Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation

Cyanobacteria have shaped the earth's biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signaling, adaptation, and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry toward the detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labeling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2382 proteins and 183 phosphorylation events and quantifying 2111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 h. Among the proteins with increased phosphorylation, the PII signaling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.
Assessment of the Antiviral Properties of Recombinant Porcine SP-D against Various Influenza A Viruses In Vitro

The emergence of influenza viruses resistant to existing classes of antiviral drugs raises concern and there is a need for novel antiviral agents that could be used therapeutically or prophylacticaly. Surfactant protein D (SP-D) belongs to the family of C-type lectins which are important effector molecules of the innate immune system with activity against bacteria and viruses, including influenza viruses. In the present study we evaluated the potential of recombinant porcine SP-D as an antiviral agent against influenza A viruses (IAVs) in vitro. To determine the range of antiviral activity, thirty IAVs of the subtypes H1N1, H3N2 and H5N1 that originated from birds, pigs and humans were selected and tested for their sensitivity to recombinant SP-D. Using these viruses it was shown by hemagglutination inhibition assay, that recombinant porcine SP-D was more potent than recombinant human SP-D and that especially higher order oligomeric forms of SP-D had the strongest antiviral activity. Porcine SP-D was active against a broad range of IAV strains and neutralized a variety of H1N1 and H3N2 IAVs, including 2009 pandemic H1N1 viruses. Using tissue sections of ferret and human trachea, we demonstrated that recombinant porcine SP-D prevented attachment of human seasonal H1N1 and H3N2 virus to receptors on epithelial cells of the upper respiratory tract. It was concluded that recombinant porcine SP-D holds promise as a novel antiviral agent against influenza and further development and evaluation in vivo seems warranted.
Psychosocial predictors of intentions to comply with bariatric surgery guidelines

An increasing body of research suggests that many patients have difficulty adopting the eating guidelines after weight-loss surgery, thereby reducing the long-term success of the procedure. Given such difficulties, it is possible that the typical preoperative education regarding post-surgical eating behavior guidelines is ineffective in motivating some individuals to comply. Presently, no accurate predictors of intentions to comply with post-bariatric surgery guidelines have been identified. In the present pilot study, a psychosocial intervention based on protection motivation theory (PMT) was presented to patients undergoing bariatric surgery. PMT is a well-established preventive health model that has been utilized in a variety of health domains. Participants for this study were recruited before undergoing bariatric surgery, and were randomly assigned to one of two groups: PMT group vs. control. In addition to routine messages from the bariatric surgeon, participants in the PMT group received an intervention based in PMT that focused on the importance of adhering to post-surgical eating behavior guidelines and how best to adhere to these guidelines. Participants in the control group received standard of care information from the bariatric surgeon. Results indicated that the PMT intervention did not have a significant impact. However, follow-up analyses revealed that two aspects of PMT, perceived self-efficacy and perceived threat of not following the guidelines, predicted patients' intentions to comply with post-surgical guidelines. Findings are discussed in terms of the methodological compromises that resulted from the applied research setting as well as promising avenues for future investigation.
Renin-angiotensin system gene polymorphisms in children with Henoch—Schönlein purpura in West China

It has been suggested that renin-angiotensin system (RAS) gene polymorphism is involved in the pathogenesis of Henoch—Schönlein purpura (HSP) with conflicting reports. We therefore investigate the effect of RAS gene polymorphism on HSP susceptibility and severity in a Chinese cohort. The study included 142 children with HSP and 218 healthy controls that were genotyped for RAS gene polymorphisms. Significantly, differences of T174M-T and ACE-D frequency were found between HSP patients and controls (p alleo = .002, ORalleo = 2.001; p alleo = .007, OR alleo = 1.533, respectively). We also found correlations between ACE-I/D and Agt T174M with multiple organ involvements, with significant differences in ACE-D in renal groups (p < 0.05) and Agt T174M in non-renal (p joint = .002, p GI = .042). Furthermore, decreasing M235T-T and increasing ACE-D were found associated with serious renal complications (p = .019, p = .016). Additionally, ACE-I/D and T174M were significantly associated with high clinical score patients, as opposed to low clinical score patients, when patients were scored depending on the severity of overall complications (p = .045, p = .026). We suggest that RAS gene polymorphisms (ACE-I/D, M235T or T174M) are significantly associated with susceptibility to HSP, organ involvement, and disease severity, which largely account for individual prognosis.
High resolution radio astronomy using very long baseline interferometry

Very long baseline interferometry, or VLBI, is the observing technique yielding the highest-resolution images today. Whilst a traditionally large fraction of VLBI observations is concentrating on active galactic nuclei, the number of observations concerned with other astronomical objects such as stars and masers, and with astrometric applications, is significant. In the last decade, much progress has been made in all of these fields. We give a brief introduction to the technique of radio interferometry, focusing on the particularities of VLBI observations, and review recent results which would not have been possible without VLBI observations.
A $Q$-Modification Neuroadaptive Control Architecture for Discrete-Time Systems

This brief extends the new neuroadaptive control framework for continuous-time nonlinear uncertain dynamical systems based on a Q -modification architecture to discrete-time systems. As in the continuous-time case, the discrete-time update laws involve auxiliary terms, or Q-modification terms, predicated on an estimate of the unknown neural network weights which in turn involve a set of auxiliary equations characterizing a set of affine hyperplanes. In addition, we show that the Q -modification terms in the discrete-time update law are designed to minimize an error criterion involving a sum of squares of the distances between the update weights and the family of affine hyperplanes.
Badlands as a hot spot of petrogenic contribution to riverine particulate organic carbon to the Gulf of Lion (NW Mediterranean Sea)

Determining the riverine carbon fluxes to oceans is critical for an improved understanding of C budgets and biogeochemical cycles (C, O) over a broad range of spatial and time scales. Among the particulate organic carbon (POC) involved in these fluxes, those yielded by sedimentary rocks (petrogenic POC: pPOC) remain somewhat uncertain as to their source on continental surfaces. Based on time series from long‐term observatories, we refine the POC and sediments flux of the Rhône River, one of the major tributaries to the Mediterranean Sea. Radiocarbon measurements on a set of riverine samples and forward modelling were used to (i) determine a modelled pPOC content and pPOC/POC ratio for each sample set, (ii) assess pPOC flux delivered to the NW Mediterranean Sea, and (iii) estimate the badlands contribution from the Durance catchment to both the pPOC and to sediment discharges. The weighted pPOC flux contributes up to 26% of the POC flux (145 Gg yr‐1) discharged into the Mediterranean Sea, whereas the weighted pPOC content reaches 0.31 wt%. Despite their low contributive surface area (0.2%), badlands provide, respectively, 12, 3.5 and 14% of the pPOC, POC and sediment fluxes to the Rhône River. Consequently, such rocks can be considered as a major source of pPOC and sediments for the NW Mediterranean Sea and potentially for oceans. We suggest that river‐dominated ocean margins, such as the Rhône River, with badlands in their catchment could export a significant amount of pPOC to the oceans. Copyright © 2018 John Wiley & Sons, Ltd.
Activated protein C in normal human pregnancy and pregnancies complicated by severe preeclampsia: A therapeutic opportunity?*

ObjectivesGiven the efficacy and safety of recombinant human activated protein C (rhAPC) in the systemic inflammatory response syndrome, this study was designed to review the evidence for a role for APC in the pathogenesis of preeclampsia. Preeclampsia is a proinflammatory and procoagulant state, and it is a pregnancy-specific condition that mimics the systemic inflammatory response syndrome. rhAPC reduces mortality in patients with systemic inflammatory response syndrome and could potentially have a role as disease-modifying therapy in preeclampsia. To determine which patients would be offered rhAPC, the literature pertaining to fetal/neonatal outcomes for preeclampsia remote from term, transplacental transport of protein C, and pregnancy experience with the compound were reviewed. Data SourcesMEDLINE, review papers, hand searches of relevant nonindexed journals, and the bibliographies of relevant textbooks and articles reviewed. Study SelectionRandomized controlled trials were considered to provide the best quality of clinical data. Case-control series were considered over uncontrolled data. Some data were not available in the published literature (e.g., neonatal outcomes at various gestational ages and birthweights after a hypertensive pregnancy; and transplacental transfer of protein C), and these data were determined by us. Data ExtractionData were extracted by systematic review onto data collection sheets. Because of the quality of the data, this review is primarily qualitative. Data SynthesisAPC levels fall during normal gestation, returning to normal values by 6 wks postpartum. Limited data suggest that early onset preeclampsia is a state of further, and inappropriate, reduction in APC. Preeclampsia resembles systemic inflammatory response syndrome in this regard. After hypertensive pregnancies, neonates have a 50% chance of intact survival if delivered after 27 + 0 wks of gestation with a birthweight of >600 g. It would seem ethical to offer women with preeclampsia with <50% chance of intact perinatal survival novel and potentially disease-modifying therapy such as rhAPC, especially as there is no transplacental transfer of protein C. Limited evidence would support the use of rhAPC in women with severe postpartum preeclampsia. ConclusionsSufficient data exist to support the use of rhAPC in phase II clinical studies for women with either early onset preeclampsia or severe or deteriorating postpartum disease.
Gram Negative Bacteria Are Associated with the Early Stages of Necrotizing Enterocolitis

Introduction Necrotizing enterocolitis (NEC) affects 5–10% of infants born weighing less than 1500 g. Most models of NEC recapitulate late-stage disease with gut necrosis and elevated inflammatory mediators. Evaluation of NEC at earlier, less lethal stages of disease will allow investigation of initial disease triggers and may advance our understanding of temporal relationships between factors implicated in NEC pathogenesis. In this manuscript, we describe our investigation of early NEC and test the hypothesis that bacteria and inflammatory mediators differ between animals with early NEC and disease free animals. Methods On DOL7 C3HeB/FeJ pups were fed liquid formula with 1×104 Streptococcus thoraltensis, Serratia marcescens, and Pseudomonas aeruginosa every 3 h. To initiate NEC, pups underwent asphyxia (100% N2 for 90 s) and hypothermia (4°C for 10 min) after feeding. Pups were euthanized at 72 h. Intestines were collected for histologic NEC scoring and DNA/RNA extraction. Bacterial populations were identified by 16S rRNA pyrosequencing and principal component analysis (PCA). RNA isolates underwent QRT-PCR for Toll-like Receptor 4 (TLR4) and inducible nitric oxide synthase (iNOS). Results Despite histologic, intestinal damage in mice with NEC, no gross necrosis was observed suggesting early disease. QRT-PCR yielded no difference between groups in TLR4 or iNOS mRNA levels. PCA demonstrated relative clustering of microbial communities based on presence or absence of NEC. 16S pyrosequencing demonstrated similar phyla between groups (Firmicutes and Proteobacteria predominated in all animals). However, the colonic microbiota of animals with NEC had more Citrobacter (p<0.01), Klebsiella (p<0.05), and Tatumella (p<0.05), while that of animals without NEC had more Streptococcus (p<0.01) and Enterococcus (p<0.01). Conclusion Citrobacter, Klebsiella, and Tatumella are associated with NEC. Differential colonic bacteria were identified despite the lack of inflammatory mediator elevation traditionally associated with NEC. This suggests a temporal relationship between bacteria and inflammatory mediators such that alterations in gut microbiota are associated with early NEC, while inflammatory mediator elevation is associated with advanced NEC.
The Changing Spatial Extent of Rivers and Floodplains and its Implications for Flooding: The Case of Kumasi, Ghana

xviii List of Abbreviations . xx Chapter 1 Introduction . 1 1.1 The Key Issue: changes affecting rivers, floodplains and flooding . 1 1.2 Urban areas in Ghana as a case study . 3 1.3 Research gaps, questions and aim . 7 1.4 Research approach and methods . 11 1.5 Thesis Outline . 13 Chapter 2 Literature review . 15 2.
PREDATOR‐DRIVEN PHENOTYPIC DIVERSIFICATION IN GAMBUSIA AFFINIS

Abstract Predation is heterogeneously distributed across space and time, and is presumed to represent a major source of evolutionary diversification. In fishes, fast‐starts–udden, high‐energy swimmingbursts–are often importan tin avoiding capture during a predator strike. Thus, in the presence of predators, we might expect evolution of morphological features that facilitate increased fast‐start speed. We tested this hypothesis using populations of western mosquitofish (Gambusia affinis) that differed in level of predation by piscivorous fish. Body morphology of G. affinis males, females, and juveniles diverged in a consistent manner between predatory environments. Fish collected from predator populations exhibited a larger caudal region, smaller head, more elongate body, and a posterior, ventral position of the eye relative to fish from predator‐free populations. Divergence in body shape largely matched a priori predictions based on biomechanical principles, and was evident across space (multiple populations) and time (multiple years). We measured maximum burst‐swimming speed for male mosquitofish and found that individuals from predator populations produced faster bursts than fish from predator‐free populations (about 20% faster). Biomechanical models of fish swimming and intrapopulation morphology‐speed correlations suggested that body shape differences were largely responsible for enhanced locomotor performance in fish from predator populations. Morphological differences also persisted in offspring raised in a common laboratory environment, suggesting a heritable component to the observed morphological divergence. Taken together, these results strongly support the hypothesis that divergent selection between predator regimes has produced the observed phenotypic differences among populations of G. affinis. Based on biomechanical principles and recent findings in other species, it appears that the general ecomorphological model described in this paper will apply for many aquatic taxa, and provide insight into the role of predators in shaping the body form of prey organisms.
An adaptive PLL tuning system architecture combining high spectral purity and fast settling time

An adaptive phase-locked loop (PLL) architecture for high-performance tuning systems is described. The architecture combines contradictory requirements posed by different performance aspects. Adaptation of loop parameters occurs continuously, without switching of loop filter components, and without interaction from outside of the tuning system. The relationship of performance aspects (settling time, phase noise, and spurious signals) to design variables (loop bandwidth, phase margin, and loop filter attenuation at the reference frequency) are presented, and the basic tradeoffs of the new concept are discussed. A circuit implementation of the adaptive PLL, optimized for use in a multiband (global) car-radio tuner IC, is described in detail. The realized tuning system achieved state-of-the-art settling time and spectral purity performance in its class (integer-N PLLs): a signal-to-noise ratio of 65 dB, a 100-kHz spurious reference breakthrough signal under -81 dBc, and a residual settling error of 3 kHz after 1 ms, for a 20-MHz frequency step. It simultaneously fulfills the speed requirements for inaudible frequency hopping and the heavy signal-to-noise ratio specification of 64 dB.
Becoming a nurse: “it’s just who I am”

In any research study, researchers situate themselves, either explicitly or implicitly, within a variety of frameworks when studying phenomena. From a research perspective, the study will be more robust if these frameworks and the accompanying assumptions are compatible with each other; otherwise, the project may lack coherence. Ricoeur offers a methodological perspective—that is, an interpretive theory as reflected in mimesis, which is congruent with his ontological theory of self identity (ipse- and idem-identity). To illustrate Ricoeur’s frameworks when researching the self identities, I use examples from a research study in which I asked senior nursing students to explore their experience of becoming a nurse. I do not intend for this article to be a comprehensive research report, but I present it as an exemplar of how Ricoeur’s ideas can guide other researchers studying self identity. I labelled my study a narrative research project and assumed that becoming a nurse means developing a self identity as a nurse. While self identity is often framed in psychological terms, Ricoeur uses a philosophical perspective when exploring this concept. I conclude the paper by suggesting (a) that Ricoeur can guide any project in which researchers ask participants to describe “becoming” a person with illness, sickness or disease, and (b) that educators of healthcare professional students can improve the educative experience by purposefully considering how a student’s ontological self affects that student’s practice.
Conservation of polyproline II helices in homologous proteins: Implications for structure prediction by model building

Left‐handed polyproline II (PPII) helices commonly occur in globular proteins in segments of 4–8 residues. This paper analyzes the structural conservation of PPII‐helices in 3 protein families: serine proteinases, aspartic proteinases, and immunoglobulin constant domains. Calculations of the number of conserved segments based on structural alignment of homologous molecules yielded similar results for the PPII‐helices, the α‐helices, and the β‐strands. The PPII‐helices are consistently conserved at the level of 100–80% in the proteins with sequence identity above 20% and RMS deviation of structure alignments below 3.0 Å. The most structurally important PPII segments are conserved below this level of sequence identity. These results suggest that the PPII‐helices, in addition to the other 2 secondary structure classes, should be identified as part of structurally conserved regions in proteins. This is supported by similar values for the local RMS deviations of the aligned segments for the structural classes of PPII‐helices, α‐helices, and β‐strands. The PPII‐helices are shown to participate in supersecondary elements such as PPII‐helix/α‐helix. The conservation of PPII‐helices depends on the conservation of a supersecondary element as a whole. PPII‐helices also form links, possibly flexible, in the interdomain regions. The role of the PPII‐helices in model building by homology is 2‐fold: they serve as additional conserved elements in the structure allowing improvement of the accuracy of a model and provide correct chain geometry for modeling of the segments equivalenced to them in a target sequence. The improvement in model building is demonstrated in 2 test studies.
A physiological increase in maternal cortisol alters uteroplacental metabolism in the pregnant ewe

Fetal nutrient supply is dependent, in part, upon the transport capacity and metabolism of the placenta. The stress hormone, cortisol, alters metabolism in the adult and fetus but it is not known whether cortisol in the pregnant mother affects metabolism of the placenta. In this study, when cortisol concentrations were raised in pregnant sheep by infusion, proportionately more of the glucose taken up by the uterus was consumed by the uteroplacental tissues while less was transferred to the fetus, despite an increased placental glucose transport capacity. Concomitantly, the uteroplacental tissues produced lactate at a greater rate. The results show that maternal cortisol concentrations regulate uteroplacental glycolytic metabolism, producing lactate for use in utero. Prolonged increases in placental lactate production induced by cortisol overexposure may contribute to the adverse effects of maternal stress on fetal wellbeing.