Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudoreplication and the Design of Ecological Field Experiments

Pseudoreplication is defined. as the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates are not statistically independent. In ANOVA terminology, it is the testing for treatment effects with an error term inappropriate to the hypothesis being considered. Scrutiny of 176 experi- mental studies published between 1960 and the present revealed that pseudoreplication occurred in 27% of them, or 48% of all such studies that applied inferential statistics. The incidence of pseudo- replication is especially high in studies of marine benthos and small mammals. The critical features of controlled experimentation are reviewed. Nondemonic intrusion is defined as the impingement of chance events on an experiment in progress. As a safeguard against both it and preexisting gradients, interspersion of treatments is argued to be an obligatory feature of good design. Especially in small experiments, adequate interspersion can sometimes be assured only by dispensing with strict random- ization procedures. Comprehension of this conflict between interspersion and randomization is aided by distinguishing pre-layout (or conventional) and layout-specifit alpha (probability of type I error). Suggestions are offered to statisticians and editors of ecological j oumals as to how ecologists' under- standing of experimental design and statistics might be improved.
Consumer Innovativeness Model of Indonesian Young People in Adopting Electronic Products

It is important for marketers to understand how innovators respond to the introduction of new products. This paper investigates consumer innovativeness (CI) from meta-analysis study as suggested by Nasution and Garnida [2011] and examines the simultaneous impacts of CI on new product adoption. Nasution and Garnida [2010] proposed three different perspectives in conceptualizing the CI model. First, the generalist stream that represents a generalized personality trait that engenders consumers to adopt new product. Second, the particularist stream that focuses on product adoption behavior within a specific domain of interest. Third, the integrator perspective that proposes to integrate these two streams by putting domain-specific innovativeness as a mediating factor in relationship between general innovativeness trait and new product adoption. A structural equation model is used to test hypotheses using empirical data from 607 respondents in electronic products adoption. The result shows that the integrator perspective provides the best model in representing the empirical data. The finding of the integrator perspective reveals that domain specific CI mediates the relationship between general innovativeness trait and new product adoption. Specifically, subjective knowledge and hedonic idea shopping enhances the actuality of new products. The findings provide an explanation to the less than consistent relationship between consumer innovativeness and new product adoption. However, a single research context of electronic products and student sample may become one of the limitations and future studies needed to replicate the perspective of CI in different research contexts for greater generalizability and the use of non-student sample. The findings have implications for the innovation adoption theory, for managers involved in the introduction of new products, and for future research on innovation adoption. Keywords: Consumer Innovativeness, innovation, electronic, adoption
Immunogenicity of a serogroup B meningococcal vaccine against multiple Neisseria meningitidis strains in infants.

BACKGROUND The serogroup B meningococcus is responsible for the majority of cases of meningococcal disease in temperate countries. Infants and young children <2 years of age are at greatest risk of disease. This study assessed the immunogenicity in infants of a serogroup B meningococcal outer membrane protein vaccine that has been used extensively in disease outbreaks in Cuba and several Latin American countries and shown to be efficacious in teenagers. METHOD One hundred five healthy infants entering the routine vaccination schedule in Havana, Cuba, were given either 2 or 3 doses of the serogroup B meningococcal vaccine VA-MENGOC-BC at 3.5, 5.5 and 7.5 months of age. Immune response pre- and postvaccination was determined by the conventional serum bactericidal assay (SBA), a more sensitive novel whole blood bactericidal assay (WBA) and immunoglobulin ELISA. RESULTS In 52 and 46% of infants >50% killing of the vaccine serogroup B strain (B:4:P1.19,15) and serogroup C strain, respectively, was demonstrated by the WBA after 2 doses of the vaccine. Serum bactericidal activity (4-fold increase in titer) was induced in only 27% against the vaccine serogroup B strain and in 14% against the serogroup C strain. The changes in WBA and SBA were mirrored by the serogroup B and C immunoglobulin ELISA. Cross-reactive immunogenicity against other (heterologous) serogroup B strains was demonstrated for one of the four further strains assessed by WBA. By age 16 to 18 months SBA, WBA and ELISA responses had declined considerably. The addition of a third dose of vaccine did not appear to significantly influence immunogenicity at 17 months of age. CONCLUSION The serogroup B outer membrane protein vaccine VA-MENGOC-BC induces a demonstrable immune response in infants against both the serogroup B vaccine strain and against a serogroup C strain. Cross-reactive immunogenicity against other (heterologous) serogroup B strains is limited in this age group.
Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2

In the last twenty years, three separate coronaviruses have left their typical animal hosts and became human pathogens. An area of research interest is coronavirus transcription regulation that uses an RNA-RNA mediated template-switching mechanism. It is not known how different transcriptional stoichiometries of each viral gene are generated. Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5’-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. TRS independent transcripts were detected as likely non-polyadenylated. Additionally, a novel conserved sequence motif was discovered at either end of the TRS independent splice junctions. While similar both SARS viruses generated similar TRS independent transcripts they were more abundant in SARS-CoV-2. TRS independent gene regulation requires investigation to determine its relationship to viral pathogenicity.
Virus-host protein-protein interactions between human papillomavirus 16 E6 A1 and D2/D3 sub-lineages: variances and similarities

High-risk strains of human papillomavirus are causative agents for cervical and other mucosal cancers with type 16 being the most frequent. Compared to the European Prototype (A1, denoted “EP”), the Asian-American (D2/D3, denoted “AA”) sub-lineage or “variant” is reported to have increased abilities to promote carcinogenesis. Few global interactome studies have looked at protein-protein interactions (PPIs) between host proteins and variants of the key transforming E6 protein. We applied a primary human foreskin keratinocyte model transduced with EP and AA variant E6 genes and co-immunoprecipitated expressed E6 proteins along with interacting cellular proteins to detect virus-host binding partners. We reasoned that, due to single nucleotide polymorphisms, AAE6 and EPE6 may have unique PPIs with host cellular proteins—conferring gain or loss of function—resulting in varied abilities to promote carcinogenesis. Using liquid chromatography-mass spectrometry and stringent interactor selection criteria based on the number of peptides, we identified 25 candidates: 6 unique to each of AAE6 and EPE6, along with 13 E6 targets common to both AAE6 and EPE6. We also applied a more inclusive process based on pathway selection and discovered 171 target proteins: 90 unique AAE6 and 61 unique EPE6 along with 20 common E6 targets between the two sub-lineages. Interpretations for both approaches were made using databases such as UniProt, BioGRID and Reactome. Detected E6 targets are implicated in important hallmarks of cancer: deregulating Notch and other signaling, energetics and hypoxia, DNA replication and repair, and immune response. Validation experiments, such as reverse co-immunoprecipitation and RNA interference, are required to substantiate these findings. Here, we provide an unprecedented resource for new research questions in HR HPV biology. The current data also underline our lab’s driving hypothesis that E6, being a “master regulator” in HPV-positive cancers, is an excellent candidate for anti-cancer treatment strategies. Author Summary Chronic infection with high-risk human papillomavirus (HPV) type 16 is the most prevalent cause of cervical and other mucosal cancers. The E6 oncoproteins of the European Prototype (EP) and the Asian-American (AA) HPV variants differentially promote carcinogenesis. We looked at protein-protein interactions between host proteins and two key HPV variant E6 proteins of these strains to reveal how high risk HPVs cause cancer, based on the proteins they bind to in infected cells. Our methodology combined molecular biology and data mining techniques using widely available databases. We confirmed and discovered novel virus-host associations that explained how HPV AA and EP variants differ in their carcinogenic capabilities, and confirmed the candidacy of the E6 protein as a viable target for HPV therapies.
A Bitter Pill to Swallow: The Rise and Fall of the Tablet Computer

Tablet computers (or tablet PCs) are a form of mobile personal computer with large, touch-sensitive screens operated using a pen, stylus, or finger; and the ability to recognize a user's handwriting? a process known as "pen computing. " The first of these devices, which appeared at the end of the 1980s, generated a huge amount of interest in the computer industry, and serious amounts of investment money from venture capitalists. Pen computing was seen as the next wave of the silicon revolution, and the tablet computer was seen as a device everyone would want to use. It was reported in 1991 that "Nearly every major maker of computers has some type of pen-based machine in the works. "l Yet in the space of just a few years, the tablet computer and the notion of pen computing sank almost without a trace.2 Following a series of disastrous product launches and the failure of a number of promising start-up companies, the tablet computer was discred ited as an unfulfilled promise. It no longer represented the future of mobile computing, but instead was derided as an expensive folly? an irrelevant sideline in the history of the computer. This article traces the early development of pen comput ing, the appearance, proliferation, and disappearance of the tablet computer, and explores possible reasons for the demise of this partic ular class of product.
In situ classification of cell types in human kidney tissue using 3D nuclear staining

To understand the physiology and pathology of disease, capturing the heterogeneity of cell types within their tissue environment is fundamental. In such an endeavor, the human kidney presents a formidable challenge because its complex organizational structure is tightly linked to key physiological functions. Advances in imaging-based cell classification may be limited by the need to incorporate specific markers that can link classification to function. Multiplex imaging can mitigate these limitations, but requires cumulative incorporation of markers, which may lead to tissue exhaustion. Furthermore, the application of such strategies in large scale 3-dimensional (3D) imaging is challenging. Here, we propose that 3D nuclear signatures from a DNA stain, DAPI, which could be incorporated in most experimental imaging, can be used for classifying cells in intact human kidney tissue. We developed an unsupervised approach that uses 3D tissue cytometry to generate a large training dataset of nuclei images (NephNuc), where each nucleus is associated with a cell type label. We then devised various supervised machine learning approaches for kidney cell classification and demonstrated that a deep learning approach outperforms classical machine learning or shape-based classifiers. Specifically, a custom 3D convolutional neural network (NephNet3D) trained on nuclei image volumes achieved a balanced accuracy of 80.26%. Importantly, integrating NephNet3D classification with tissue cytometry allowed in situ visualization of cell type classifications in kidney tissue. In conclusion, we present a tissue cytometry and deep learning approach for in situ classification of cell types in human kidney tissue using only a DNA stain. This methodology is generalizable to other tissues and has potential advantages on tissue economy and non-exhaustive classification of different cell types.
Assessing temperature-dependent competition between two invasive mosquito species

Invasive mosquitoes are expanding their ranges into new geographic areas and interacting with resident mosquito species. Understanding how novel interactions can affect mosquito population dynamics is necessary to predict transmission risk at invasion fronts. Mosquito life-history traits are extremely sensitive to temperature and this can lead to temperature-dependent competition between competing invasive mosquito species. We explored temperature-dependent competition between Aedes aegypti and Anopheles stephensi, two invasive mosquito species whose distributions overlap in India, the Middle East, and North Africa. We followed mosquito cohorts raised at different intraspecific and interspecific densities across five temperatures (16°C - 32°C) to measure traits relevant for population growth and to estimate species' per capita growth rates. We then used these growth rates to derive each species competitive ability at each temperature. We find strong evidence for asymmetric competition at all temperatures, with Ae. aegypti emerging as the dominant competitor. This was primarily due to differences in larval survival and development times across all temperatures that resulted in a higher estimated intrinsic growth rate and competitive tolerance estimate for Ae. aegypti compared to An. stephensi. Synthesis and applications: The spread of An. stephensi into the African continent could lead to urban transmission of malaria, an otherwise rural disease, increasing the human population at risk and complicating malaria elimination efforts. Competition has resulted in habitat segregation of other invasive mosquito species, and our results suggest that it may play a role in determining the distribution of An. stephensi across its invasive range.
Design of Universal Simulation Platform for Avionics

For lack of universality and flexibility in current avionics simulator, a universal semi-physical simulation platform was designed. The innovation is that a simulation database used to describe the behavior, attribute and interface information of avionics was proposed, and simulation is realized by software's analysis to the database filled with the information. Because the object to be simulated is separated from simulation software, the universality and flexibility of the platform are enhanced greatly. Now this simulation platform has been successfully used in the union simulation experimentation of one airplane's avionics system
A New Efficient Permanent-Magnet Vernier Machine for Wind Power Generation

This paper proposes a new outer-rotor permanent-magnet (PM) vernier machine for direct-drive wind power generation, which can offer low-speed operation to directly capture wind power, and enable high-speed rotating field design to maximize the power density. Compared with its mechanical gear counterpart, the proposed machine can eliminate the mechanical wear and tear as well as gear transmission loss, thus improving the generation reliability and efficiency. The key is to newly introduce the flux-modulation poles which can effectively modulate the high-speed rotating field of the armature windings and the low-speed rotating field of the PM outer rotor. By using the time-stepping finite-element method, the proposed machine can be accurately analyzed. Hence, its performances are quantitatively compared with other PM vernier machines, thus verifying its validity.
R&D Reduces Firms' ’Incentives to Create Divisions

I study a game in which two firms create independent divisions, then they choosewhether to do R&D so as to reduce their divisions' marginal costs, and then the divisions compete in the market. I provide necessary and sufficient conditions under which the game has an equilibrium in pure strategies, and I show that the game has an equilibrium only if each firm threatens that if the rival creates more divisions it will use R&D to foreclose the market. The case we find the literature, in which firms flood the market with their divisions, should happen only in industries with low returns to R&D.
Detection and Identification of Triple Phosphate Crystals and Calcium Oxalate Crystals in Human Urine Sediment Using Harr Feature, Adaptive Boosting and Support Vector Machine via Open CV

The importance of pattern recognition technology to help doctors during clinical diagnosis for urine crystals will be the topic in this paper. The paper focused on creating a program that would detect and identify both triple phosphate and calcium oxalate crystals from a urine sediment sample. By doing so, the professional who is supposed to conduct the diagnosis through visual inspection of microscope slides containing urine sample, aiming to identify crystals, bacteria and other relevant elements, resulting in a laborious task, will take less time in doing so and furthermore, lessen the probability for human error. Tests showed that the system was capable of detecting and classifying with accuracy of higher than 90%, individual as high as 89.70% and specificity of over 93% for both crystals.
Coordinated Link Sharing Behavior as a Signal to Surface Sources of Problematic Information on Facebook

Despite widespread concern over the role played by disinformation during recent electoral processes, the intrinsic elusiveness of the subject hinders efforts aimed at estimating its prevalence and effect. While there has been proliferation of attempts to define, understand and fight the spread of problematic information in contemporary media ecosystems, most of these attempts focus on detecting false content and/or bad actors. For instance, several existing studies rely on lists of problematic content or news media sources compiled by fact-checkers. However, these lists may quickly become obsolete leading to unreliable estimates. Using media manipulation as a frame, along with a revised version of the “coordinated inauthentic behavior” original definition, in this paper, we argue for a wider ecological focus. Leveraging a method designed to detect “coordinated links sharing behavior” (CLSB), we introduce and assess an approach aimed at creating and keeping lists of potentially problematic sources updated by analyzing the URLs shared on Facebook by public groups, pages, and verified profiles. We show how CLSB is consistently associated with higher risks of encountering problematic news sources across three different datasets of news stories and can be thus used as a signal to support manual and automatic detection of problematic information.
Economics of recreation and tourism

: Evaluation of the websites in tourism is a developing area of research. DMO websites are official representatives of the tourism destinations; they aim to attract more tourists. Therefore, it is essential to evaluate website in order to make timely changes, and maintain qualitative website, which is able to attract and keep attention of web users and is able to grow prospective tourists’ interest towards the promoted tourism destination. This paper presents an evaluation model and framework for the assessment of the tourism DMO website success in web-users and tourists attraction. The model presented in this paper is based on D&M IS Success model, with influence from TAM model, Rocha’s Global quality website evaluation framework and Lee and Kozar’s model for the investigation of the effect of website quality on e-business success.
MET-COFEA: a liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation.

In this paper, we present a novel liquid chromatography/mass spectrometry (LC/MS) data processing and analysis platform, MET-COFEA (METabolite COmpound Feature Extraction and Annotation). MET-COFEA detects and clusters chromatographic peak features for each metabolite compound by first comprehensively evaluating retention time and peak shape criteria and then annotating the associations between each peak's observed m/z value with the corresponding metabolite compound's molecular mass. MET-COFEA integrates a series of innovative approaches, including novel mass trace based extracted-ion chromatogram (EIC) extraction, continuous wavelet transform (CWT)-based peak detection, and compound-associated peak clustering and peak annotation algorithms. On the basis of the deduced neutral molecular mass and retention time, we have also developed a new alignment algorithm that uses compound-associated peak groups instead of individual peaks to align the same metabolite compound across samples from different electrospray ionization (ESI) modes, different instruments, even different experimental conditions. MET-COFEA has been systematically tested on a series of LC/MS profiles of mixed standards at different concentrations as well as real untargeted LC/MS plant metabolomics data. We compared the performances of MET-COFEA with the existing publicly available tools at LC/MS peak analysis level and demonstrated its excellent performance in this arena. MET-COFEA is freely available at http://bioinfo.noble. org/manuscript-support/met-cofea/.
The role of convenience yield in going-private transactions

In this paper we examine the liquidity aspects of going private transactions and introduce the concept of liquidity regeneration which describes the valuation benefit accruing to a listed parent with more liquid stock squeezing out a relatively more illiquid subsidiary. We develop a theoretical model to proxy this convenience yield effect by the differential cost of transacting in the parent versus its subsidiary stock and find it significantly influential on the economics of the decision to take a listed company private. By the means of a liquidity arbitrage, parent shareholders may take advantage of the double benefit of a lower bidding price, improved cumulative abnormal returns and thinner liquidity discount, post a successful deal consummation. Our results justify that relatively higher target illiquidity underlies superior abnormal returns and lower takeover premiums, to the degree that parent companies may indulge in manipulating their subsidiary stock liquidity to maximize their returns.