Miracle-dz/UniFAR-FTUs huggingface dataset:
Gas exchange, water relations and their relationships with photochemical reflectance index in Quercus ilex plants during water stress and recovery.

Diffusional limitations to photosynthesis (A), relative water content (RWC) and their association with photochemical reflectance index (PRI) were studied in holm oak (Quercus ilex L.) saplings subjected to water stress and subsequent water stress relief. RWC decreased sharply as drought progressed. Following rewatering, RWC gradually increased to pre-stress values. A, stomatal conductance (gs), mesophyll conductance (gm), total conductance (gt), and PRI changed in parallel with RWC. A decrease in A resulted from coordinated suppression in leaf conductance. As water stress progressed, A measured in non-photorespiratory conditions (A1%O2) became more than 3 times higher compared to that recorded at 21% [O2], indicating that photorespiration likely increased in response to water stress. A1%O2 was significantly correlated with all leaf conductances. A1%O2 was limited more by gs than by gm, indicating that higher gm favors photosynthesis over photorespiration. There was a significant linear correlation between RWC and PRI. Significant non-linear relationships were also found both between PRI and A and PRI and gt. These data imply that PRI may clearly detect normal and stressed status of holm oak, but it is not very informative when plants are severely stressed. Overall, our data indicate that: a) PRI is an important indicator of leaf water status as evident from RWC; b) because leaf conductance did not limit photosynthesis when photorespiration was suppressed, holm oak, and in general sclerophyllous species, will respond to future elevated [CO2] significantly more than mesophyllous plants; c) PRI can be used to predict changes in the performance of holm oak subjected to physiological water stress, whereas caution is needed under severe drought. © 2014 Friends Science Publishers
The histone code: what proteomics has taught us

4 Introduction 5 Mass spectrometry as a tool to study chromatin biology 6 The histone code 8 Identifying novel histone modifications using MS 9 Quantification of histone PTMs 10 Gene locus-specific histone analysis 13 Identifying epigenetic readers 14 Conclusion 15 Acknowledgements 17 References 18
Chemistry of riming: the retention of organic and inorganic atmospheric trace constituents

Abstract. During free fall in clouds, ice hydrometeors such as snowflakes and ice particles grow effectively by riming, i.e., the accretion of supercooled droplets. Volatile atmospheric trace constituents dissolved in the supercooled droplets may remain in ice during freezing or may be released back to the gas phase. This process is quantified by retention coefficients. Once in the ice phase the trace constituents may be vertically redistributed by scavenging and subsequent precipitation or by evaporation of these ice hydrometeors at high altitudes. Retention coefficients of the most dominant carboxylic acids and aldehydes found in cloud water were investigated in the Mainz vertical wind tunnel under dry-growth (surface temperature less than 0 °C) riming conditions which are typically prevailing in the mixed-phase zone of convective clouds (i.e., temperatures from −16 to −7 °C and a liquid water content (LWC) of 0. 9 ± 0. 2 g m−3). The mean retention coefficients of formic and acetic acids are found to be 0. 68 ± 0. 09 and 0. 63 ± 0. 19. Oxalic and malonic acids as well as formaldehyde show mean retention coefficients of 0. 97 ± 0. 06, 0. 98 ± 0. 08, and 0. 97 ± 0. 11, respectively. Application of a semi-empirical model on the present and earlier wind tunnel measurements reveals that retention coefficients can be well interpreted by the effective Henry's law constant accounting for solubility and dissociation. A parameterization for the retention coefficients has been derived for substances whose aqueous-phase kinetics are fast compared to mass transport timescales. For other cases, the semi-empirical model in combination with a kinetic approach is suited to determine the retention coefficients. These may be implemented in high-resolution cloud models.
Nitrogen Metabolism and Excretion

Protein Turnover in Animals, D.F. Houlihan, C.G. Carter, and I.D. McCarthy Molecular Aspects of Carbamoyl Phosphate Synthesis, P.M. Anderson Nitrogen and Buoyancy in Marine Organisms, N. Sanders and J. Childress Nitrogen Metabolism and Excretion for Cell Volume Regulation in Invertebrates, R.P. Henry Membrane Transport and Nitrogenous Solute Balance in Molluscs, S.H. Wright and D.S. Neufeld Nitrogen Metabolism, Excretion, Osmoregulation, and Cell Volume Regulation in Elasmobranchs, L. Goldstein and D.F. Perlman Nitrogen Excretion in Terrestrial Crustaceans, M.J. O'Donnell and J.C. Wright Nitrogen Metabolism and Excretion in Locusts, J.F. Harrison Molecular Aspects of Ureogenesis in Amphibians, B.G. Atkinson Excretory Nitrogen Metabolism in Reptiles and Birds, J.W. Campbell Nitrogen Excretion in Reptiles, W.H. Dantzler Urea Synthesis in Mammals, A.J. Meijer Urea and Ammonium Transport in the Mammalian Kidney, M.A. Knepper and C. -L. Chou Gene Expression and Development of Hepatic Nitrogen Metabolic Pathways, M.A. Dingemanse and W.H. Lamers Maternal-Fetal Transfer of Nitrogen in Chondrichthyans, G.A. Kormanik Nitrogen Excretion in Teleostean Fish: Adaptive Relationships to Environment, Ontogenesis, and Viviparity, B. Korsgaard, T.P. Mommsen, and P.A. Wright Uptake and Effects of Nitrite and Nitrate in Animals, F.B. Jensen Nitric Oxide Synthesis, J.M. Fukuto Index
Cloning and expression of superoxide dismutase from Sarcoptes scabiei in Escherichia coli

Sarcoptes scabiei is a disease-causing parasitic mite of humans and animals that is prevalent worldwide. The parasite lives in burrows in the epidermis of its host. These burrows are formed by a combination of mechanical destruction by the mite and secretion of various factors.The enzyme superoxide dismutase (SOD) catalyzes the dismutation of superoxide into oxygen and hydrogen peroxide. As such, it is an important antioxidant defense in nearly all cells exposed to oxygen. In this project, the enzyme was expressed in transformed Escherichia coli cells. The SOD cDNA from S. scabiei was ligated into two different expression vectors: pPU16 and pET-14b. The S. scabiei SOD open reading frame reported here is 696 nucleotides long and yields a protein with a molecular weight of  69.5 kDa. Only one of the constructs was successfully created, using pPU16. The construct was designated pPU110 and has a sequence coding for a hexahistidine tag downstream of the SOD cDNA and has a sequence coding for the maltose binding protein (MBP) upstream.The expression plasmid pPU110 was verified by DNA-sequencing and the tested in different expression experiments. Analysis using SDS-PAGE showed that recombinant fusion SOD could be readily expressed in E.coli.
Effects of Application Attributes of Coffee Chains on Consumer’s Repurchase Decision-Making Processes

This study explores the impacts of application attributes of coffee chains on consumer’s re-purchase decision-making processes in the context of coffee chains. We posited coffee quality, service quality, and physical environment as key service attributes of coffee chains and personalization, usefulness, economy, and convenience as key application attributes. The moderating effect of application attributes on the relationship between consumer satisfaction and repurchase intention was investigated. The theoretical framework was tested based on 382 consumers who frequently visit coffee chains and install their applications. PLS method was used to analysis the hypotheses. The theoretical model accounts for 48.1% of variance in customer satisfaction and 41.6% of variance in repurchase intention. The analysis results showed that personalization and convenience play an moderating effect on consumer’s repurchase decision-making processes. Coffee quality and physical environment were found to have significant effects on customer satisfaction, while service quality does not significantly influence consumer satisfaction. Brand image has a significant effect on customer satisfaction and repurchase intention.
The Contribution of DNA Interstrand Crosslinks to Aging

DNA damage is hypothesized to be a driver of aging. In support of this, DNA damage and genetic mutations, resulting from replication of that damage, both increase in the nuclear genome as organisms age. Furthermore, long-lived species are relatively resistant to genotoxic stress. Conversely, organisms with DNA repair-deficient or genome instability disorders have decreased lifespans and age rapidly, which supports this theory. One main source of endogenous DNA damage is reactive oxygen species (ROS) generated by mitochondria. While it is true that ROS can damage other macromolecules in the cell, DNA is the only one that is repaired rather than replaced, illustrating the dire consequences of DNA damage. If repair is not 100% complete over a lifetime, it stands to reason that this unrepaired damage could be a major contributor to aging. Ercc1-/Δ mice are deficient in multiple DNA repair pathways and therefore suffer more DNA damage than normal mice. As a consequence, they age prematurely, modeling a human progeroid syndrome. This makes them a useful in vivo system for studying the contribution of DNA damage to aging. For this reason, we challenged the mice with a chemotherapeutic crosslinking agent to determine if DNA damage promotes aging, with an environmental contaminant and a diet of polyunsaturated fatty acids to see if these promote DNA damage and aging. We found that a particular class of lesions, DNA interstrand crosslinks, accelerate aging associated changes through a cytostatic, rather than cytotoxic mechanism. We also exposed the mice to a specialized antioxidant to test the hypothesis that mitochondrial-derived reactive oxygen species are the cause of endogenous DNA damage that promotes aging. Collectively, these studies identified genes, environmental influences and therapeutics that impact lifespan and healthspan. In total, the studies strongly support the hypothesis that DNA damage can promote degenerative changes associated with aging. These studies have public health significance as they reveal multiple novel strategies to decrease the DNA damage burden, therefore presenting potential opportunities to improve quality of life in old age.
New technologies and quality of trout and carp aquafeed.

The objective of our researches was to examine efficiency of installed extruder and vacuum coater, and benefits of applied technology in trout and carp feed, and to determine physico-chemical composition and nutritional value of this feed in comparison to fish feed made by renowned world producers. The quality fish feed production is a complex technological procedure that requires great knowledge but also an adequate equipment. A satisfactory preparation of raw material, extrusion, as well as, the use of the vacuum coater, are certainly necessary segments in the technological lines for the feed production for such kind of an animal. Obtained production results indicate that feed manufactured in our facility generates same results as the feed of three renowned world feed producers. The results obtained at the end of trial show that floating pellets for carp, particularly in group 1, had somewhat increased performance benefits (growth rate and FCR) as compared to sinking pellets.
Impact de l'levage sur la structure gntique des populations mditerranennes de Dicentrarchus labrax

Recu le 8 avril 2004 ; Accepte le 7 octobre 2004 Resume – Une analyse phylogeographique de quinze echantillons de Dicentrarchus labrax dont cinq sont originaires de Mediterranee occidentale, sept de Mediterranee orientale et trois echantillons d’elevage en provenance de trois piscicultures francaises a ete effectuee a partir du polymorphisme de six locus microsatellites. Parmi les echantillons orientaux, trois ne se regroupent pas en fonction de leur origine geographique, mais plutot avec le groupe occidental. Ces echantillons presentent egalement une diversite allelique legerement reduite, indiquant qu’ils proviennent d’un nombre limite de geniteurs d’origine occidentale. Parmi les stocks d’elevage, un seul montre une reduction significative de la variabilite genetique, ce qui indique que ces cheptels sont ouverts et font largement appel a des geniteurs sauvages. L’utilisation d’alevins d’origine occidentale pour ensemencer les premieres fermes d’elevage du bassin oriental remonte au plus tard au debut des annees 80. Ceci souleve la question des mecanismes biologiques expliquant le maintien de poissons d’origine occidentale dans un contexte oriental pendant au moins deux ou trois generations.
Cholesterol crystals enhance TLR2- and TLR4-mediated pro-inflammatory cytokine responses of monocytes to the proatherogenic oral bacterium Porphyromonas gingivalis

Cholesterol deposits and pro-inflammatory cytokines play an essential role in the pathogenesis of atherosclerosis, a predominant cause of cardiovascular disease (CVD). Epidemiological evidence has linked periodontal disease (PD) with atherosclerotic CVD. Accordingly, viable periodontal pathogens, including Porphyromonas gingivalis, have been found in atherosclerotic plaques in humans and mice. We aimed to determine whether cholesterol crystals (CHCs) and oral bacteria synergize in the stimulation of human monocytes. Incubation of human monocytes with CHCs induced secretion of interleukin (IL)-1β, tumor necrosis factor (TNF)-α, IL-6, and IL-8. Moreover, CHCs markedly enhanced secretion of IL-1β by monocytes stimulated with the toll-like receptor (TLR) 4 agonist Escherichia coli lipopolysaccharide (LPS), and the TLR2 agonist Staphylococcus aureus lipoteichoic acid. Notably, CHCs also enhanced IL-1β secretion induced by P. gingivalis LPS and IL-1β secretion induced by whole P. gingivalis bacteria. This enhancement was abrogated by the NLRP3 inflammasome inhibitors Z-YVAD-FMK and glibenclamide. CHCs had no effect on cytokine production induced by P. gingivalis gingipains. Taken together, our findings support that CHCs, via stimulation of NLRP3 inflammasomes, act in synergy with the periodontal pathogen P. gingivalis to promote monocyte secretion of pro-atherogenic cytokines.
Phytochemical evaluation and anti-tuberculosis activity of selected nine ethnomedicinal plants

Tuberculosis is one of the leading infectious disease and health burden in the world. It has been estimated that, one third of world’s population including 40% from India estimated to be infected with tuberculosis. As plants are the important sources of diverse range of bioactive principles. The revival of interests in plant derived drugs is mainly due to the current widespread belief that green medicine is safe and more dependable than expensive synthetic drugs, which have adverse side. In this study nine healthy plants with medicinally potential were collected and different extracts were prepare to evaluate its phytochemical study and anti-tubercular activity on Mycobacterium smegmatis using two different models. There are many similarities between Mycobacterium smegmatis and the much more virulent obligate pathogens that are Mycobacteria. On the basis of both the models, form nine selected plants three plants A. vasika, O. sanctum and A. galanga shows maximum anti-tuberculosis activity at the MIC 100 μg/ml, 250 μg/ml and 250 μg/ml respectively. The present study has revealed the importance of plant extracts to control Mycobacterial infections which are being a threat to human health and for the development of alternate, safe and effective medicines.
Lactoferrin : an anti‐inflammatory molecule released by apoptotic cells to inhibit granulocyte migration

5 Introduction . 8 Apoptosis . 8 Burkitt’s Lymphoma . 38 Polymorphonuclear Leukocytes . 49 Leukocytes and Tumour . 87 Lactoferrin . 115 Thesis Aims . 141 Materials and Methods . 142 Antibodies, Reagents and Culture Media . 142 Cell Isolation and Culture . 144 Biochemical Analysis . 149 In vitro Chemotaxis Assay . 151 Lactoferrin Absorption Experiments . 152 Short Hairpin RNA (shRNA)‐Mediated Lactoferrin Expression Knock‐Down . 153 Reverse‐Transcription PCR (RT‐PCR) Analysis . 156 In vivo BL Tumour Xenografts and Peritonitis Model . 160 Immunohistochemistry . 161 In vivo Model of Peritonitis . 162 Time‐lapse Video Microscopy . 163 Measurement of [Ca]i. 164 Immunolabelling and Flow Cytometry . 164 Proliferation Assay . 165 Direct ELISA (Enzyme‐Linked Immunosorbent Assay) for Lactoferrin . 166 Immunoblot Analysis . 166 Induction of Apoptosis and Primary Necrosis . 168 Quantification of Apoptosis and Cell Cycle Analysis . 169 Statistical Analysis . 170 Results . 171 Apoptotic cells actively release factors that inhibit neutrophil migration . 171 Biochemical characterisation of the neutrophil migration inhibitory factor(s) . 179 Biochemical characterisation of the neutrophil migration inhibitory factor(s) . 179 Lactoferrin is actively released from BL cells and specifically inhibits neutrophil chemotaxis in vitro and in vivo . 191 Lactoferrin inhibits neutrophil chemotaxis towards a range of chemoattractants without interfering or impairing the chemoattractant activity. 221
The Prediction and Analysis of Inter- and Intra-Species Protein-Protein Interaction

Protein-protein interactions (PPIs) are essential to cellular processes. Recent developments of high-throughput technologies have uncovered vast numbers of PPIs. However, the experimental evidences are mostly for intra-species interactions of model organisms, especially human. Studies of non-human organisms and inter-species PPIs are few. For organisms such as Arabidopsis thaliana, the experimentally detected 5990 PPIs are estimated to be less than 3% of the entire A. thaliana interactome (M. Lin et al., 2011). The accuracy of high-throughput PPI experiments is also doubtful (Mrowka et al., 2001; Sprinzak et al., 2003; von Mering et al., 2002). To resolve the above issues, several computational methods have been developed to evaluate and predict PPIs. This chapter focuses on direct PPIs which involve physical interactions of proteins, provides a brief overview of the reliabilities of high-throughput PPI detection technologies, and discusses the weakness and strength of important PPI computational prediction and evaluation methods. The major repositories which store, evaluate, and analyse both detected and predicted PPIs are also introduced.
Paracrine and autocrine functions of PDGF in malignant disease.

Growth factors and their receptors are frequently activated by mutations in human cancer. Platelet-derived growth factor (PDGF)-B and its tyrosine kinase receptor, the PDGF β-receptor, have been implicated in autocrine transformation as well as paracrine stimulation of tumor growth. The availability of clinically useful antagonists motivates evaluation of PDGF inhibition in these diseases.In chronic myelomonocytic leukemia with t(5;12), parts of the transcription factor TEL and the PDGF β-receptor are fused, generating a constitutively signaling protein. Oligomerization and unique phosphorylation pattern of TEL-PDGFβR was demonstrated, as well as the transforming activity of TEL-PDGFβR, which was sensitive to PDGF β-receptor kinase inhibition.Dermatofibrosarcoma protuberans (DFSP) is characterized by a translocation involving the collagen Iα1 and PDGF B-chain genes. The COLIA1-PDGFB fusion protein was processed to mature PDGF-BB and transformed fibroblasts in culture. The PDGF antagonist STI571 inhibited growth of COLIA1-PDGFB transfected cells and primary DFSP cells in vitro and in vivo through induction of apoptosis.Paracrine effects of PDGF-DD, a ligand for the PDGF β-receptor, were evaluated in a murine model of malignant melanoma. PDGF-DD production accelerated tumor growth and altered the vascular morphology in experimental melanomas.A validated immunohistochemical procedure for PDGF β-receptor detection was established and applied to normal tissues and more than 280 tumor biopsies. Perivascular and stromal expression was detected in 90% and 50%, respectively, of human tumors.Recently, non-transformed cells in the tumor microenvironment have emerged as targets in cancer therapy. Selective sensitization of tumor fibroblasts to paclitaxel by STI571 was evaluated in vitro and in a xenograft model. Whereas neither drug alone caused growth inhibition, combination of the two significantly reduced tumor growth, suggesting anti-stromal therapy as a possible treatment modality in solid tumors.
Brain Activity Tracking Using Smart Eyewear

© Proceedings of the CHI 2017 Workshop on Amplification and Augmentation of Human Perception, May 07, 2017, Denver, CO, USA. Copyright is held by the owner/author(s). Abstract This paper describes our approach towards the concept of a brain fitness tracker. A wearable sensing platform that is capable of tracking cognitive load and mental state of the user. We discuss some of the promising sensing modalities, implementations and approaches as well as physiological mechanisms that can give us valuable insights on the cognitive processes.
Anaerobic Induction of Isocitrate Lyase and Malate Synthase in Submerged Rice Seedlings Indicates the Important Metabolic Role of the Glyoxylate Cycle

The glyoxylate cycle is a modified form of the tricarboxylic acid cycle that converts C2 compounds into C4 dicarboxylic acids at plant developmental stages. By studying submerged rice seedlings,we revealed the activation of the glyoxylate cycle by identifying the increased transcripts of mRNAs of the genes of isocitrate lyase (ICL) and malate synthase (MS), two characteristic enzymes of the glyoxylate cycle. Northern blot analysis showed that ICL and MS were activated in the prolonged anaerobic environment.The activity assay of pyruvate decarboxylase and ICL in the submerged seedlings indicated an 8.8-fold and 3.5-fold increase over that in the unsubmerged seedlings, respectively. The activity assay of acetyl-coenzyme A synthetase in the submerged seedlings indicated a 3-fold increase over that in the unsubmerged seedlings, which is important for initiating acetate metabolism. Consequently, we concluded that the glyoxylate cycle was involved in acetate metabolism under anaerobic conditions.
MUSCLE DEVELOPMENT IN AMPHIOXUS: MORPHOLOGY, BIOCHEMISTRY, AND MOLECULAR BIOLOGY

ABSTRACT This review concerns the structure and biochemistry of muscle in amphioxus. Most work has focused on the segmented swimming (axial) muscles. These muscles derive from the medial wall of the somites, which arise as evaginations from the gut wall. The myotomal muscle cells of amphioxus, unlike those of vertebrates, never fuse, but remain mononucleate, contain only one myofibril, and span the entire length of the myotome. The muscle cells are very thin and lack a T-tubule system. There are two, maybe three, types of fibers. Innervation is via muscle tails, which contact the basal lamina of the nerve cord. The notochord is also composed of striated muscle cells, which similarly send muscle tails to the nerve cord. Less is known about the biochemistry of muscle. The notochord, like molluskan catch muscle, contains paramyosin. Among the muscle-specific proteins sequenced are alkali myosin light chain, troponin C and sarcoplasmic calcium-binding proteins, calcium-vector protein, and its target protein c.