Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploration, quantification, and mitigation of systematic error in high-throughput approaches to gene-expression profiling : implications for data reproducibility

Technological and methodological advances in the fields of medical and life-sciences have, over the last 25 years, revolutionised the way in which cellular activity is measured at the molecular level. Three such advances have provided a means of accurately and rapidly quantifying mRNA, from the development of quantitative Polymerase Chain Reaction (qPCR), to DNA microarrays, and second-generation RNA-sequencing (RNA-seq). Despite consistent improvements in measurement precision and sample throughput, the data generated continue to be affected by high levels of variability due to the use of biologically distinct experimental subjects, practical restrictions necessitating the use of small sample sizes, and technical noise introduced during frequently complex sample preparation and analysis procedures. A series of experiments were performed during this project to profile sources of technical noise in each of these three techniques, with the aim of using the information to produce more accurate and more reliable results. The mechanisms for the introduction of confounding noise in these experiments are highly unpredictable. The variance structure of a qPCR experiment, for example, depends on the particular tissue-type and gene under assessment while expression data obtained by microarray can be greatly influenced by the day on which each array was processed and scanned. RNA-seq, on the other hand, produces data that appear very consistent in terms of differences between technical replicates, however there exist large differences when results are compared against those reported by microarray, which require careful interpretation. It is demonstrated in this thesis that by quantifying some of the major sources of noise in an experiment and utilising compensation mechanisms, either preor post-hoc, researchers are better equipped to perform experiments that are more robust, more accurate, and more consistent.
Characterization of splicing mechanisms by single-molecule fluorescence

CHARACTERIZATION OF SPLICING MECHANISMS BY SINGLE-MOLECULE FLUORESCENCE by KRISHANTHI SANJEEWANI KARUNATILAKA May 2011 Advisor: Prof. David Rueda Major: Chemistry (Biochemistry) Degree: Doctor of Philosophy Group II introns rank amongst the largest self-splicing ribozymes found in bacteria and organellar genomes of various eukaryotes. Interestingly, these ribozymes can self-splice via two transesterification reactions that resemble nuclear pre-mRNA splicing in eukaryotes (54,55). Despite the diversity in primary sequences, group II introns posses highly conserved secondary structures consisting of six domains (D1-D6). To perform its function, the large multidomain group II intron RNA must adopt the correctly folded structure (52). As a result, in vitro splicing of these introns requires high ionic strength and elevated temperatures. In vivo, this process is mainly assisted by protein cofactors (37). However, the exact mechanism of protein-mediated splicing of group II intron RNA is still not known.
The Epidemiology of HIV-1 Transmitted Drug Resistance

textabstractThe human immunodeficiency virus (HIV) was first discovered in 1983. In 2009, it was estimated that 33.3 (31.4 -35.3) million individuals are infected with HIV worldwide. In that year 1.8 (1.6-2.1) million people died from HIV. Although the virus continues to spread, the number of new infections has fallen from an estimated 3.2 (3.0 -3.5) million in 1997 to 2.6 (2.3 – 2.8) million in 2009. There are several explanations for this decrease. First, the use of antiretrovirals has slowed down the epidemic by suppressing viral replication and thereby the HIV RNA load [2]. This RNA load is a key factor in determining transmissibility of HIV. Second, sexual risk behaviour has decreased in most countries. Third, HIV prevalence follows an ‘S’ curve, like any infectious disease where it start slowly and gradually. In the final phase of the epidemic, people are either no longer infectious (due to effective treatment) or deaths outnumber new cases, so that the total number alive and infected passes its peak and begin to decline or reach a plateau. The majority of new HIV infections continue to occur in sub-Saharan Africa. Here, an estimated 1.8 (1.6 -2.0) million people were newly infected in 2009 and 22.5 million (20.9 -24.2) people were living with HIV in this region (figure 1). In Europe, the HIV-1 epidemic is much smaller, with an estimated 130,000 (110,000-160,000) newly infected in Western and Central Europe in 2009. This results in 820,000 (720,000-910,000) individuals living with HIV-1 and a prevalence of 0.2% in this region.
Lawrie's Meat Science

This highly regarded book remains a standard work for both students and professionals in the meat industry. Its basic theme remains the central importance of biochemistry in understanding the production, storage, processing and eating quality of meat. At a time when so much controversy surrounds meat production and nutrition, Meat Science provides a clear guide, which takes the reader from the growth and development of meat animals, through the conversion of muscle to meat, to the point of consumption. This new edition incorporates significant advances in meat science during the past ten years.
Habitat case studies

Many important issues in conservation biology are more clearly visible on islands than on continental mainlands. Islands are natural laboratories for demonstrating the dynamic nature of life and the consequences both of natural selection and of the human conquest of planet earth (Cook et al. 2006). In recent years, islands have also been places where large-scale experiments in the conservation of endemic species and the management of invasive species have led to huge practical advances in conservation biology. The literature on conservation on islands is enormous, and in this chapter we summarize a few of the key topics that concern island managers worldwide, with exemplary case studies from the islands shown in Figure 12.1. Conservation biogeography
Syntrophic oxidation of butyrate and ethanol

Vasilij Leonidovič Omeljanskij (Василий Леонидович Омелянский, also transliterated as Omelianski, Omelianskii, Omeliansky or Omelyansky) (1867-1928) was the only student to S. N. Vinogradskij, the discoverer of microbial chemoautotrophy. At the beginning of the 20 century, Omeljanskij founded a school of thought based on Vinogradskij’s discoveries and theories in Russia and the USSR. Omeljanskij followed the research interests of Vinogradskij and did pioneering work on methanogenesis and nitrogen fixation. He published the first Russian textbook on microbiology, “Principles of microbiology” (“Основы микробиологии“) in 1909, followed by numerous other articles popularizing the young science field microbiology and Vinogradskij’s school in Russia. Omeljanskij published internationally in German, French and English, thus representing a cross-border type of scientist. Today, both the international and Russian scientific community can positively refer to Omeljanskij’s lifework. His path of life exemplifies the common origin of national science traditions which grew apart the last century.
Tyk2-Signaling Plays an Important Role in Host Defense against Escherichia coli through IL-23-Induced IL-17 Production by γδ T Cells1

Tyrosine kinase 2 (Tyk2), a member of the JAK-signal transducer family, is involved in intracellular signaling triggered by various cytokines, including IL-23. We have recently reported that resident γδ T cells in the peritoneal cavity of naive mice produced IL-17 in response to IL-23. In this study, we examined importance of Tyk2-mediated signaling in the IL-17 production by γδ T cells using Tyk2 deficient (−/−) mice. γδ T cells in the peritoneal cavity of Tyk2−/− mice displayed effecter/memory phenotypes and TCR V repertoire similar to those in Tyk2+/+ mice and produced comparable level of IL-17 to those in Tyk2+/+ mice in response to PMA and ionomycin, indicating normal differentiation to IL-17-producing effectors in the absence of Tyk2-signaling. However, γδ T cells in Tyk2−/− mice produced less amount of IL-17 in response to IL-23 in vitro than those in Tyk2+/+ mice. Similarly, γδ T cells in the peritoneal cavity of Tyk2−/− mice showed severely impaired IL-17 production after an i.p. infection with E. coli despite comparable level of IL-23 production to Tyk2+/+ mice. As a consequence, Tyk2−/− mice showed a reduced infiltration of neutrophils and severely impaired bacterial clearance after Escherichia coli infection. These results indicate that Tyk2-signaling is critical for IL-23-induced IL-17 production by γδ T cells, which is involved in the first line of host defense by controlling neutrophil-mediated immune responses.
Screening of insecticides against the mulberry fruit gall midge Cotarina sp.

In recent years, a kind of mulberry pests which were known as the mulberry gall midge Cotarina sp. in different mulberry planting areas occurred popularly in China. This study aims to screening high efficacy and low toxicity insecticides for controlling Cotarina sp. The current study can help understand integrated pest management (IPM) of Cotarina sp. by scientific and reasonable insecticide use. Field experiment was carried out to investigate eight insecticides, treated with 3 concentration gradients. The result shows that Imidacloprid, Thiamethoxam, Cyromazine, Bifenthrin and Cypermethrin·Profenofos had high control effect on the mulberry gall midge.Their pesticide residues were all less than Chinese Standard GB2763-2016, which means that they were feasible to control this pest. This paper shows that, to control Cotarina sp. in fruit mulberry production, 10% Imidacloprid WP with 2000~3000 dilution and 25% Thiamethoxam WDG with 1500~2500 dilution and 80% Cyromazine WDG with 1500~2000 dilution are the best. 2.5% Bifenthrin EW with 1000~1500 dilution and 440g/l Cypermethrin·Profenofos EC with 1000~2000 dilution should be used by selection. However, Bifenthrin or Cypermethrin·Profenofos cannot be used in mulberry field for both fruits and leaves, so as to avoid causing silkworm poisoning.
Osteology of the axial and appendicular skeletons of the meagre, Argyrosomus regius (Sciaenidae) and early skeletal development at two rearing facilities

Summary The meagre (Argyrosomus regius) is a new species for aquaculture diversification, presenting a high economic value and a high growth rate, reaching 1 kg year )1 . The occurrence of deformities, which generally appear in cultured larvae at early stages, is problematic for aquaculture since they reduce fish fitness and profitability. Knowledge about the stages of skeletal formation is essential to accurately assess deformities in hatchery produced fish. Here, we describe the osteology of the axial skeleton and unpaired fins of the meagre. Based on this data, the osteological development of meagre larvae reared at the IPIMAR and IRTA-SCR, under different rearing conditions, was compared. Although little literature is available on the osteology of teleosts from the same taxonomic group, the skeletal composition of the meagre is comparable to that of other Sciaenidae. All skeletal structures considered appeared at earlier stages in larvae reared at IPIMAR, which presented a more advanced skeletal development in comparison to larvae of comparable length reared at IRTA-SCR that were submitted to lower temperature and light intensity, and reduced photoperiod regimes.
R46K /R125K Mutation of PKP2 Instigates H9c2 Cell Hypertrophy

Plakophilin 2, an armadillo protein, is a constituent of the desmosomal protein complex. Its function is very important in the maintenance of the integrity of tissues exposed to mechanical stress, such as the cardiac tissues. Mutations in the PKP2 gene complex has been implicated in the development of (Arrhythmogenic Cardiomyopathy (ACM), a condition that predisposes athletes to sudden cardiac death, occurring mostly during sporting activities. In this study, we examined the effect of R46K-R125K mutations on the cardiac cells using H9c2 cells. Results show that H9c2 cells bearing mutant (R46K-R125K) gene for PKP2 develop cell hypertrophy after 24 hours, although the mechanisms inducing hypertrophy is currently unknown. However, R46 and R125 are known hotspots for arginine methylation, the authors propose that hypertrophy induction may be associated with factors related to defects in arginine methylation at these sites. Short Communication Onwuli and Beltran-Alvarez; AJRCD, 1(1): 1-7, 2019; Article no.AJRCD. 46470 2
Fauna of the Mediterranean Hydrozoa

This study provides a systematic account of the hydrozoan species collected up to now in the Mediterranean Sea. All species are described, illustrated and information on morphology and distribution is given for all of them. This work is the most complete fauna of hydrozoans made in the Mediterranean. The fauna includes planktonic hydromedusae, benthic polyps stages and the siphonophores. The Hydrozoa are taken as an example of inconspicuous taxa whose knowledge has greatly progressed in the last decades due to the scientific research of some specialists in the Mediterranean area. The number of species recorded in the Mediterranean almost doubled in the last thirty years and the number of new records is still increasing. The 457 species recorded in this study represents the 12% of the world known species. The fauna is completed with classification keys and a glossary of terms with the main purpose of facilitating the identification of all Meditrranean hydrozoan species
Molecular studies of the pathogenic free-living amoeba, Acanthamoeba

Molecular Studies of the Pathogenic Free-living Amoeba, Acanthamoeba By Kimberley A. Durham Ubiquitous amoebae from the genus Acanthamoeba are associated with two main serious infections: The more common eye disease acanthamoeba keratitis (AK), which can result in blindness, and the rare and often fatal disease affecting the central nervous system, granulomatous amoebic encephalitis (GAE). The traditional morphological taxonomic system for Acanthamoeba is based on cyst size and shape, and divides the amoebae into three groups (I, II and III). Since the discovery that cyst shape can be modified by culture conditions, the classic system has become largely redundant. A more robust system has been developed, based on the nucleotide sequence of the 18S rRNA (Rns) gene. It types Acanthamoeba into 15 T-groups, with most species including environmental and clinical clumped into three groups T3, T4 and T11, with little resolution between them. Although speciation does not help cure patients directly, it can provide valuable information regarding disease epidemiology and ultimately benefit patient prognosis. Here a system to better resolve strains has been developed, using the mitochondrial cytochrome oxidase subunit 1 and 2 (cox1/2) gene sequence. When used in conjunction with the T-group system, resolution between strains including those with a T3, T4 or T11 genotype is obtained. Additionally the combined approach identified a mixed infection in a patient suffering with AK, and the occurrence of Acanthamoeba strains with multiple alleles of 18S and cox1/2 genes. The combined use of both genotyping systems was used to investigate an unprecedented outbreak of GAE within a Swedish hospital. Results confirmed Acanthamoeba had infected several immunocompromised paediatrics from a single ICU, and the source was from within the unit’s water system. In vitro assays were used to test the strains pathogenic abilities and sensitivities to antimicrobial compounds, identifying if they are more virulent than typical strains of Acanthamoeba.
Etude de l'activation de la transmission du Turnip mosaic virus par pucerons

Beaucoup de virus de plante sont transmis selon le mode non-circulant par vecteurs hemipteres, souvent des pucerons. Ce mode de propagation repand les virus tres rapidement d’un hote a l’autre, ce qui cause d’innombrables degâts sur de nombreuses cultures d'interet agronomique. Actuellement, le manque de connaissances sur leur processus de transmission constitue un frein pour le developpement de methodes de lutte efficaces. Recemment, des resultats ont montre qu’un virus modele, le Cauliflower mosaic virus (CaMV, genre Caulimovirus), repond a l'arrivee de son vecteur puceron en formant, a ce moment precis et de maniere reversible, des complexes transmissibles du virus, obligatoire pour son acquisition par le puceron. Ce phenomene extraordinaire nomme « activation de la transmission (AT) » controle l’acquisition du virus et donc sa transmission. Il constitue une decouverte majeure pour la transmission non-circulante et ouvre de nombreuses perspectives de recherche dont celle d’elargir ce phenomene a autres virus pour savoir si l’AT est un phenomene generalise dans la propagation des virus.Dans cette optique, nous nous sommes interesses a un virus non apparente au CaMV, le Turnip mosaic virus (TuMV), un Potyvirus, egalement transmis par pucerons. La transmission du TuMV depend de l’interaction directe de la particule virale et de la proteine virale facteur assistant de la transmission (HC-Pro). En effet, HC-Pro doit former avec la particule un complexe transmissible, seule forme du virus pouvant etre acquis par le vecteur. Nos resultats montrent que le TuMV utilise l’AT et qu’elle est dependante de la presence d’especes reactives de l’oxygene (ROS) et de la signalisation calcique. L’AT du TuMV est correlee avec la formation d’oligomeres par ponts disulfures de HC-Pro et avec la formation des complexes transmissibles HC-Pro/particules virales dans les cellules vegetales. Notre analyse pharmacologique a montre que l’AT du CaMV dependait egalement de la presence des ROS et de la signalisation calcique. Ces deux voies de signalisation sont donc impliquees dans les etapes presumees precoces de l’AT du CaMV et du TuMV. Des experiences avec d’autres composes ont mis en evidence que les etapes suivantes de l’AT sont differentes pour les deux virus. Une recherche d’eliciteurs de l’AT a ete initiee mais n’a pour l’instant pas permis d’en identifier un.Ces resultats ont mis en evidence l’existence de l’AT pour un deuxieme genre de virus non-circulant, suggerant qu’il pourrait s’agir d’un mode de transmission general. Ces nouvelles donnees ouvrent, d’un point de vu applique, de nouvelles perspectives pour les strategies de lutte, visant a interrompre specifiquement le processus de l’AT.
Substrate‐modulated reactions of putidamonooxin

1 4-Methoxybenzoate monooxygenase is fairly nonspecific. The enzyme system with putidamonooxin as its oxygen-activating component catalyses:(a) O-, S- and N-demethylation; (b) the oxygenation of 4-methylbenzoate and 4-methylmercaptobenzoate, with formation of 4-carboxybenzyl alcohol and 4-carboxyphenylmethyl sulfoxide, respectively, and (c) attack of the aromatic ring of 4-and 3-hydroxybenzoate and 4-aminobenzoate, yielding 3,4-dihydroxybenzoate and 4-amino-3-hydroxybenzoate, respectively. 2 Compounds which are bound by the active sites of putidamonooxin have two essential features in common: a planar aromatic ring system, and a free carboxyl group attached to it. 3 By a substrate-modulated reaction putidamonooxin can be induced to function not only as a monoxygenase but also as a peroxotransferase, i.e. it incorporates both atoms of the activated oxygen molecule into a substrate molecule. This finding supports the hypothesis that a mesomeric state of the iron · peroxo complex, [FeO2]+, is indeed the active oxygenating species of putidamonooxin. 4 The lifetime of the ternary complex consisting of enzyme · iron-peroxo-complex · substrate is significantly prolonged by uncoupling and partially uncoupling substrates, except when it is inactivated by protonation of the iron · peroxo complex by a proton transported into the active sites by a special kind of substrate (i.e. isomers of monoaminobenzoate), with the direct formation of H2O2. 5 The lifetime of the active oxygen species is determined by (a) the rate of the oxygenation reaction in the presence of tight-coupling substrates and (b) the rate of the oxygenation reaction as well as detoxification by the availability of a dissociable proton in the presence of partial uncoupling (and uncoupling) substrate analogues. 6 The rate of the oxygenation reaction depends on the lifetime of the active oxygen species, [FeO2]+, in the presence of partial uncoupling substrates. 7 The iron · peroxo complex attacks an aromatic ring system according to the empiric rules of electrophilic substitution, whereas the attack of aliphatic substituents at the aromatic ring is controlled by steric criteria.
Comparative analysis of results of numerical simulation of cyber-physical biosensor systems on the basis of lattice differential equations

Summary. The article deals with the comparative analysis of the results of numerical modeling of mathematical models of cyber-physical biosensor systems on hexagonal and rectangular lattices using lattice differential equations. The main attention is given to the mathematical description of the discrete population dynamics in combination with the dynamic logic of the studied models. The lattice differential equations with delay are proposed to simulate antigen-antibody interaction within hexagonal and rectangular biopixels. Appropriate spatial operators have been used to model the interaction between biopixels similar to the phenomenon of diffusion. The paper presents the results of numerical simulations in the form of phase plane images and lattice images of the probability of antigen to antibody binding in the biopixels of cyberphysical biosensor systems for antibody populations relative to antigen populations. The obtained experimental results make it possible to carry out a comparative analysis of the stability of mathematical models of cyberphysical immunosensory systems on hexagonal and rectangular lattices using lattice differential equations. It is concluded that at a constant delay value ) 25 . 0 , 0 [ for the model on the hexagonal lattice and
Judging the levels of violence: Factors that influence assessment of severity of violent acts and their consequences.

To what extent do people vary in their judgment of the severity of violent acts and their consequences? The present study investigates this in two experiments (total N=2490, US & UK adult sample) in which participants were presented with several tasks (Rating task, Ranking task, Financial compensation task) designed to assess consistent patterns in judgments of the severity of violent acts. As age and educational level increased so did judged severity of violent acts. However, overall ordering of the violent acts from least to most violent was the same across both experiments. Severity ratings were lower in the US compared with the UK sample (study 1), but compensation requests were on average higher in the US (M=$160,235) compared with the UK sample (M=$16,160) (Study 2). Moreover, as details of the consequences of the violent acts increased, so did compensation requests (Study 2). We conclude that the absolute ordering of violent acts by severity remains the same irrespective of individual differences. Individual differences account for differences in the judged degree of severity of violence, and in particular cultural factors influences the amount of financial compensation requested.
ARSENIC REPRESSES MYOGENESIS AND NEUROGENESIS THROUGH EPIGENETIC MECHANISMS, REPRESSED TRANSCRIPTION FACTORS, AND ALTERED WNT SIGNALING PATHWAY

36 Introduction 38 Methods 41 Results 44 Discussion 46 Acknowledgements 51 References 52 Table 58 Figures 59 III. SODIUM ARSENITE REPRESSES THE EXPRESSION OF MYOGENIN IN C2C12 MOUSE MYOBLAST CELLS THROUGH HISTONE MODIFICATIONS AND ALTERED EXPRESSION OF EZH2 AND IGF-1 64 Abstract 65 Introduction 67 Methods 70 65 Introduction 67 Methods 70