Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical methods for analyzing genetic sequencing association studies

Case-control genetic sequencing studies are increasingly being conducted to identify rare variants associated with complex diseases. Oftentimes, these studies collect a variety of secondary traits–quantitative and qualitative traits besides the case-control disease status. Reusing the data and studying the association between rare variants and secondary phenotypes provide an attractive and cost effective approach that can lead to discovery of new genetic associations. In Chapter 1, we carry out an extensive investigation of the validity of ad hoc methods, which are simple, computationally efficient methods frequently applied in practice to study the association between secondary phenotypes and single common genetic variants. Though other researchers have investigated the same problem, we make two key contributions to existing literature. First, we show that in taking an ad hoc approach, it may be desirable to adjust for covariates that affect the primary disease in the secondary phenotype model, even though these covariates are not necessarily associated with the secondary phenotype in the population. Second, we show that when the disease is rare, ad hoc methods can lead to severely biased estimation and inference if the true disease model follows a nonlogistic model such as the probit model. Spurious associations can be avoided by including interaction terms in the fitted regression model. Our results are justified theoretically and via simulations, and illustrated by a genome-wide association study of smoking using a lung cancer case-control study. In Chapter 2, we consider the problem of testing associations between secondary phenotypes and sets of rare genetic variants. We show that popular region-based methods such as the burden test and the sequence kernel association test (SKAT) can only be applied under the same conditions as those applicable to ad hoc methods (Chapter 1). For a more
EFFECTS OF COMPOST ON THE AVAILABILITY OF NITROGEN AND PHOSPHORUS IN STRONGLY ACIDIC SOILS

Strongly acidic soil is a major problem in Taiwan. The application of organic fertilizers is an important practice in increasing the productivity of such soils. However, the transformation and availability of phosphorus in the soil will be more complex if organic fertilizers are used in strongly acidic soils. This paper discusses the effect of using composted animal manure on the availability of nitrogen and phosphorus in strongly acidic soils in Taiwan. The development of phosphocompost and its application to strongly acidic soils are also discussed.
The relationships between snail1 and estrogen receptor signaling in breast cancer cells

The loss of hormonal dependency of breast tumor cells is often accompanied with the appearance of epithelial‐mesenchymal transition (EMT) features and increase in cell metastasis and invasiveness. The central role in the EMT belongs to transcription factors Snail responded for the decrease in E‐cadherin expression and cell contacts, stimulation of cell mobility and invasiveness. Aim was to study the relationships between estrogen receptor machinery and Snail1 signaling, and mechanism of Snail1 regulation in hormone‐resistant breast cancer cells. The experiments were performed on the estrogen‐dependent MCF‐7 breast cancer cells, estrogen‐hyposensitive MCF‐7/LS subline generated through long‐term cultivation of the parental cells in steroid‐free medium, and ER‐negative estrogen‐resistant HBL‐100 cells. Snail1, estrogen receptor, p65 NF‐κB, E‐cadherin levels were analyzed by Western blot. We found that decrease in the estrogen dependency is correlated with increase in Snail1 expression and activity, we demonstrated the Snail1 involvement in the negative regulation of ER, and showed that Snail1 inhibition partially restores the sensitivity of the estrogen‐hyposensitive cells to antiestrogen tamoxifen. Furthermore, NF‐κB was found to serve as a positive regulator of Snail1 in breast cancer cells, and simultaneous inhibition of NF‐κB and Snail1 resulted in additional increase in cell response to tamoxifen. In general, the results obtained demonstrate the phenomenon of Snail1 activation in the hormone‐resistant breast cancer cells, and show that Snail1 and NF‐κB may serve as an important targets in the treatment of breast cancer, both estrogen‐dependent and estrogen‐independent tumors. J. Cell. Biochem. 113: 2147–2155, 2012. © 2012 Wiley Periodicals, Inc.
Insider Trading B-Side: Relevance, Timeliness and Position Influence

Objective – Our main objective is to analyze the impacto f insider trading on stock investments’ decision. Design/methodology/approach – We used an online survey, obtaining 271 valid answers. To analyze our data, we used some parametric (t and F Anova), and non-parametric techniques (Mann-Whitney and Kruskal-Wallis). Findings – We find that insider tradings are relevant to investment decisions, and the timeliness also exert an influence to this kind of decision, especially abnormal trades. Practical implications – In practical terms, our results suggests that the Brazilian Securities and Exchange Commission (CVM) must update the Brazilian insider trading regulation to achieve the objective to protect investors. In the investors point of view, this possible update could improve investors’ ability to control insiders and follow his activities as well as to mimic his trades. Originality/value – The originality of our paper is an analysis of relevance, timeliness and influence of position in a firm as “determinants” of investment decisions. We use these three specific characteristics to criticize the Brazilian insider trading regulation.
Sustainability Standards for Palm Oil

This article investigates the integration of smallholders into voluntary certification schemes, exemplified by smallholder certification under the Roundtable on Sustainable Palm Oil in Indonesia (RSPO). It identifies the main barriers to the adoption of standards by smallholders and the specific compliance challenge in the context of RSPO smallholder certification, thereby contributing to the growing literature on the effectiveness of voluntary sustainability standards. It discusses findings on smallholder certification, focusing on antecedent variables as potential adoption determinants at the level of smallholders, smallholder organization, and the institutional context. The empirical findings suggest that smallholders, and specifically independent smallholders, often lack both the information and the degree of organization that certification demands. The article also identifies the most important compliance challenges for independent smallholders in relation to land titles, seedlings, pesticide usage, fertilization, and documentation and outlines how smallholders can be supported so that they can be included in certification schemes.
Exaptation dynamics and entrepreneurial performance: : evidence from the internet video industry

This paper explores entrepreneurial strategy by analyzing the Internet video industry. Data on entrants to the Chinese Internet video industry from 2006 to 2011 reveal how those that adapt to shifts in the environment outperform less flexible firms. The paper also shows how exaptive processes, including strategic commitment to user communities, increase resilience in start-ups that face such shifts. These findings introduce an expanded view of entrepreneurial strategy by directly linking strategic choice to venture performance and clarifying the role of exaptation in entrepreneurship.
Validity in psychological measurement : an investigation of test norms

A psychological test may be defined as an objective and standardized measure of a sample of behaviour. The interpretation of test results is usually based on comparing an individual’s performance to norms based on a representative sample of the population. The present study examined the norms of popular adult tests. The validity of the Wartegg drawing test (WZT) was studied using two rating scales, the Toronto Alexithymia Scale and the Beck Depression Inventory as criterion tests. Weak to moderate correlations were found. It is concluded that the WZT has some validity in the assessment of Alexithymia. Efforts to develop a psychometrically valid and reliable method of interpreting the WZT should be continued. Crossnational and historical analyses of the norms of Wechsler’s adult intelligence scale (WAIS) were performed. The results show that the Finnish WAIS III test norms are distorted in the younger age groups. Significant cross-national and cross-generational differences in relative subtest scores, test profiles were also observed. Differences in general intelligence cannot explain such variations, and educational and cultural factors probably underlie the observed differences. It is suggested that the concept of a national IQ profile is useful for cross-national test validation studies. The validity of a validity scale, the Chapman Infrequency Scale, was studied in the context of a survey study. Results showed that careless responding is significantly more frequent among psychiatric patients relative to healthy respondents. The common procedure of excluding careless responders from final samples may affect the results of survey studies targeting individuals with psychiatric symptoms. Cut-off scores for exclusion should be flexible and chosen according to the demographic and health characteristics of the sample. In conclusion, the results of this study underscore the need for up-to-date and representative test norms for valid test interpretation.
Acoustic Signal Characteristics Analysis of Underwater Plasma Source Pulse Discharge based on Variational Mode Decomposition Algorithm

In order to study the variational mode decomposition (VMD) algorithm for the analysis of acoustic signal characteristics of underwater plasma sound source pulse discharge, a simulation model of central control module is established by using VMD algorithm. The whole hardware circuit takes the FPGA (Field Programmable Gate Array) chip as the intelligent control center of the central control module, and combining with the minimum composed of basic power supply circuit, clock circuit, reset circuit and configuration circuit, the model is used to analyze the characteristics of acoustic signals. The results show that the uncertainties of these parameters also affect the performance of VMD. In VMD decomposition, the smaller the equilibrium constraint parameters are, the larger the bandwidth of each modal component is, the more likely the phenomenon of center frequency overlap and mode aliasing will occur. The larger the equilibrium constraint parameters are, the smaller the bandwidth of each component signal will be, and the phenomenon of center frequency overlap and mode aliasing will disappear. Through analysis, it is proposed that the general equilibrium constraint parameters can be taken as sampling frequency fs in practice. The acoustic signal of VMD applied to underwater plasma sound source pulse discharge is analyzed, and the results are as expected. It provides a theoretical basis and practical basis for its application in underwater plasma acoustic signal characteristics analysis. This is of great significance to the study of VMD as an underwater plasma source for the analysis of acoustic signal characteristics of pulse discharge.
Telomere Maintenance Mechanisms in Cancer

Tumour cells can adopt telomere maintenance mechanisms (TMMs) to avoid telomere shortening, an inevitable process due to successive cell divisions. In most tumour cells, telomere length (TL) is maintained by reactivation of telomerase, while a small part acquires immortality through the telomerase-independent alternative lengthening of telomeres (ALT) mechanism. In the last years, a great amount of data was generated, and different TMMs were reported and explained in detail, benefiting from genome-scale studies of major importance. In this review, we address seven different TMMs in tumour cells: mutations of the TERT promoter (TERTp), amplification of the genes TERT and TERC, polymorphic variants of the TERT gene and of its promoter, rearrangements of the TERT gene, epigenetic changes, ALT, and non-defined TMM (NDTMM). We gathered information from over fifty thousand patients reported in 288 papers in the last years. This wide data collection enabled us to portray, by organ/system and histotypes, the prevalence of TERTp mutations, TERT and TERC amplifications, and ALT in human tumours. Based on this information, we discuss the putative future clinical impact of the aforementioned mechanisms on the malignant transformation process in different setups, and provide insights for screening, prognosis, and patient management stratification.
Novel Deep Learning Model for Traffic Sign Detection Using Capsule Networks

Convolutional neural networks are the most widely used deep learning algorithms for traffic signal classification till date but they fail to capture pose, view, orientation of the images because of the intrinsic inability of max pooling layer.This paper proposes a novel method for Traffic sign detection using deep learning architecture called capsule networks that achieves outstanding performance on the German traffic sign dataset.Capsule network consists of capsules which are a group of neurons representing the instantiating parameters of an object like the pose and orientation by using the dynamic routing and route by agreement algorithms.unlike the previous approaches of manual feature extraction,multiple deep neural networks with many parameters,our method eliminates the manual effort and provides resistance to the spatial variances.CNNs can be fooled easily using various adversary attacks and capsule networks can overcome such attacks from the intruders and can offer more reliability in traffic sign detection for autonomous vehicles.Capsule network have achieved the state-of-the-art accuracy of 97.6% on German Traffic Sign Recognition Benchmark dataset (GTSRB).
Breast cancer awareness through smart mobile healthcare applications from Indian doctors' perspective

Breast cancer is the most common cancer in women worldwide, with nearly 14.1 million cases diagnosed globally in 2012. In the same year, there were 8.2 million deaths from cancer in the world making breast cancer the second most common cancer overall. Also, India has one of the highest cases of breast cancer. According to WHO, for the year 2012, an estimated 144,937 women in India were newly detected with breast cancer and 70,218 women died of breast cancer in the same year, more than any other country in the world. This indicates a beginning of an epidemic which requires effective intervention to reduce the incidence of breast cancer, thereby reducing mortality. In the last few years, a lot of global initiatives on breast cancer have been taken by the World Health Organization (WHO), the International Breast Cancer Research Foundation (IBCRF) and Pink Ribbon International (PBI). These international bodies are addressing and creating awareness on breast cancer. One such initiative is the mobile applications that can can provide people with breast cancer, survivors, and caregivers convenient resources and tools to guide them through their treatment and keep their life more organized. Many researchers and scientists have come up with mobile health (m-health) apps to prevent and promote breast cancer awareness to the public. Though there are many mobile apps available on itunes and google play, people are not aware of the apps' purpose or it is not promoted well. The main purpose of this article is to analyse how breast cancer health apps (such as iBreastCheck) can help in primary prevention, early diagnosis and palliative care of breast cancer in India from doctors' perspective. Focus group and questionnaire survey was carried out to understand the adoption and acceptance of mobile health apps for breast cancer awareness by doctors for the Indian public. The focus group and the online survey statistical results demonstrates the need and importance of using mobile health apps to prevent, detect and treat breast cancer, which means Indian doctors have a positive approach towards recommending breast cancer mobile health apps to women.
Yield Curve Dynamics: Regional Common Factor Model

In this paper, we focus on thorough yield curve modelling. We build on extended classical NelsonSiegel model, which we further develop to accommodate unobserved regional common factors. We centre our discussion on Central European currencies’ yield curves: CZK, HUF, PLN and SKK. We propose a model to capture regional dynamics purely based on state space formulation. The contribution of this paper is twofold: we examine regional yield curve dynamics and we quantify regional interdependencies amongst considered currencies’ yield curves. We conclude that the CZK yield curve possesses its own dynamics corresponding to country specifi c features, whereas other currencies’ yield curves are strongly infl uenced by the regional level, the regional slope factor or both.
Dermatitis Herpetiformis: A Common Extraintestinal Manifestation of Coeliac Disease

Dermatitis herpetiformis (DH) is a common extraintestinal manifestation of coeliac disease presenting with itchy papules and vesicles on the elbows, knees, and buttocks. Overt gastrointestinal symptoms are rare. Diagnosis of DH is easily confirmed by immunofluorescence biopsy showing pathognomonic granular immunoglobulin A (IgA) deposits in the papillary dermis. A valid hypothesis for the immunopathogenesis of DH is that it starts from latent or manifest coeliac disease in the gut and evolves into an immune complex deposition of high avidity IgA epidermal transglutaminase (TG3) antibodies, together with the TG3 enzyme, in the papillary dermis. The mean age at DH diagnosis has increased significantly in recent decades and presently is 40–50 years. The DH to coeliac disease prevalence ratio is 1:8 in Finland and the United Kingdom (U.K.). The annual DH incidence rate, currently 2.7 per 100,000 in Finland and 0.8 per 100,000 in the U.K., is decreasing, whereas the reverse is true for coeliac disease. The long-term prognosis of DH patients on a gluten-free diet is excellent, with the mortality rate being even lower than for the general population.
Assessment of Soil-Water Infiltration Dynamics of Waste Oil Polluted Terrestrial Habitat Under Macrophytic Remediation: A Window for Automobile Workshops

Automobile workshops are the hub of waste oil sources among other sources of pollution with it attendance consequence of physico-edaphic alterations of the terrestrial soil habitat. This research was aimed at reevaluating the demonstrated potential of three hydrocarbon tolerant leguminous species; in view of their application in automobile workshop surroundings. Field and laboratory analysis of the physico-edaphic parameters were carried out using universally acceptable standard methods. Result has recorded enhanced infiltration rate by phytotechnology among Peltophorum pterocarpium (Pp), Leucaena leucocephala (Ll) and Crotolaria retusa (Cr) waste oil soils in the order Pp<Cl<Ll ; in which P. pterocarpum has increased infiltration at lesser time rate of 1.07 ± 0.31, 1.51 ± 0.02, 2.48 ± 0.35 and 3.13 ± 1.45 across levels of treatment with significant difference ( p<0.05 ). This was correspondingly in direct relationship with the significantly enhanced particle size (87.73%) of sand, and 2.61g/cm 3 particle density, reduced bulk density (0.83g/cm 3 ), 68% porosity increase and reduced organic matter content of 2.65%, total hydrocarbon content reduction of 1.8mg/g, high efficiency of 55% hydrocarbon removal, 34.40 bioaccumulation quotient and 24.63% reduction in crusting hazard of sealing recorded. Conclusively, P. pterocarpum can be proposed for automobile workshops as a proactive measure and containment absorbent among other hydrocarbon restoration approach against envisaged waste oil discharge. Keywords: Crusting hazard, total hydrocarbon, root formation, bioaccumulation quotient and particle size. DOI : 10.7176/JEES/9-3-07 Publication date :March 31 st 2019
A Patient Suffering from Pneumatosis Cystoid Intestinalis

Article history: Received: 17 Sep 2010 Accepted: 18 Oct 2010 Available online: 20 June 2011 Pneumatosis Cystoid Intestinalis (PCI) is a relatively rare disorder that occurs in different parts of the stomach and intestines as gas-filled cysts. It is predicted to be prevalent among 0/20/03% of the population. In 85% of cases, Pneumatosis Cystoid Intestinalis is caused by a specific disease. In this article, a patient will be introduced who was admitted 3 days after the pelvic trauma presented with symptoms of intestinal obstruction. The conducted examinations showed generalized abdominal tenderness and in CXR plenty of free air was observed under the diaphragm. After the primary diagnosis of intestinal obstruction (ileus), the patient was put under laparotomy. During laparotomy, PCI was seen under the intestinal serosa and a significant amount of air was released and many parts of contusion were observed in the small intestine along with fibrin formation without pus which was restored and the patient was discharged in a well general condition. Copyright© 2012 Zahedan University of Medical Sciences. All rights reserved.
Beyond Deductive Methods in Program Analysis

Building effective program analysis tools is a challenging endeavor: analysis designers must balance multiple competing objectives, including scalability, fraction of false alarms, and the possibility of missed bugs. Not all of these design decisions are optimal when the analysis is applied to a new program with different coding idioms, environment assumptions, and quality requirements. Furthermore, the alarms produced are typically accompanied by limited information such as their location and abstract counter-examples. We present a framework DIFFLOG that fundamentally extends the deductive reasoning rules that underlie program analyses with numerical weights. Each alarm is now naturally accompanied by a score, indicating quantities such as the confidence that the alarm is a real bug, the anticipated severity, or expected relevance of the alarm to the programmer. To the analysis user, these techniques offer a lens by which to focus their attention on the most important alarms and a uniform method for the tool to interactively generalize from human feedback. To the analysis designer, these techniques offer novel ways to automatically synthesize analysis rules in a data-driven style. DIFFLOG shows large reductions in false alarm rates and missed bugs in large, complex programs, and it advances the state-of-the-art in synthesizing non-trivial analyses.
Erdheim-Chester Disease: Case Report with Aggressive Multisystem Manifestations and Review of the Literature

Erdheim-Chester disease (ECD) is an extremely rare and aggressive form of non-Langerhans cell histiocytosis. ECD usually presents with bone pain in adults aged 40–60. Its etiology is unknown but it is thought to be either a reactive or neoplastic disorder. Recently, mutation of the proto-oncogene BRAF (BRAFV600E) has been found in more than 50% of cases. The multisystemic form of ECD is associated with significant morbidity, which may arise due to histiocytic infiltration of critical organ systems. The common sites of involvement are the skeleton, central nervous system, cardiovascular system, lungs, retroperitoneum, and skin. Current available treatment is interferon alpha as the first line of treatment. Treatment with other agents is based on anecdotal case reports. Cladribine, anakinra, and vemurafenib (BRAF inhibitor) are currently advocated as promising second-line treatments for patients whose response to interferon alpha is unsatisfactory. Herein, we are reporting a middle-aged Saudi male patient with an aggressive type of ECD and highlighting the clinical, radiological, and pathological manifestations associated with ECD and the various treatment options and patient follow-up.