Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of TRIM Genes in Different Immune Cells and Mechanism of Regulation of Their Expression: Implications for the Immune Response to Pathogens

The tripartite motif (TRIM) proteins are important in a variety of cellular functions including antiviral activity. We systematically analyzed mRNA expression of representative TRIMs in primary mouse macrophages, myeloid and plasmacytoid dendritic cells, and a selection of CD4+ T cell subsets. These cells have different effector functions in innate and adaptive immune responses, to a large extent due to the different patterns of cytokines that they produce. Here, we defined four clusters of TRIM genes based on their selective expression in these cell subsets. The first group of TRIMs was preferentially expressed in CD4+T cells and contained the COS-FN3 motif. Additional TRIMs were identified that showed up-regulation in macrophages and dendritic cells upon influenza virus infection in a type-I IFN dependent manner suggesting that they may play a role in anti-viral responses. However, stimulation of macrophages and mDC with LPS and double stranded RNA also led to type-I IFN dependent up-regulation of these TRIM genes, suggesting that their expression is not directly regulated by the virus, and that they may have broader functions in innate immune responses. In support of the proposed role of TRIMs in anti-viral responses, a subset of the type-I IFN dependent TRIMs mapped to mouse chromosome 7, syntenic to human chromosome 11 where TRIMs such as TRIM5, shown to have anti-viral activity, are localized. Consistent with these findings, up-regulation of the same TRIM genes in human macrophages was mainly observed under conditions which resulted in the induction of IFNβ (in this case by LPS and IFNγ stimulations), as observed by reanalysis of a previously published microarray study. Within the group of TRIMs induced by viruses in macrophages and dendritic cells via a type-I IFN dependent mechanism we distinguish two clusters on the basis of TRIM expression in CD4+ T cells. A fourth group of TRIMs was constitutively expressed in plasmacytoid dendritic cells independently of viral infection or signalling through the type-I IFN receptor. Our findings on expression and regulation of TRIMs may help to develop potential strategies for determining functions of this diverse family of molecules in immune cells.
Adaptive Backstepping Tracking Control for an over–Actuated DP Marine Vessel with Inertia Uncertainties

Abstract Designing a tracking control system for an over-actuated dynamic positioning marine vessel in the case of insufficient information on environmental disturbances, hydrodynamic damping, Coriolis forces and vessel inertia characteristics is considered. The designed adaptive MIMO backstepping control law with control allocation is based on Lyapunov control theory for cascaded systems to guarantee stabilization of the marine vessel position and heading. Forces and torque computed from the adaptive control law are allocated to individual thrusters by employing the quadratic programming method in combination with the cascaded generalized inverse algorithm, the weighted least squares algorithm and the minimal least squares algorithm. The effectiveness of the proposed control scheme is demonstrated by simulations involving a redundant set of actuators. The evaluation criteria include energy consumption, robustness, as well accuracy of tracking during typical vessel operation.
Saving large fish through harvest slots outperforms the classical minimum-length limit when the aim is to achieve multiple harvest and catch-related fisheries objectives

We address the problem of optimal size-selective exploitation in an age-structured fish population model by systematically examining how density- and size-dependency in growth, mortality and fecundity affect optimal harvesting patterns when judged against a set of common fisheries objectives. Five key insights are derived. First, while minimum-length limits often maximize the biomass yield, exploitation using harvest slots (i.e., regulations that protect both immature and very large individuals) can generate within 95% of maximum yield, and harvest slots generally maximize the number of fish that are harvested. Second, density-dependence in growth and size-dependent mortality predict more liberal optimal size-limits than those derived under assumptions of no density and size-dependence. Third, strong density-dependence in growth maximizes the production of trophy fish in the catch only when some modest harvest is introduced; the same holds for numbers harvested, when the stock-recruitment function follows the Ricker-type. Fourth, the inclusion of size-dependent maternal effects on fecundity or egg viability has only limited effects on optimal size limits, unless the increase in fecundity with mass (“hyperallometry”) is very large. Extreme hyperallometry in fecundity also shifts the optimal size-limit for biomass yield from the traditional minimum-length limit to a harvest slot. Fifth, harvest slots generally provide the best compromises among multiple objectives. We conclude that harvest slots, or more generally dome-shaped selectivity to harvest, can outperform the standard minimum-length selectivity. The exact configuration of optimal size limits crucially depends on objectives, local fishing pressure, the stock-recruitment function and the density and size-dependency of growth, mortality and fecundity.
Trna Aminoacylation: New Protein Players And New Reactions

TRNA AMINOACYLATION: NEW PROTEIN PLAYERS AND NEW REACTIONS by WHITNEY N. WOOD May 2019 Advisor: Dr. Tamara L. Hendrickson Major: Chemistry (Biochemistry) Degree: Doctor of Philosophy Protein translation must usually occur with high accuracy for an organism to survive. However, Helicobacter pylori, Staphylococcus aureus, and many other microorganisms including important human pathogens, lack one or more aminoacyl-tRNA synthetase (aaRS), the enzymes that typically aminoacylate tRNAs for ribosomal translation. These organisms must use an indirect pathway to aminoacylate some tRNAs. Specifically, H. pylori lacks the genes that encode for asparaginyl- and glutaminyl-tRNA synthetases (AsnRS and GlnRS, respectively). Instead, H. pylori uses a two-step, indirect pathway to synthesize Asn-tRNAAsn and Gln-tRNAGln. This process requires two misacylating tRNA synthetases (a non-discriminating aspartyl-tRNA synthetase, ND-AspRS, and a misacylating glutamyl-tRNA synthetase 2, GluRS2) and a glutamine-dependent amidotransferase called GatCAB. We have recently discovered a protein called Hp0100 that promotes formation of a stable complex between ND-AspRS, Hp0100, and GatCAB called the Asn-transamidosome. Hp0100 enhances GatCAB’s ability to produce both Asn-tRNAAsn and Gln-tRNAGln and it hydrolyzes ATP in the presence of either Asp-tRNAAsn or Glu-tRNAGln, the precursors to Asn-tRNAAsn and Gln-tRNAGln, respectively. (Red text indicates misacylation.) This dissertation focuses on three different research projects. Chapter 2 describes our evaluation of a shortened ortholog of Hp0100 from S. aureus. Full-length orthologs of Hp0100 are restricted to the e-proteobacteria; however, we have recently discovered truncated orthologs comprising the N-terminal 2/3 of Hp0100 outside of this clade. The truncated ortholog from S. aureus (Sa2591) is compared to Hp0100 to assess if it is a functional ortholog of Hp0100. The predicated model structure of Sa2591 showed several conserved cysteine residues clustered together with a CXXC motif next to one of the ATPase active sites. Chapter 3 focuses on our characterization of this putative metal-binding site and Sa2591’s potential involvement in the synthesis of a tRNA modification. Chapter 4 reports our discovery that some aaRSs hydrolyze ATP to ADP in the presence of tRNA. All aminoacyl-tRNA synthetases (aaRSs) catalyze the ATP-dependent aminoacylation of tRNAs, producing AMP and PPi as side products. We are unaware of any evidence that aaRSs can produce ADP instead of AMP. We characterized this activity in 25 different aaRSs and propose a function for ADP formation.
Effects of forest management on the phenology of early-flowering understory herbs

Many organisms respond to anthropogenic environmental change through shifts in their phenology. In plants, flowering is largely driven by temperature, and therefore affected by climate change. However, on smaller scales climatic conditions are also influenced by other factors, including habitat structure. A group of plants with a particularly distinct phenology are the understorey herbs in temperate forests. In these forests, management alters tree species composition and stand structure and, as a consequence, light conditions and microclimate. Forest management should thus also affect the phenology of understorey herbs. To test this, we recorded the flowering phenology of 20 early-flowering herbs on 100 forest plots varying in management intensity, from near-natural to intensely managed forests, in Central and Southern Germany. We found that in forest stands with a high management intensity the plants flowered on average about two weeks later than in unmanaged forests. This was largely because management also affected microclimate (e.g. spring temperatures of 5.9 °C in managed coniferous, 6.7 in managed deciduous and 7.0 °C in unmanaged deciduous plots), which in turn affected phenology, with plants flowering later on colder and moister forest stands (+4.5 days per −1°C and 2.7 days per 10 % humidity increase). Among forest characteristics, the main tree species as well as the age, overall crown projection area, structural complexity and spatial distribution of trees had the greatest influence on microclimate. Our study demonstrates that forest management alters plant phenology, with potential far-reaching consequences for the ecology and evolution of understorey communities. More generally, our study suggests that besides climate change other drivers of environmental change, too, can influence the phenology of organisms.
Risk factors associated with in-hospital falls reported to the Patient Safety Commitee of a teaching hospital

ABSTRACT Objective To investigate the use of fall-risk-increasing drugs among patients with falls reported to the Patient Safety Office of a hospital, and to identify the factors associated with high risk for fall. Methods A cross-sectional study, carried out in a teaching hospital. The study population was the universe of fall reports received by the Patient Safety Office. The dependent variable was a high risk for falls. The Medication Fall Risk Score was used to measure fall risk. Descriptive, univariate and multivariate analyses were performed. Results Of the 125 fall reports in the study, 38 (30.4%) were in 2014, 26 (20.8%) in 2015, and 61 (48.8%) in 2016. Half of the patients (63; 50.4%) were classified as high fall risk and 74 (59.2%) had two or more risk factors for the event. The most frequently used drug classes were opioids (25%), anxiolytics (19.7%), beta-blockers (9.9%), angiotensin II antagonists (7%) and vascular-selective calcium channel blockers (7%). After the adjusted analysis, the factors associated with falls were amputation (odds ratio: 14.17), female sex (odds ratio: 2.98) and severe pain (odds ratio: 5.47). Conclusion Medications are an important contributor to in-hospital falls, and the Medication Fall Risk Score can help identify patients at a high risk for falls.
Movement abilities and brain development in preschoolers born very preterm

Aim To examine how healthy preschoolers born very preterm (VPT) with and without significant movement impairments differ from full term (FT) controls in subcortical brain volume measures and white matter diffusion properties. Method A case-control, observational study of fifty-four VPT-born and 32 FT-born children were administered the Movement Assessment Battery for Children – Second Edition (MABC-2) and underwent MRI within 6-months of starting kindergarten. Selected subcortical structural volumes, fractional anisotropy (FA), and mean diffusivity (MD) of selected white matter tracts were compared across VPT children with movement impairments (VPT-abnormal), and VPT and FT children without movement impairments. Results The VPT-abnormal group had higher MD in the corpus callosum and inferior frontal-occipital fasciculus and lower FA in the anterior thalamic radiations, corpus callosum, and cingulum than the FT group. The forceps major was particularly affected in the VPT-abnormal group compared with the VPT and FT groups without movement impairments. Both VPT groups had reduced brainstem and cerebellar white matter volumes and larger lateral ventricles compared to the FT group. Interpretation Movement impairments in healthy VPT preschoolers were associated with more abnormalities in white matter integrity and reduced subcortical brain volumes most likely reflecting a greater extent of white matter damage associated with their very preterm birth.
Serum copeptin might improve risk stratification and management of aortic valve stenosis: a review of pathophysiological insights and practical implications

Over recent decades, the prevalence of aortic valve stenosis (AVS) has been constantly increasing possibly owing to the aging of general population. Severe AVS as determined by an aortic valve area (AVA) of <1 cm2 has been regarded as a serious clinical condition potentially associated with a variety of adverse outcomes, including sudden cardiac death (SCD). However, patients with severe AVS (in the absence of overt high-risk features) are usually evaluated and managed exclusively based on symptomatology or imperfect prognostic tools including exercise testing and biomarkers, with a potential risk of mismanagement, suggesting the need for further objective risk stratifiers in this setting. Within this context, copeptin (C-terminal pro-vasopressin), a novel neurohormone widely considered as the surrogate marker of the arginine–vasopressin (AVP) system, may potentially serve as a reliable prognostic and therapeutic guide (e.g. timing of aortic valvular intervention) in patients with severe AVS largely based on its hemodynamic, fibrogenic as well as autonomic implications in these patients. Accordingly, the present paper aims to discuss clinical and pathophysiological implications of copeptin in the setting of AVS along with a summary of biomarkers and other prognostic tools used in this setting.
Scale Both Confounds and Informs Characterization of Species Coexistence in Empirical Systems

Identifying stable coexistence in empirical systems is notoriously difficult. Here, we show how spatiotemporal structure and complex system dynamics can confound two commonly used stability metrics in empirical contexts: response to perturbation and invasion rate when rare. We use these metrics to characterize stable coexistence across a range of spatial and temporal scales for five simulated models in which the ability of species to coexist in the long term is known a priori and for an empirical old field successional time series. We term the resulting multivariate distribution of metrics a “stability fingerprint. ” In accordance with a wide range of classic and recent studies, our results demonstrate that no combination of empirically tractable metrics or measurements is guaranteed to “correctly” characterize coexistence. However, we also find that heuristic information from the stability fingerprint can be used to broadly characterize dynamic behavior and identify circumstances under which particular combinations of species are likely to persist. Moreover, stability fingerprints appear to be particularly well suited for matching potential theoretical models to observed dynamics. These findings suggest that it may be prudent to shift the focus of empirical stability analysis away from quantifying single measures of stability and toward more heuristic, multivariate characterizations of community dynamics.
Isolation and Identification of Components from Wasabi (Wasabia japonica Matsumura) Flowers and Investigation of Their Antioxidant and Anti-inflammatory Activities

Wasabi (Wasabia japonica Matsumura) is a perennial plant, and its rhizome is widely used as a pungent spice. Wasabi rhizome has been reported to have various physiological activities, but the flower has not been studied in depth. The aim of the present study was to isolate compounds from wasabi flowers and clarify their antioxidant and anti-inflammatory activities. Three phenylpropanoids, one alkaloid and seven flavonoids were isolated from wasabi flowers. Among them, 2"-O-trans sinapoyl isovitexin was identified as a novel compound. Five compounds inhibited 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity, with IC50 values of less than 100 μM. Luteolin isolated in this study was found to inhibit nitric oxide production in macrophage-like J774.1 cells, with an IC50 value of 24.1 ± 4.4 μM. Our results indicate that the phenolic compounds in wasabi flowers are effective ingredients for antioxidant and anti-inflammatory activities. For these reasons, wasabi flowers are expected to be used effectively as a functional food.
An update on the CardioMEMS pulmonary artery pressure sensor

Heart failure (HF) is one of the most important healthcare issues due to its prevalence, high morbidity and mortality, as well as its economic burden. A shift in the healthcare model towards reducing inpatient hospitalizations might have a significant impact on HF-related costs and quality of life. Recently, wireless monitoring has begun to be an essential part of the management in the patient with HF. The CardioMEMS HF system is one of the best examples pertaining to the success in this field. This article will discuss the CardioMEMS HF system and the rationale behind its development.
Diffusion of HRM to Europe and the Role of US MNCs: Introduction to the Special Issue

There has been considerable debate both among scholars and policy makers concerning the extent to which national systems of industrial relations (IR) and human resource management (HRM) systems are converging. In Europe this debate has concerned both convergence within Europe and convergence between European systems and those of non-European states, most notably the USA. The convergence thesis rests essentially on the notion of competitive isomorphism: that is as firms are increasingly faced with similar competitive environments globally, they will adopt similar (optimally efficient) management practices. For example, a significant part of the European convergence debate concerns whether, in Europe, collective employee relations, mediated by representative institutions are being replaced by HRM management systems designed to establish a direct and individualised relationship between organization and employee. Some commentators have attributed this trend to the influence of a model of HRM derived from practices in the USA and increasingly adopted in Europe. Multinational companies (MNCs) have become of particular importance to this thesis. First, they are often seen as an important channel for the transmission of management practices from one country to another, in particular from the USA to Europe. Second, the transferability of management practices from one national context to another is a matter of considerable practical importance for managers in MNCs. Third, the economic importance of large MNCs and their border spanning nature means that their activities have particular salience to legislators and regulators. This special issue addresses these concerns in three ways. First reviews of the development of HRM in the USA and in Germany and evidence on convergence of HRM practices in Europe help us consider both what may be being transmitted from the USA and the evidence for its transmission. Second three papers, provide different kinds of evidence on the convergence or barriers to convergence of HRM practices between Europe and the USA and the role of MNCs in that transmission. Finally, the special issue concludes with three reviews of in all six books each of which are relevant to the concerns of this special issue.
Competition and Information Deception in Online Social Networks

ABSTRACT This study empirically examines the role of competition in determining intentions toward personal information deception (PID) among users of online social network (OSN) sites. PID refers to OSN users intentionally misrepresenting or refusing to disclose online personal information. The research proposes that consumers’ intentions toward PID depend on their desire for online competition with other OSN users, which in turn depends on user appraisals of available status and hedonic benefits, as well as established social norms around competition. An analysis of data gathered from 499 OSN participants (students enrolled at a state university in the southeastern United States) shows that competitive desires represent an important antecedent of PID behavior in OSN contexts. Theoretical and practical implications of the research are also discussed.
Fault Diagnosis in Nonlinear Hybrid Systems

Abstract The problem of fault diagnosis in hybrid systems is investigated. It is assumed that the hybrid systems under consideration consist of a finite automaton, a set of nonlinear difference equations and the so-called mode activator that coordinates the action of the other two parts. To solve the fault diagnosis problem, hybrid residual generators based on both diagnostic observers and parity relations are used. It is shown that the hybrid nature of the system imposes some restrictions on the possibility of creating such generators. Sufficient solvability conditions of the fault diagnosis problem are found. Examples illustrate details of the solution.
Gains through selection for grain yield in a winter wheat breeding program

Increased genetic gains for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selection R values across several selection approaches including phenotypic (PS), marker-based (MS), genomic (GS), and a combination of PS and GS. Five populations of Washington State University (WSU) winter wheat breeding lines evaluated from 2015 to 2018 in Lind and Pullman, WA, USA were used in the study. Selection was conducted by selecting the top 20% of lines based on observed yield (PS strategy), genomic estimated breeding values (GS), presence of yield “enhancing” alleles of the most significant single nucleotide polymorphism (SNP) markers identified from genome-wide association mapping (MS), and high observed yield and estimated breeding values (PS+GS). Overall, PS compared to other individual strategies showed the highest response. However, when combined with GS, a 23% improvement in R for yield was observed, indicating that gains could be improved by complementing traditional PS with GS. Using GS alone as a selection strategy for grain yield should be taken with caution. MS was not that successful in terms of R relative to the other selection approaches. Altogether, we demonstrated that gains through increased response to selection for yield could be achieved in the WSU winter wheat breeding program by implementing different selection strategies either exclusively or in combination.