Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography

The ability to infer the parameters of positive selection from genomic data has many important implications, from identifying drug-resistance mutations in viruses to increasing crop yield by genetically integrating favorable alleles. Although it has been well-described that selection and demography may result in similar patterns of diversity, the ability to jointly estimate these two processes has remained elusive. Here, we use simulation to explore the utility of the joint site frequency spectrum to estimate selection and demography simultaneously, including developing an extension of the previously proposed Jaatha program (Mathew et al., 2013). We evaluate both complete and incomplete selective sweeps under an isolation-with-migration model with and without population size change (both population growth and bottlenecks). Results suggest that while it may not be possible to precisely estimate the strength of selection, it is possible to infer the presence of selection while estimating accurate demographic parameters. We further demonstrate that the common assumption of selective neutrality when estimating demographic models may lead to severe biases. Finally, we apply the approach we have developed to better characterize the within-host demographic and selective history of human cytomegalovirus (HCMV) infection using published next generation sequencing data.
A mobile driver safety system: Analysis of single-channel EEG on drowsiness detection

Recent studies reveal that driving without sufficient sleep would increase the risk of road traffic accident. With the aim to facilitate a safer driving experience, eye activity detection algorithm were studied actively. Though the use of wired multi-channel brain computer interface (BCI) to monitor driver's mental state has shown promising results, but the actual practicality were limited by its inconvenience. Consequently, we examined the effectiveness of a wireless and wearable single-channel BCI in detecting driver's eye-states. Using the NeuroSky MindWave headset that entailed a single-electrode for prefrontal cortex, we observed an increment of low alpha activity during the transition from eyes-open to eyes-closed state. A monitoring system to keep drivers awake by means of alarm notifications is then implemented using adaptive percentage threshold algorithm for alarm-triggering purpose. Through simulation, our algorithm has demonstrated an EEG eye-states recognition system with: adequate detection rate of 31% per second, negligible false alarm rate of 0.5%, and minimum latency of 2 seconds.
Plant Virus-Derived Small Interfering RNAs Originate Predominantly from Highly Structured Single-Stranded Viral RNAs

ABSTRACT RNA silencing is conserved in a broad range of eukaryotes and includes the phenomena of RNA interference in animals and posttranscriptional gene silencing (PTGS) in plants. In plants, PTGS acts as an antiviral system; a successful virus infection requires suppression or evasion of the induced silencing response. Small interfering RNAs (siRNAs) accumulate in plants infected with positive-strand RNA viruses and provide specificity to this RNA-mediated defense. We present here the results of a survey of virus-specific siRNAs characterized by a sequence analysis of siRNAs from plants infected with Cymbidium ringspot tombusvirus (CymRSV). CymRSV siRNA sequences have a nonrandom distribution along the length of the viral genome, suggesting that there are hot spots for virus-derived siRNA generation. CymRSV siRNAs bound to the CymRSV p19 suppressor protein have the same asymmetry in strand polarity as the sequenced siRNAs and are imperfect double-stranded RNA duplexes. Moreover, an analysis of siRNAs derived from two other nonrelated positive-strand RNA viruses showed that they displayed the same asymmetry as CymRSV siRNAs. Finally, we show that Tobacco mosaic virus (TMV) carrying a short inverted repeat of the phytoene desaturase (PDS) gene triggered more accumulation of PDS siRNAs than the corresponding antisense PDS sequence. Taken together, these results suggest that virus-derived siRNAs originate predominantly by direct DICER cleavage of imperfect duplexes in the most folded regions of the positive strand of the viral RNA.
Subjective quality assessment of an adaptive video streaming model

With the recent increased popularity and high usage of HTTP Adaptive Streaming (HAS) techniques, various studies have been carried out in this area which generally focused on the technical enhancement of HAS technology and applications. However, a lack of common HAS standard led to multiple proprietary approaches which have been developed by major Internet companies. In the emerging MPEG-DASH standard the packagings of the video content and HTTP syntax have been standardized; but all the details of the adaptation behavior are left to the client implementation. Nevertheless, to design an adaptation algorithm which optimizes the viewing experience of the enduser, the multimedia service providers need to know about the Quality of Experience (QoE) of different adaptation schemes. Taking this into account, the objective of this experiment was to study the QoE of a HAS-based video broadcast model. The experiment has been carried out through a subjective study of the end user response to various possible clients’ behavior for changing the video quality taking different QoE-influence factors into account. The experimental conclusions have made a good insight into the QoE of different adaptation schemes which can be exploited by HAS clients for designing the adaptation algorithms.
H-rev107 Regulates Cytochrome P450 Reductase Activity and Increases Lipid Accumulation

H-rev107 is a member of the HREV107 type II tumor suppressor gene family and acts as a phospholipase to catalyze the release of fatty acids from glycerophospholipid. H-rev107 has been shown to play an important role in fat metabolism in adipocytes through the PGE2/cAMP pathway, but the detailed molecular mechanism underlying H-rev107-mediated lipid degradation has not been studied. In this study, the interaction between H-rev107 and cytochrome P450 reductase (POR), which is involved in hepatic lipid content regulation, was determined by yeast two-hybrid screen and confirmed by using in vitro pull down assays and immunofluorescent staining. The expression of POR in H-rev107-expressing cells enhanced the H-rev107-mediated release of arachidonic acid. However, H-rev107 inhibited POR activity and relieved POR-mediated decreased triglyceride content in HtTA and HeLa cervical cells. The inhibitory effect of H-rev107 will be abolished when POR-expressing cells transfected with PLA2-lacking pH-rev107 or treated with PLA2 inhibitor. Silencing of H-rev107 using siRNA resulted in increased glycerol production and reversion of free fatty acid-mediated growth suppression in Huh7 hepatic cells. In summary, our results revealed that H-rev107 is also involved in lipid accumulation in liver cells through the POR pathway via its PLA2 activity.
Cellular retinol-binding protein I, a regulator of breast epithelial retinoic acid receptor activity, cell differentiation, and tumorigenicity.

BACKGROUND Retinoic acid receptor (RAR) activation induces cell differentiation and may antagonize cancer progression. Cellular retinol-binding protein I (CRBP-I) functions in retinol storage and its expression is lower in human cancers than in normal cells. We hypothesized that retinol storage might be linked to RAR activation and thus that lowered CRBP-I function might impair RAR activity and cell differentiation. METHODS Sarcoma virus 40-immortalized human mammary epithelial cells (MTSV1-7) devoid of CRBP-I were transfected with wild-type CRBP-I or CRBP-I point mutants with low RA binding affinity. The subcellular localization of CRBP-I was investigated in these cells and in wild-type or CRBP-I null mouse mammary epithelial cells (MECs), using indirect immunofluorescence and sucrose gradient fractionation. RAR activity was assessed using reporter gene assays. Acinar differentiation and in vivo tumor growth were assessed in reconstituted basement membrane and athymic mice, respectively. RESULTS In cells expressing wild-type CRBP-I but not the CRBP-I mutants, CRBP-I was found mainly in lipid droplets, the retinol storage organelle, and this localization was associated with promotion of retinol storage by wild-type CRBP-I only. RAR activity was higher and acinar differentiation was observed in cells expressing wild-type but not mutant CRBP-I. RAR antagonist treatment blocked and chronic RA treatment mimicked, the CRBP-I induction of cell differentiation. Finally, CRBP-I suppressed tumorigenicity in athymic mice. CONCLUSIONS Physiologic RAR activation is dependent on CRBP-I-mediated retinol storage, and CRBP-I downregulation chronically compromises RAR activity, leading to loss of cell differentiation and tumor progression.
Capital Adequacy, Bank Behavior and Crisis: Evidence from Emergent Economies

Using the simultaneous equations model, this paper examines the impact of capital requirements on bank risk-taking during the recent financial crisis. It also explores the relationship between capital and risk decisions and the impact of economic instability on this relationship. By analyzing the data of 46 commercial banks between 2004 and 2014 from four Middle East countries, the study concludes a positive effect of regulatory pressure on bank capital and bank risk taking. The findings reveal also that banks close to the minimum regulatory capital requirements improve their capital adequacy by increasing their capital and decreasing their risk taking. Furthermore, the results show that economic crisis positively affects bank risk changes, suggesting that banks react to the impact of uncertainty by increasing their risk taking. Finally, the estimations show a positive correlation between banks profitability and increase in capital, indicating that profitable banks can more easily improve their capitalization through retained earnings rather than issuing new securities. Keywords: bank regulation, risk taking, bank capital, crisis.
A Study of Cytological Evaluation of Bronchial Washing and Brushing In Bronchogenic Carcinoma

Bronchogenic carcinoma is undoubtedly one of the major killer diseases worldwide. Pulmonary cytology is a simple and resourceful method of early diagnosis of bronchogenic carcinoma. The use of bronchoscope has increased the variety of diagnostic specimen obtainable and extended the scope of cyto-pathology. We carried out a study to demonstrate the value of cytological examination of bronchial brushing and washing in diagnosis of bronchogenic carcinoma in our settings. 69 patients of clinically and radiologically suspected brochogenic carcinoma attending the Dr. B. Borooah Cancer Institute (Guwahati) as well as in Dept. of Pathology, Gauhati Medical College and hospital were selected for one year. Out of total 69 cases bronchial brushing carried out in 42 cases and bronchial washing carried out in 27 cases. In bronchial brushing cytology a positive diagnosis of malignancy was established in 30 cases (71.43%) and in bronchial washing diagnosis of malignancy was found in 8 cases. Bronchoscopic biopsy was successfully done in 40 cases and histopathological diagnosis of malignancy was made in 29 cases. Out of 29 cases of carcinoma confirmed by histology, cytology was consistent in 26 cases. The bronchial cytology revealed sensitivity (89.96%), specificity (90.9%), positive predictive rate (96.3%), accuracy (90%), false negative rate (10.34%) and false positive rate (9.1%). During the bronchoscopic procedure there was no major complication or fatality. Thus bronchial brushing and washing has firmly established its role in the early diagnosis of brochogenic carcinoma because it is safe, rapid and cost -effective and importantly gives a higher rate of sensitivity and accuracy.
Establishment of a New Cell Line from Lepidopteran Epidermis and Hormonal Regulation on the Genes

When an insect molts, old cuticle on the outside of the integument is shed by apolysis and a new cuticle is formed under the old one. This process is completed by the epidermal cells which are controlled by 20-hydroxyecdysone (20E) and juvenile hormone. To understand the molecular mechanisms of integument remolding and hormonal regulation on the gene expression, an epidermal cell line from the 5th instar larval integument of Helicoverpa armigera was established and named HaEpi. The cell line has been cultured continuously for 82 passages beginning on June 30, 2005 until now. Cell doubling time was 64 h. The chromosomes were granular and the chromosome mode was from 70 to 76. Collagenase I was used to detach the cells from the flask bottom. Non-self pathogen AcMNPV induced the cells to apoptosis. The cell line was proved to be an epidermal cell line based on its unique gene expression pattern. It responded to 20E and the non-steroidal ecdysone agonist RH-2485. Its gene expression could be knocked down using RNA interference. Various genes in the cell line were investigated based on their response to 20E. This new cell line represents a platform for investigating the 20E signaling transduction pathway, the immune response mechanism in lepidopteran epidermis and interactions of the genes.
Genetic Modification of Cancer Cells Using Non-Viral, Episomal S/MAR Vectors for In Vivo Tumour Modelling

The development of genetically marked animal tumour xenografts is an area of ongoing research to enable easier and more reliable testing of cancer therapies. Genetically marked tumour models have a number of advantages over conventional tumour models, including the easy longitudinal monitoring of therapies and the reduced number of animals needed for trials. Several different methods have been used in previous studies to mark tumours genetically, however all have limitations, such as genotoxicity and other artifacts related to the usage of integrating viral vectors. Recently, we have generated an episomally maintained plasmid DNA (pDNA) expression system based on Scaffold/Matrix Attachment Region (S/MAR), which permits long-term luciferase transgene expression in the mouse liver. Here we describe a further usage of this pDNA vector with the human Ubiquitin C promoter to create stably transfected human hepatoma (Huh7) and human Pancreatic Carcinoma (MIA-PaCa2) cell lines, which were delivered into “immune deficient” mice and monitored longitudinally over time using a bioluminometer. Both cell lines revealed sustained episomal long-term luciferase expression and formation of a tumour showing the pathological characteristics of hepatocellular carcinoma (HCC) and pancreatic carcinoma (PaCa), respectively. This is the first demonstration that a pDNA vector can confer sustained episomal luciferase transgene expression in various mouse tumour models and can thus be readily utilised to follow tumour formation without interfering with the cellular genome.
Robust Tracking: Keeping Adaptivity but Refusing to Drift

Tracking with a discriminative classifier becomes popular recently. The online updating makes it easy to adapt to target appearance variations. However, this also brings drifting problem. It’s necessary to find a tracking method with strong adaptivity and anti-drifting ability. In this paper, an online semi-supervised boosting method is proposed at first, and based on it, we propose a novel tracking framework that treats samples differently when updating the classifier under different conditions. This tracking framework can significantly alleviate the drifting problem and keep adaptive enough to appearance variations. Experimental results on challenging videos show that our method can track accurately and robustly， and outperform many other state-of-the-art trackers.
The impacts of external factors on the growth of Chinese entrepreneurial enterprises

Purpose – The purpose of this paper is to explore the key external factors that are impacting on the performance of Chinese entrepreneurial enterprise (EE). Design/methodology/approach – A linear regression model was developed that comprised three types of organisations(government, university and R&D institute, agency, financial institution) and three kinds of environmental factors(legal and institutional environment, culture, geographic location) which greatly influence Chinese venture enterprises growth. The model was validated using 91 responses obtained through a questionnaire survey carried out in Shanghai, Zhejiang, Jiangsu and Fujian Province of China.Findings – Evidence suggests that a fine relationship with a financial organisation positively impacts on the growth of EEs and a close relationship with government shows a disadvantageous impact on the EE's growth. The significant influence of environmental factors appeared to come from entrepreneurial culture and atmosphere.Practical implications – T.
Evidence on the Presence of Representativeness Bias in Investor Interpretation of Consistency in Sales Growth

We document that consistent patterns of high or low sales growth that are incongruent with underlying fundamentals are followed by significant stock price reversals. In contrast, no stock return reversals are found for firms that achieve the same level of sales growth in an inconsistent manner. Furthermore, future earnings announcement returns mimic the pattern of abnormal stock returns documented for the Consistent- and Inconsistent-Growth portfolios, respectively, corroborating our main findings. Our results are robust to controls for the magnitude of sales growth, fundamental strength, business cycle risk exposures, and standard risk factors. Our evidence is consistent with representativeness bias affecting investor interpretation of consistency in sales growth patterns. This paper was accepted by Mary Barth, accounting .
Managing in Turbulence: How the Capacity for Resilience Influences Creativity

How do companies manage to compete in a marketplace marked by turbulence, and not be outcompeted? In our study we assess the resources used to create resilience in organizations and how each of these resources relates to organizational creativity. We show that organizational resilience is positively related to organizational creativity. Specifically, our study highlights that cognitive, emotional, and structural resources are important resources for organizations wanting to become creative. Our results are based upon a pilot in‐depth qualitative case study followed by a survey of medium‐sized firms. The results in our study advance the emergent literature on resilience and on the practical applications of resilience in organizations. From a practical point of view, managers may realize that they have to develop a capacity for resilience (i.e. what they have to do) in order to have a creative organization, but a far bigger challenge is to understand the how; how the capacity for resilience is built. Our research shows that if managers truly want to manage in turbulence and still have a creative organization, they need to put a strong emphasis on the soft skills in the organization, in addition to the structural resources.
Nonlinear neural representation of emotional feelings elicited by dynamic naturalistic stimulation

Emotions guide organisms in constantly changing dynamic environments. While the majority of previous studies have assessed neural basis of emotions elicited by impoverished stimuli (e.g., pictures or words), it has been shown that dynamic naturalistic stimuli (e.g., movies and stories) elicit stronger subjective emotional experiences. Here, we studied the neural basis of subjective feelings of pleasantness and unpleasantness (i.e., emotional valence) and emotional arousal by presenting sixteen participants with thirteen emotional and neutral movie clips during 3-Tesla fMRI scanning. After scanning, the participants viewed the clips again and rated their moment-to-moment subjective experience of valence and arousal. These participant-wise experiential time series were used to model each participant’s brain activity during viewing of the movies, while factoring out contributions of physical stimulus features. The results suggest that a set of cortical and subcortical areas encode subjective feelings in nonlinear fashion; we observed a quadratic (U-shaped) dependency between the experienced emotional valence and BOLD signal in insula, somatosensory cortex, anterior and middle cingulate cortices, hypothalamus and thalamus, inferior frontal gyrus, and in medial prefrontal and orbitofrontal cortex. We propose that this network of brain areas represents the subjectively experienced valence as deviations from the neutral emotional state.
Segment Reporting Practices in Australia: Has IFRS 8 Made a Difference?

This study examines changes in segment reporting in Australia following the adoption of the international accounting standard, IFRS 8 Operating Segments. We analyse segment disclosures of the top 200 companies listed on the Australian Stock Exchange in their pre- and post-adoption of AASB 8, the equivalent Australian standard to IFRS 8. Our findings indicate that the number of reportable segments and the extent of disclosure have increased post-adoption of AASB 8. Contrary to expectations, however, there is very little change in the identification of reportable segments. Companies, in general, have managed to retain their segment reporting formats and disclosures from the pre-AASB 8 period.
Phosphorylation Analysis by Mass Spectrometry

The mass spectrometric analysis of protein phosphorylation is still far from being routine, and the outcomes thereof are often unsatisfying. Apart from the inherent problem of substoichiometric phosphorylation, three arguments as to why phosphorylation analysis is so problematic are often quoted, including (a) increased hydrophilicity of the phosphopeptide with a concomitant loss during the loading onto reversed-phase columns, (b) selective suppression of the ionization of phosphopeptides in the presence of unmodified peptides, and (c) lower ionization/detection efficiencies of phosphopeptides as compared with their unmodified cognates. Here we present the results of a study investigating the validity of these three arguments when using electrospray ionization mass spectrometry. We utilized a set of synthetic peptide/phosphopeptide pairs that were quantitated by amino acid analysis. Under the applied conditions none of the experiments performed supports the notions of (a) generally increased risks of losing phosphopeptides during the loading onto the reversed-phase column because of decreased retention and (b) the selective ionization suppression of phosphopeptides. The issue of ionization/detection efficiencies of phosphopeptides versus their unphosphorylated cognates proved to be less straightforward when using electrospray ionization because no evidence for decreased ionization/detection efficiencies for phosphopeptides could be found.
Web-Store Aesthetics in E-Retailing : A Conceptual Framework and Some Theoretical l Implications

Noam Tractinsky is a Senior Lecturer of Information Systems Engineering at Ben-Gurion University of the Negev, Beer Sheva 84105, Israel, tel. +972 8 647 2226, noamt@bgu.ac. il. Oded Lowengart is a Senior Lecturer of Marketing, Department of Business Administration, School of Management, BenGurion University of the Negev, Beer Sheva 84105, Israel, tel +972 8 647 2447, odedl@bgu.ac. il. The authors wish to thank the editor and the anonymous reviewers for their valuable comments and suggestions.