysis to assess the effect of changed funding on ambulance use could be used to the influence of other locally relevant factors contributing to ambulance use.
Papillomavirus contains cis-acting sequences that can suppress but not regulate origins of DNA replication

Bovine papillomavirus (BPV) DNA has been reported to restrict its own replication and that of the lytic simian virus 40 (SV40) origin to one initiation event per molecule per S phase, which suggests BPV DNA replication as a model for cellular chromosome replication. Suppression of the SV40 origin required two cis-acting BPV sequences (NCOR-1 and -2) and one trans-acting BPV protein. The results presented in this paper confirm the presence of two NCOR sequences in the BPV genome that can suppress polyomavirus (PyV) as well as SV40 origin-dependent DNA replication as much as 40-fold. However, in contrast to results of previous studies on SV40, most of the suppression of the PyV origin was due to NCOR-1, a 512-bp sequence that functioned independently of distance or orientation with respect to the PyV origin and that was not required for BPV DNA replication. Moreover, NCOR-1 alone or together with NCOR-2 did not restrict the ability of the PyV ori to reinitiate replication within a single S phase and did not require any BPV protein to exert suppression. Furthermore, NCOR-1 did not suppress BPV origin-dependent DNA replication except in the presence of PyV large tumor antigen (T-ag). Since NCOR-1 suppression of PyV origin activity also varied with T-ag concentration, suppression of origins by NCOR sequences appeared to require papovavirus T-ag. Therefore, it is unlikely that NCOR sequences are involved in regulating BPV DNA replication. When these results are taken together with those from other laboratories, BPV appears to be a slowly replicating version of papovaviruses rather than a model for origins of DNA replication in eukaryotic cell chromosomes.