Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-scale proteomic screen and signal transduction analysis used to study embryonic gonad and germ cell development

Research Doctorate - Doctor of Philosophy (PhD)%%%%In the fields of sex determination, embryonic gonad development and germ cell differentiation, much effort has been placed in performing large-scale screens anchored in RNA and DNA technologies. Whilst these technologies have identified new candidate genes, they are unable to provide expression data for functionally active gene products. Recent improvements in the sensitivity of proteomic screening technologies have made analysis of the embryonic gonadal proteome experimentally feasible. Thus, major aims of my PhD were to generate a data set of gonadal proteins expressed at the time of sex determination, and to identify differentially expressed proteins that potentially regulate early events in gonadogenesis, germ cell development and sex differentiation. To detect and identify gonadal proteins, I used two-dimensional nano-flow liquid chromatography and tandem mass spectrometry. I identified 1037 proteins which primarily serve in RNA post-transcriptional modification and trafficking, protein synthesis and folding, and post-translational modification. Over 300 proteins were not identified in a similar transcriptomic study. Over 60 proteins were identified with potential links to human disorders of sexual development (DSDs). I identified four proteins up-regulated in the ovary and three proteins up-regulated in the testis at a critical time point in sex determination. I also identified five proteins increasing, and three proteins decreasing, in expression during early testis development. Two of these temporally-regulated proteins are associated with human DSDs. The majority of these expression differences have not been detected at the transcript level. These data provide novel targets potentially controlling events in gonadogenesis, sex determination and germ cell differentiation. Recently, the field of germ cell sex differentiation was revolutionised with the discovery that retinoic acid (RA) initiates meiosis in female embryonic germ cells, and that the RA-degrading enzyme CYP26B1 inhibits meiosis in male germ cells, which consequently cease mitotic division till after birth. How these somatic environmental factors regulate the transition from mitosis to meiosis or mitotic arrest remains unanswered. p38 MAP kinase (MAPK) signalling initiates mitotic arrest in other differentiating cell types. Thus, a specific aim of my PhD was to investigate the role of p38 MAPK in controlling male germ cell differentiation. To address this aim experimentally, I analysed expression of p38 MAPK in embryonic gonads and found it to be activated in differentiating male germ cells. I then blocked p38 MAPK signalling and found that male germ cells expressed pluripotency and meiosis-associated proteins in a similar pattern to their female counterparts, and that testes exhibited more meiotic germ cells. These data suggest that p38 MAPK signalling contributes to meiosis inhibition in testicular germ cells, and potentially directs them towards quiescence. The studies outlined in this thesis…
A Survey of Multifragment Rendering

In the past few years, advances in graphics hardware have fuelled an explosion of research and development in the field of interactive and real‐time rendering in screen space. Following this trend, a rapidly increasing number of applications rely on multifragment rendering solutions to develop visually convincing graphics applications with dynamic content. The main advantage of these approaches is that they encompass additional rasterised geometry, by retaining more information from the fragment sampling domain, thus augmenting the visibility determination stage. With this survey, we provide an overview of and insight into the extensive, yet active research and respective literature on multifragment rendering. We formally present the multifragment rendering pipeline, clearly identifying the construction strategies, the core image operation categories and their mapping to the respective applications. We describe features and trade‐offs for each class of techniques, pointing out GPU optimisations and limitations and provide practical recommendations for choosing an appropriate method for each application. Finally, we offer fruitful context for discussion by outlining some existing problems and challenges as well as by presenting opportunities for impactful future research directions.
The State of the Art in Map‐Like Visualization

Cartographic maps have been shown to provide cognitive benefits when interpreting data in relation to a geographic location. In visualization, the term map‐like describes techniques that incorporate characteristics of cartographic maps in their representation of abstract data. However, the field of map‐like visualization is vast and currently lacks a clear classification of the existing techniques. Moreover, choosing the right technique to support a particular visualization task is further complicated, as techniques are scattered across different domains, with each considering different characteristics as map‐like. In this paper, we give an overview of the literature on map‐like visualization and provide a hierarchical classification of existing techniques along two general perspectives: imitation and schematization of cartographic maps. Each perspective is further divided into four principal categories that group common map‐like techniques along the visual primitives they affect. We further discuss this classification from a task‐centered view and highlight open research questions.
OLAP Querying of Document Stores in the Presence of Schema Variety

Document stores are preferred to relational ones for storing heterogeneous data due to their schemaless nature. However, the absence of a unique schema adds complexity to analytical applications. In a previous paper we have proposed an original approach to OLAP on document stores; its basic idea was to stop ﬁghting against schema variety and welcome it as an inherent source of information wealth in schemaless sources. In this paper we focus on the querying phase, showing how queries can be directly rewritten on a heterogeneous collection in an inclusive way, i
Comparing the performance of 11 crop simulation models in predicting yield response to nitrogen fertilization

SUMMARY Eleven widely used crop simulation models (APSIM, CERES, CROPSYST, COUP, DAISY, EPIC, FASSET, HERMES, MONICA, STICS and WOFOST) were tested using spring barley (Hordeum vulgare L.) data set under varying nitrogen (N) fertilizer rates from three experimental years in the boreal climate of Jokioinen, Finland. This is the largest standardized crop model inter-comparison under different levels of N supply to date. The models were calibrated using data from 2002 and 2008, of which 2008 included six N rates ranging from 0 to 150 kg N/ha. Calibration data consisted of weather, soil, phenology, leaf area index (LAI) and yield observations. The models were then tested against new data for 2009 and their performance was assessed and compared with both the two calibration years and the test year. For the calibration period, root mean square error between measurements and simulated grain dry matter yields ranged from 170 to 870 kg/ha. During the test year 2009, most models failed to accurately reproduce the observed low yield without N fertilizer as well as the steep yield response to N applications. The multi-model predictions were closer to observations than most single-model predictions, but multi-model mean could not correct systematic errors in model simulations. Variation in soil N mineralization and LAI development due to differences in weather not captured by the models most likely was the main reason for their unsatisfactory performance. This suggests the need for model improvement in soil N mineralization as a function of soil temperature and moisture. Furthermore, specific weather event impacts such as low temperatures after emergence in 2009, tending to enhance tillering, and a high precipitation event just before harvest in 2008, causing possible yield penalties, were not captured by any of the models compared in the current study.
Corporate Social Responsibility and Capital Market Regulation: Empirical Evidence from Coastal Regions of China

ABSTRACT Li, Y. and Fu, X.F. , 2020. Corporate social responsibility and capital market regulation: Empirical evidence from coastal regions of China. In: Qiu, Y. ; Zhu, H. , and Fang, X. (eds.), Current Advancements in Marine and Coastal Research for Technological and Sociological Applications. Journal of Coastal Research, Special Issue No. 107, pp. 413-418. Coconut Creek (Florida), ISSN 0749-0208. This study investigates whether corporate social responsibility (CSR) mitigates or contributes to the corporate capital market regulation. We use annual report inquiry letters and conducted the survey among the listed companies in coast regions of China. We find a significantly negative association between firms' CSR and the probability of receiving an annual report inquiry letter. Our study will be useful to firms and shareholders who want to reduce business risks and to investors who want to use inquiry letter information to make decisions.
Tail-tolerance as a Systems Principle not a Metric

Tail-latency tolerance (or just simply tail-tolerance) is the ability for a system to deliver a response with low-latency nearly all the time. It it typically expressed as a system metric (e.g., the 99th or 99.99th percentile latency) or as a service-level objective (e.g., the maximum throughput so that the tail latency is below a desired threshold). We advocate instead that modern datacenter systems should incorporate tail-tolerance as a core systems design principle and not a metric to be observed, and that tail-tolerant systems can be built out of large and complex applications whose individual components may suffer from latency deviations. This is analogous to fault-tolerance, where a fault-tolerant system can be built out of unreliable components. The general solution is for the system to control the applied load and keep it under the threshold that violates the latency SLO. We propose to augment RPC semantics with an architectural layer that measures the observed tail latency and probabilistically rejects RPC requests maintaining throughput under the threshold that violates the SLO. Our design is application-independent, and does not make any assumptions about the request service time distribution. We implemented a proof of concept for such a tail-tolerant layer using programmable switches, called SVEN. We demonstrate that the approach is suitable even for microsecond-scale RPCs with variable service times. Moreover, our approach does not induce measurable overheads, and can maintain the maximum achieved throughput very close to the load level that would violate the SLO without SVEN.
PosEdiOn: Post-Editing Assessment in PythOn

There is currently an extended use of post-editing of machine translation (PEMT) in the translation industry. This is due to the increase in the demand of translation and to the significant improvements in quality achieved by neural machine translation (NMT). PEMT has been included as part of the translation workflow because it increases translators’ productivity and it also reduces costs. Although an effective post-editing requires enough quality of the MT output, usual automatic metrics do not always correlate with post-editing effort. We describe a standalone tool designed both for industry and research that has two main purposes: collect sentence-level information from the post-editing process (e.g. post-editing time and keystrokes) and visually present multiple evaluation scores so they can be easily interpreted by a user.
Multimodality assessment of sleep outcomes in people living with HIV performed using validated sleep questionnaires

Studies conducted in people living with HIV (PLHIV) report high rates of sleep disturbance, without a clear explanation as to cause or effect. Therefore, we proposed use of multiple validated questionnaires that would allow a more comprehensive evaluation of sleep quality in PLHIV. We administered eight validated sleep and wellbeing questionnaires, recording different aspects of sleep in order to provide a comprehensive description of sleep quality, quantity, daytime functioning, wakefulness, and general wellbeing. Associations with demographics and clinical data were analyzed by univariable/multivariable analyses. Of 254 subjects 99% were male (98% men who have sex with men), 88% white, mean age 41 (SD ± 9.9) years, HIV duration eight years (SD ± 6.3), 94% were on antiretroviral therapy, mean CD4 cell count was 724 cells/mm3, 81% had HIV RNA<40 copies/ml, 72% were university educated, and 60% used ‘chemsex’ drugs. Almost half (45%) reported poor sleep quality, 22% insomnia, 21% daytime sleepiness, and 33% fatigue. As individual factors, HIV duration ≥10 years, anxiety, depression, and recreational drug use were associated with poor quality sleep, fatigue, and poorer functional outcomes (p ≤ 0.05). The prevalence of sleep disturbance was high in our cohort of PLHIV. Sleep disturbance was associated with longer duration of HIV infection, depression, anxiety, and recreational drug use.
Uses of pathogen detection data to estimate vaccine direct effects in case–control studies

The fact that many pathogens can be carried or shed without causing symptoms complicates the interpretation of microbiological data when diagnosing certain infectious disease syndromes. Diagnostic criteria that attribute symptoms to a pathogen which is detectable, whether it is or is not the aetiological agent of disease, may lead to outcome misclassification in epidemiological studies. Case–control studies are commonly undertaken to estimate vaccine effectiveness (VE) and present an opportunity to compare pathogen detection among individuals with and without clinically relevant symptoms. Considering this study context, we present a mathematical framework yielding simple estimators for the direct effects of vaccination on various aspects of host susceptibility. These include protection against acquisition of the pathogen of interest and protection against progression of this pathogen to disease following acquisition. We assess the impact of test sensitivity on these estimators and extend our framework to identify a ‘vaccine probe’ estimator for pathogen-specific aetiological fractions. We also derive biases affecting VE estimates under the test-negative design, a special case enrolling only symptomatic persons. Our results provide strategies for estimating pathogen-specific VE in the absence of a diagnostic gold standard. These approaches can inform the design and analysis of studies addressing numerous pathogens and vaccines.
How disease constrains the evolution of social systems

Animal populations are occasionally shocked by epidemics of contagious diseases. The ability of social systems to withstand epidemic shocks and mitigate disruptions could shape the evolution of complex animal societies. We present a mathematical model to explore the potential impact of disease on the evolutionary fitness of different organizational strategies for populations of social species whose survival depends on collaborative efficiency. We show that infectious diseases select for a specific feature in the organization of collaborative roles—cohort stability—and that this feature is costly, and therefore unlikely to be maintained in environments where infection risks are absent. Our study provides evidence for an often-stated (but rarely supported) claim that pathogens have been the dominant force shaping the complexity of division of labour in eusocial societies of honeybees and termites and establishes a general theoretical approach for assessing evolutionary constraints on social organization from disease risk in other collaborative taxa.
Identification of new host signaling pathways hijacked by bacterial pathogens during infection

11 RESUMO . 13 INTRODUCTION . 15 I. BACTERIAL PATHOGENS . 17 I.A. Listeria monocytogenes . 17 I.A. 1. Overview . 17 I.A. 2. Listeriosis . 19 I.A. 3. Cellular infection cycle . 21 I.A. 4. Major virulence factors . 24 I.A. 4.1. Internalins A and B . 24 I.A. 4.2. Listeriolysin O and phospholipases . 25 I.A. 4.3. Actin assembly-inducing protein (ActA) . 26 I.A. 4.4. PrfA . 27 I.B. Enterobacteriaceae . 28 I.B. 1. Yersinia . 28 I.B. 1.1. Yersiniosis . 29 I.B. 1.2. Cellular infection mechanisms. 29 I.B. 2. Pathogenic E. coli . 34 I.B. 2.1. EPEC and EHEC. 36 I.B. 2.1.1. Virulence effectors. 37 II. POST-TRANSLATIONAL MODIFICATIONS IN BACTERIAL INFECTION . 40 II.A. Protein phosphorylation . 40 II.A. 1. Phosphorylation in Lm infection . 41 II.A. 2. Phosphorylation and other bacterial infections . 44 III. MYOSINS . 47 III.A. Structure, classification and function . 47 III.B. Non-muscle myosin IIA (NM-IIA) . 49 III.B. 1. NM-IIA structure . 50 III.B. 2. Regulation of NM-IIA activity . 51 III.B. 3. Cellular functions of NM-IIA . 52 III.C. Myosins and bacterial infection . 52 PROJECT PRESENTATION . 55 RESULTS . 59 I. SRC-DEPENDENT TYROSINE PHOSPHORYLATION OF NON-MUSCLE MYOSIN HEAVY CHAIN-IIA RESTRICTS LISTERIA MONOCYTOGENES CELLULAR INFECTION . 61 II. NMHC-IIA-INTERACTING PROTEINS . 87 III. KERATINS . 101 GENERAL DISCUSSION . 111 GENERAL PERSPECTIVES . 117 REFERENCES . 121 ANNEX . 161
Education and Cognitive Functioning Across the Life Span

Cognitive abilities are important predictors of educational and occupational performance, socioeconomic attainment, health, and longevity. Declines in cognitive abilities are linked to impairments in older adults’ everyday functions, but people differ from one another in their rates of cognitive decline over the course of adulthood and old age. Hence, identifying factors that protect against compromised late-life cognition is of great societal interest. The number of years of formal education completed by individuals is positively correlated with their cognitive function throughout adulthood and predicts lower risk of dementia late in life. These observations have led to the propositions that prolonging education might (a) affect cognitive ability and (b) attenuate aging-associated declines in cognition. We evaluate these propositions by reviewing the literature on educational attainment and cognitive aging, including recent analyses of data harmonized across multiple longitudinal cohort studies and related meta-analyses. In line with the first proposition, the evidence indicates that educational attainment has positive effects on cognitive function. We also find evidence that cognitive abilities are associated with selection into longer durations of education and that there are common factors (e.g., parental socioeconomic resources) that affect both educational attainment and cognitive development. There is likely reciprocal interplay among these factors, and among cognitive abilities, during development. Education–cognitive ability associations are apparent across the entire adult life span and across the full range of education levels, including (to some degree) tertiary education. However, contrary to the second proposition, we find that associations between education and aging-associated cognitive declines are negligible and that a threshold model of dementia can account for the association between educational attainment and late-life dementia risk. We conclude that educational attainment exerts its influences on late-life cognitive function primarily by contributing to individual differences in cognitive skills that emerge in early adulthood but persist into older age. We also note that the widespread absence of educational influences on rates of cognitive decline puts constraints on theoretical notions of cognitive aging, such as the concepts of cognitive reserve and brain maintenance. Improving the conditions that shape development during the first decades of life carries great potential for improving cognitive ability in early adulthood and for reducing public-health burdens related to cognitive aging and dementia.
Antibiotic resistance genes as an emerging environmental contaminant

Emerging contaminants, including pharmaceutical and personal care products, are receiving considerable attention owing to their potential to negatively impact the environment and to pose risks to human health. The widespread use of antibiotics and their fate and transport in the environment pose further risks with respect to public health and the development of antibiotic resistant organisms (AROs). While the occurrence of AROs is important, there is increasing interest in antibiotic resistance genes (ARGs). An urgent need exists to improve our understanding of the mechanisms associated with the spread and development of ARGs in both clinical and veterinary settings, the human body (gastrointestinal tract and microbiome) as well as in engineered (wastewater treatment plants) and natural (soil, sediments and water) environments. This review focuses on ARGs as an emerging environmental contaminant. The factors and mechanisms involved in ARG dissemination in a variety of environments are explored in detail.
Influence of temperature on the growth of Pseudomonas putida

Lots of reports on the generation of stress by increase in temperature in the bacterial cells especially in Escherichia coli has been observed so far. Current study further emphasized such effect on the cells of Pseudomonas putida (SUBP03). Conventional methods relating growth assessment of bacteria were employed. The optical density of bacterial cells at 600 nm (OD 600 ) in the minimal broth along with the culturable cells were assessed in the form of colony forming units (CFUs) in the minimal agar media at different temperatures (27 ° C, 30 ° C, 33 ° C, 37 ° C and 40 ° C). Morphological observations were made to further clarify the bacterial physiology and the spot tests were performed to examine the cell viability. Cells of P. putida (SUBP03) were found to grow vigorously at 30 ° C, while the growth was found to decline at lower temperature (27 ° C) and along with the increase in temperature (at 33 ° C, 37 ° C and 40 ° C). However, the morphological changes were insignificant. Furthermore, cells were noticed to completely lose culturability at 40 °C after 48 hours. Stamford Journal of Microbiology, Vol.5(1) 2015: 9-12
Control of Estrus in Gilts and Primiparous Sows

The primary controller of weaned pig output is the successful breeding of enough females in the breeding week. The number of females available for breeding is dependent on the number of sows weaned sows and service-ready gilt availability. Primiparous (P1) sows often have longer wean-estrus intervals (WEI) and increased anestrus; ensuring sufficient gilts and sows are available may require control of estrus. Stimulating estrus requires appropriate boar contact or when this is not sufficient, administration of gonadotrophins. If gonadotrophins are used expect estrus 4 to 6 d later and it is usual to breed at the induced estrus. If there is a problem of non-response the most likely cause is the females had a missed estrus are in their luteal phase. This can be resolved by feeding altrenogest for 18 d; expect cyclic animals to return 5 to 8 d later. The estrus response can be improved by gonadotrophin treatment at the end of altrenogest feeding. Female fertility is optimized by ensuring sperm deposition in the period 0 to 24 h before ovulation. This degree of accuracy may require control of ovulation by treatment with human chorionic gonadotrophin (ovulation 40-44 h later) or gonadotrophin releasing hormone (ovulation 36-40 h later). Knowing time of ovulation will allow use of other breeding technologies such as use of lower sperm numbers per dose and single inseminations.