Statistical Analysis of Avian Reproduction Studies

Avian reproduction studies for regulatory risk assessment are undergoing review by regulatory authorities, often leading to requests for statistical re-analysis of older studies using newer methods, sometimes with older study data that do not support these newer methods. We propose detailed statistical protocols with updated statistical methodology for use with both new and older studies and recommend improvements in experimental study design to set-up future studies for robust statistical analyses. There is increased regulatory and industry attention to the potential use of benchmark dose (BMD) methodology to derive the point of departure in avian reproduction studies, to be used as the endpoint in regulatory risk assessment. We present benefits and limitations of this BMD approach for older studies being re-evaluated and for new studies designed for with BMD analysis anticipated. Model averaging is recommended as preferable to model selection for BMD analysis. Even for a new study following the modified experimental design analyses with BMD methodology will only be possible for a restricted set of response variables. The judicious use of historical control data, identification of outlier data points, increased use of distributions more consistent with the nature of the data collected as opposed to forcing normality-based methods, and trend-based hypothesis tests are shown to be effective for many studies, but limitations on their applicability are also recognized and explained. Updated statistical methodologies are illustrated with case studies conducted under existing regulatory guidelines that have been submitted for product registrations. Through the adoption of improved avian reproduction study design elements combined with the suggested revised statistical methodologies the conduct, analyses, and utility of avian reproduction studies for avian risk assessments can be improved.

An Experimental Reproduction Study on Characteristics of Woodblock Printing on Traditional Korean Paper (Hanji)

The history of printing technology in Korea is studied by investigating existing ancient documents and records and comparing accumulated data and knowledge. Cultural property research requires non-destructive testing and observation with the naked eye or aided by a microscope. Researchers’ experience and knowledge are required even though they cannot guarantee the outcome. For ancient documents and records that are presumed to consist of woodblock printing, wood type printing, metal type printing, or their combinations, each researcher draws various opinions and conclusions. This often causes confusion and divides the opinions of ordinary citizens and field specialists. Among them, the criteria for judging ancient documents or books printed using woodblock and metal movable material are ambiguous. Academic research on the development history of printing technology in ancient Korea has been stagnant, and conflicts among researchers have also erupted. Involvement of national investigative agencies not specialized in cultural properties has exacerbated the situation. In this study, we investigated printing characteristics that are likely to serve as more objective judgment criteria by quantitatively analyzing the experiments of retrieving several sheets of Korean paper (Hanji) using a replicated Hunminjeongeum (訓民正音) woodblock and quantitatively analyzing the images of the printed papers. In addition, the validity and questions for the typical phenomena presented as a method for distinguishing between woodblock and metal print are reviewed. We investigated the possibility of developing new objective judgement criteria through quantitative analysis using image analysis and investigating the printing characteristics of Korean paper through a reproduction experiment of woodblock printing.

Comparative analysis of two methodological approaches to the study of endocrine disruptor alpha-cypermethrin reproductive toxicity

At present, one of the main threats to humanity is undoubtedly endocrine disruptors (ED), since they directly disrupt the processes of ensuring homeostasis, which are identical to the very essence of the concept of health, considered in valeology as the ability to maintain age-appropriate stability in conditions of sharp changes in quantitative and qualitative parameters of the triune flow of sensory, verbal and structural information. Pesticides can disrupt the physiological functioning of many endocrine chains, including the endocrine mechanisms that ensure reproductive health. The study aimed to compare the results of our studies of alpha-cypermethrin reproductive toxicity in the test system for studying gonadotoxic activity with data obtained in the test system "Three Generation Reproduction Study". The studies were performed on male and female Wistar Han rats with two generic samples of alpha-cypermethrin from different manufacturers at doses of 0.2, 1.0 and 3.0 mg/kg body weight. The exposure lasted 11 (males) and 10 (females) weeks. During the last two weeks of exposure the state of the estrous cycle, duration and frequency of each stage in females was studied. After the end of treatment functional parameters of the state of the gonads in males and the ability of animals to reproduce were examined. In males, the total sperm count, the absolute and relative number of motile germ cells, and the number of pathologically altered forms were evaluated. The results of the study showed that exposure of male and female Wistar Han rats to alpha-cypermethrin at doses of 0.2–3.0 mg/kg during gametogenesis had a toxic effect on the reproductive system characterized by impaired gonadal and reproductive functions. In our studies, alpha-cypermethrin was found to have reproductive toxicity (reduced number of corpora luteum and live fetuses, increased absolute and relative postimplantation death, reduced average weight of fetuses and litters) and endocrine-disruptive effect, having a pronounced antiandrogenic effect on males. Obvious signs of endocrine reproductive disorders (changes in testis and epididymis weight, deterioration in semen parameters, altered length of separate stages of the estrous cycle) were observed in both females and males. However, studies in a test system of three-generations did not reveal a reproductive and endocrine-disruptive effect of cypermethrin, the toxicity of which was recognized as equivalent to the toxicity of alpha-cypermethrin. The obtained results showed higher sensitivity, informative and diagnostic significance of the methods for studying gonadotoxicity than the methodology of reproductive toxicity studies in the test system “Three Generation Reproduction Study”.

Lessons Learnt on Reproducibility in Machine Learning Based Android Malware Detection

A well-known curse of computer security research is that it often produces systems that, while technically sound, fail operationally. To overcome this curse, the community generally seeks to assess proposed systems under a variety of settings in order to make explicit every potential bias. In this respect, recently, research achievements on machine learning based malware detection are being considered for thorough evaluation by the community. Such an effort of comprehensive evaluation supposes first and foremost the possibility to perform an independent reproduction study in order to sharpen evaluations presented by approaches’ authors. The question Can published approaches actually be reproduced? thus becomes paramount despite the little interest such mundane and practical aspects seem to attract in the malware detection field. In this paper, we attempt a complete reproduction of five Android Malware Detectors from the literature and discuss to what extent they are “reproducible”. Notably, we provide insights on the implications around the guesswork that may be required to finalise a working implementation. Finally, we discuss how barriers to reproduction could be lifted, and how the malware detection field would benefit from stronger reproducibility standards—like many various fields already have.

Influence of cultivation conditions on the growth activity of natural strains of lactic acid bacteria in winemaking

Характеристика ростовой активности молочнокислых бактерий (МКБ) виноделия является одним из основных критериев отбора штамма при проведении селекционных работ на лабораторном этапе определения условий его культивирования и сохранения. В работе представлены результаты изучения влияния температуры, рН среды культивирования и ее состава на ростовую активность штаммов МКБ виноделия родов Oenococcus (9 штаммов) и Lactobacillus (6 штаммов) с высокой декарбоксилирующей активностью. При проведении работ использовали методы и подходы, общепринятые при изучении микроорганизмов виноделия. Ростовую активность штаммов оценивали нефелометрическим методом по количеству биомассы, накопленной в процессе культивирования штаммов в различных условиях. Анализ полученных результатов, представленных в статье, позволил рекомендовать оптимальные значения рН и температуры для культивирования штаммов МКБ виноделия родов Lactobacillus и Oenococcus на стандартной среде MRS, а также целесообразность снижения рН среды при помощи яблочной кислоты для увеличения скорости размножения клеток. Изучение влияния таких компонентов среды, как глюкоза, пептон, Твин-80, гидроортофосфат калия, яблочная кислота на ростовую активность штаммов МКБ показало, что наиболее значимыми факторами, влияющими на их рост, являются глюкоза и яблочная кислота.. Влияние каждого фактора или их совокупности на ростовую активность МКБ может избирательно зависеть от культивируемого штамма, что подтверждает данные о генетическом разнообразии микроорганизмов данной группы и необходимости индивидуального подхода к выбору условий их культивирования. The characteristic of the growth activity of lactic acid bacteria (LAB) in winemaking is one of the main criteria of selecting a strain during the breeding work at the laboratory stage of determining the conditions for its cultivation and preservation. The article presents the results of study the effect of temperature, pH of the cultivation medium and its composition on the growth activity of winemaking LAB strains of the genera Oenococcus (9 strains) and Lactobacillus (6 strains) with high decarboxylating activity. In the working process we used methods and approaches generally accepted in the study of microorganisms in winemaking. Growth activity of strains was assessed by nephelometric method according to the amount of biomass accumulated in the process of cultivation strains under various conditions. The analysis of the results, presented in the article, made it possible to recommend the optimal pH and temperature values for the cultivation of LAB strains Lactobacillus and Oenococcus on a standard MRS medium, as well as the viability of decreasing the pH of the medium using malic acid to increase the speed of cell reproduction. Study of the influence of such environmental components as glucose, peptone, Tween-80, dipotassium hydrogenphosphate, malic acid on the growth activity of LAB strains showed that the most significant factors affecting growth are glucose and malic acid. Influence of each factor or their combination on the growth activity of LAB can selectively depend on the cultivated strain, confirming data of microorganism genetic diversity of the group and the necessity of an individual approach to the selection of cultivation conditions.

Effect of Different Honey Concentrations on Survival, Longevity and Reproduction of Trichospilus pupivorus (Hymenoptera: Eulophidae), a Parasitoid of Coconut Black-Headed Caterpillar, Opisina arenosella (Lepidoptera: Oecophoridae)

Many coconut producing countries in Asia are facing a serious infestation of Opisina arenosella (Lepidoptera: Oecophoridae) or commonly called the coconut black-headed caterpillar. Recently, the pest has been detected in the coconut (Cocos nucifera) planting area in Pahang, Malaysia. Thus, an initiative to manage the pest by using parasitoids has been started with a study on the effects of diet on survival, longevity and reproduction of naturally occurred parasitoid known as Trichospilus pupivorus (Hymenoptera: Eulophidae). The aim of this study was to identify suitable concentrations of honey that can be used in developing its rearing technique. Two independent experiments were conducted, i.e., a) survival and longevity study; and b) reproduction study. In each study, different honey concentrations were tested on ten (eight replications) and one (five replications) female parasitoids respectively. 30% honey concentrations resulted in high survival rate of the adult during early life with relatively prolonged longevity up to 6.0±0.19 days and significantly produced the highest number of progenies (105.4±0.81). The lowest survival rate was given by 60% honey and significant longevity up to 6.5±0.33 days with no progenies. Further studies on other plausible factors affecting the reproduction and fitness of progenies should also be investigated to ensure efficient rearing techniques.

A case study on the detailed reproducibility of a human cell atlas project

Reproducibility is a defining feature of a scientific discovery. Reproducibility can be at different levels for different types of study. The purpose of the Human Cell Atlas (HCA) project is to build maps of molecular signatures of all human cell types and states to serve as references for future discoveries. Constructing such a complex reference atlas must involve the assembly and aggregation of data from multiple labs, probably generated with different technologies. It has much higher requirements on reproducibility than individual research projects. To add another layer of complexity, the bioinformatics procedures involved for single-cell data have high flexibility and diversity. There are many factors in the processing and analysis of single-cell RNA-seq data that can shape the final results in different ways. To study what levels of reproducibility can be reached in current practices, we conducted a detailed reproduction study for a well-documented recent publication on the atlas of human blood dendritic cells as an example to break down the bioinformatics steps and factors that are crucial for the reproducibility at different levels. We found that the major scientific discovery can be well reproduced after some efforts, but there are also some differences in some details that may cause uncertainty in the future reference. This study provides a detailed case observation on the on-going discussions of the type of standards the HCA community should take when releasing data and publications to guarantee the reproducibility and reliability of the future atlas.