Miracle-dz/UniFAR-FTUs huggingface dataset:
The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease.
On the stabilization of LTI decentralized configurations under quadratically invariant sparsity constraints

In this paper we deal with the problem of decentralized stabilization for linear and time-invariant plants in feedback control configurations that are subject to sparsity constraints. Recent theoretical advances in decentralized control have proved that the class of stabilizing controllers, satisfying a given sparsity constraint admits a convex representation of the Youla-type, provided that the sparsity constraints imposed on the controller are quadratically invariant with respect to the plant. The most useful feature of the aforementioned results is that the sparsity constraints on the controller can be recast as convex constraints on the free parameter, which makes this approach suitable for optimal controller design methods based on convex optimization, numerical algorithms. All these procedures rely indispensably on the fact that some decentralized, stabilizing controller is a priori known, while design procedures for such a decentralized controller to initialize the aforementioned optimization schemes are not yet available. This paper provides necessary and sufficient conditions for such a plant to be stabilizable with a decentralized controller. These conditions are given in terms of the existence of a special type of doubly coprime factorization of the plant, which we call the input/output decoupled, doubly coprime factorization. More importantly, the set of all decentralized stabilizing controllers is characterized via the Youla parametrization. The sparsity constraints on the controller are also recast as convex constraints on the Youla parameter.
Are Heart Failure and Coronary Artery Bypass Surgery Patients Meeting Physical Activity Guidelines?

Purpose: The purpose of this study was to describe subjective and objective physical activity (PA) levels of two groups of cardiovascular patients who were either postcoronary artery bypass graft (CABG) surgery or diagnosed with heart failure (HF). Design: A descriptive comparative design was used for this secondary analysis of data from two prior studies. Methods: A convenience sample of 62 outpatients was used to examine PA objectively (Actiheart accelerometer) and subjectively (PA interview). Findings: Objectively, 33% of CABG patients and no HF patients met PA recommendations of ≥150 minutes per week. Subjectively, 56% of CABG and 38% of HF patients reported meeting PA guidelines recommendations. Conclusions: Few patients in this study met PA guidelines recommendations. Clinical Relevance: Innovative rehabilitation nursing practice strategies are needed (e.g., use of activity trackers, making PA a vital sign) to assist patients in gaining the knowledge and skills to be more active and adhere to PA guidelines recommendations.
RigMesh

The creation of a 3D model is only the first stage of the 3D character animation pipeline. Once a model has been created, and before it can be animated, it must be rigged. Manual rigging is laborious, and automatic rigging approaches are far from real-time and do not allow for incremental updates. This is a hindrance in the real world, where the shape of a model is often revised after rigging has been performed. In this paper, we introduce algorithms and a user-interface for sketch-based 3D modeling that unify the modeling and rigging stages of the 3D character animation pipeline. Our algorithms create a rig for each sketched part in real-time, and update the rig as parts are merged or cut. As a result, users can freely pose and animate their shapes and characters while rapidly iterating on the base shape. The rigs are compatible with the state-of-the-art character animation pipeline; they consist of a low-dimensional skeleton along with skin weights identifying the surface with bones of the skeleton.
Using CVSS in Attack Graphs

Derived from attack models, attack graphs are providing an efficient way to model attack scenarios intended against computer networks. Such graphs are using CVE database in which all known vulnerabilities are gathered. The CVSS framework is aiming to give numeric scores to each vulnerability recorded in the CVE database, which represent its characteristics and quantify its security impacts. In this paper we adapt attack graphs definition in order to be able to use them in conjunction with CVSS framework. The aim of our work is to provide a way to give an assessment of the impact of attacks on the hosts of the target network. This assessment is made using a host damage score and a network damage score, which take into account the characteristics and consequences of each atomic attack constituting an attack scenario.
Structural Requirements for Biological Activity of the Ninth and Tenth FIII Domains of Human Fibronectin*

The ninth and tenth type III domains of fibronectin each contain specific cell binding sequences, RGD in FIII10 and PHSRN in FIII9, that act synergistically in mediating cell adhesion. We investigated the relationship between domain-domain orientation and synergistic adhesive activity of the FIII9 and FIII10 pair of domains. The interdomain interaction of the FIII9-10 pair was perturbed by introduction of short flexible linkers between the FIII9 and FIII10 domains. Incremental extensions of the interdomain link between FIII9 and FIII10 reduced the initial cell attachment, but had a much more pronounced effect on the downstream cell adhesion events of spreading and phosphorylation of focal adhesion kinase. The extent of disruption of cell adhesion depended upon the length of the interdomain linker. Nuclear magnetic resonance spectroscopy of the wild type and mutant FIII9-10 proteins demonstrated that the structure of the RGD-containing loop is unaffected by domain-domain interactions. We conclude that integrin-mediated cell adhesion to the central cell binding domain of fibronectin depends not only upon specific interaction sites, but also on the relative orientation of these sites. These data have implications for the molecular mechanisms by which integrin-ligand interactions are achieved.
Credit Risk Spreads in Local and Foreign Currencies

The paper shows how-in a Merton-type model with bankruptcy-the currency composition of debt changes the risk profile of a company raising a given amount of financing, and thus affects the cost of debt. Foreign currency borrowing is cheaper when the exchange rate is positively correlated with the return on the company's assets, even if the company is not an exporter. Prudential regulations should therefore differentiate among loans depending on the extent to which borrowers have "natural hedges" of their foreign currency exposures.
Polygenic Risk for Schizophrenia Influences Cortical Gyrification in 2 Independent General Populations

Schizophrenia is highly heritable, whereas the effect of each genetic variant is very weak. Since clinical heterogeneity and complexity of schizophrenia is high, considerable effort has been made to relate genetic variants to underlying neurobiological aspects of schizophrenia (endophenotypes). Given the polygenic nature of schizophrenia, our goal was to form a measure of additive genetic risk and explore its relationship to cortical morphology. Utilizing the data from a recent genome-wide association study that included nearly 37 000 cases of schizophrenia, we computed a polygenic risk score (PGRS) for each subject in 2 independent and healthy general populations. We then investigated the effect of polygenic risk for schizophrenia on cortical gyrification calculated from 3.0T structural imaging data in the discovery dataset (N = 315) and replication dataset (N = 357). We found a consistent effect of the polygenic risk for schizophrenia on cortical gyrification in the inferior parietal lobules in 2 independent general-population samples. A higher PGRS was significantly associated with a lower local gyrification index in the bilateral inferior parietal lobles, where case-control differences have been reported in previous studies on schizophrenia. Our findings strongly support the effectiveness of both PGRSs and endophenotypes in establishing the genetic architecture of psychiatry. Our findings may provide some implications regarding individual differences in the genetic risk for schizophrenia to cortical morphology and brain development.
RNA-sequence analysis of human B-cells Material

object identifier (DOIs) and date of initial publication. by PubMed from initial publication. Citations to Advance online articles must include the digital publication). Advance online articles are citable and establish publication priority; they are indexed appeared in the paper journal (edited, typeset versions may be posted when available prior to final Advance online articles have been peer reviewed and accepted for publication but have not yet
Blood-Borne Markers of Fatigue in Competitive Athletes – Results from Simulated Training Camps

Assessing current fatigue of athletes to fine-tune training prescriptions is a critical task in competitive sports. Blood-borne surrogate markers are widely used despite the scarcity of validation trials with representative subjects and interventions. Moreover, differences between training modes and disciplines (e.g. due to differences in eccentric force production or calorie turnover) have rarely been studied within a consistent design. Therefore, we investigated blood-borne fatigue markers during and after discipline-specific simulated training camps. A comprehensive panel of blood-born indicators was measured in 73 competitive athletes (28 cyclists, 22 team sports, 23 strength) at 3 time-points: after a run-in resting phase (d 1), after a 6-day induction of fatigue (d 8) and following a subsequent 2-day recovery period (d 11). Venous blood samples were collected between 8 and 10 a.m. Courses of blood-borne indicators are considered as fatigue dependent if a significant deviation from baseline is present at day 8 (Δfatigue) which significantly regresses towards baseline until day 11 (Δrecovery). With cycling, a fatigue dependent course was observed for creatine kinase (CK; Δfatigue 54±84 U/l; Δrecovery -60±83 U/l), urea (Δfatigue 11±9 mg/dl; Δrecovery -10±10 mg/dl), free testosterone (Δfatigue -1.3±2.1 pg/ml; Δrecovery 0.8±1.5 pg/ml) and insulin linke growth factor 1 (IGF-1; Δfatigue -56±28 ng/ml; Δrecovery 53±29 ng/ml). For urea and IGF-1 95% confidence intervals for days 1 and 11 did not overlap with day 8. With strength and high-intensity interval training, respectively, fatigue-dependent courses and separated 95% confidence intervals were present for CK (strength: Δfatigue 582±649 U/l; Δrecovery -618±419 U/l; HIIT: Δfatigue 863±952 U/l; Δrecovery -741±842 U/l) only. These results indicate that, within a comprehensive panel of blood-borne markers, changes in fatigue are most accurately reflected by urea and IGF-1 for cycling and by CK for strength training and team sport players.
Replicating and Re-Evaluating the Theory of Relative Defect-Proneness

A good understanding of the factors impacting defects in software systems is essential for software practitioners, because it helps them prioritize quality improvement efforts (e.g., testing and code reviews). Defect prediction models are typically built using classification or regression analysis on product and/or process metrics collected at a single point in time (e.g., a release date). However, current defect prediction models only predict if a defect will occur, but not when, which makes the prioritization of software quality improvements efforts difficult. To address this problem, Koru et al. applied survival analysis techniques to a large number of software systems to study how size (i.e., lines of code) influences the probability that a source code module (e.g., class or file) will experience a defect at any given time. Given that 1) the work of Koru et al. has been instrumental to our understanding of the size-defect relationship, 2) the use of survival analysis in the context of defect modelling has not been well studied and 3) replication studies are an important component of balanced scholarly debate, we present a replication study of the work by Koru et al. In particular, we present the details necessary to use survival analysis in the context of defect modelling (such details were missing from the original paper by Koru et al.). We also explore how differences between the traditional domains of survival analysis (i.e., medicine and epidemiology) and defect modelling impact our understanding of the size-defect relationship. Practitioners and researchers considering the use of survival analysis should be aware of the implications of our findings.
Microparticles during long-term follow-up after acute myocardial infarction

Summary Microparticles (MPs) are formed from platelets (PMPs), endothelial cells (EMPs) and monocytes (MMPs), and in acute myocardial infarction (MI), there is an increase of MPs in the culprit artery. In this study MPs were evaluated in whole blood in 105 patients with MI at five time-points during a two-year follow-up (FU). Patients with non-ST-elevated MI had higher concentrations of CD41+MPs compared to ST-elevated MI patients (p=0.024). The concentrations of PMPs in whole blood increased during the time period (p<0.001), but no significant change over time was found for EMPs and MMPs. CD62P+MP counts were higher in MI patients with diabetes (p=0.020), and patients with hypertension had increased levels of CD14+MPs (p=0.004). The amount of CD62P+TF+MPs increased significantly during FU (p<0.001). Patients with atherosclerosis in three arterial beds, i. e. coronary, carotid and peripheral arteries, had lower concentrations of CD62P+TF+MPs (p=0.035) and CD144+TF+MPs (p=0.004) compared to patients with atherosclerosis in one or two arterial beds. Higher concentrations of CD62P+MPs early after MI were associated with an increased risk of cardiovascular events during FU, hazard ratio 3.32 (95%CI1.20–9.31). Only small variations in PMP, EMP and MMP concentrations were found during long-term FU after MI and their levels seem to reflect the underlying cardiovascular disease rather than the acute MI. PMPs expressing P-selectin might be a promising biomarker for predicting future cardiovascular events, but further studies are needed to confirm these results. Supplementary Material to this article is available online at www.thrombosis-online.com.
Healthcare provider relational quality is associated with better self-management and less treatment burden in people with multiple chronic conditions

Purpose Having multiple chronic conditions (MCCs) can lead to appreciable treatment and self-management burden. Healthcare provider relational quality (HPRQ) – the communicative and interpersonal skill of the provider – may mitigate treatment burden and promote self-management. The objectives of this study were to 1) identify the associations between HPRQ, treatment burden, and psychosocial outcomes in adults with MCCs, and 2) determine if certain indicators of HPRQ are more strongly associated than others with these outcomes. Patients and methods This is a cross-sectional survey study of 332 people with MCCs. Patients completed a 7-item measure of HPRQ and measures of treatment and self-management burden, chronic condition distress, self-efficacy, provider satisfaction, medication adherence, and physical and mental health. Associations between HPRQ, treatment burden, and psychosocial outcomes were determined using correlational analyses and independent samples t-tests, which were repeated in item-level analyses to explore which indicators of HPRQ were most strongly associated with the outcomes. Results Most respondents (69%) were diagnosed with ≥3 chronic conditions. Better HPRQ was found to be associated with less treatment and self-management burden and better psychosocial outcomes (P<0.001), even after controlling for physical and mental health. Those reporting 100% adherence to prescribed medications had higher HPRQ scores than those reporting less than perfect adherence (P<0.001). HPRQ items showing the strongest associations with outcomes were “my healthcare provider spends enough time with me”, “my healthcare provider listens carefully to me”, and “I have trust in my healthcare provider”. Conclusion Good communication and interpersonal skills of healthcare providers may lessen feelings of treatment burden and empower patients to feel confident in their self-management. Patient trust in the provider is an important element of HPRQ. Educating healthcare providers about the importance of interpersonal and relational skills could lead to more patient-centered care.
The forest or the trees: preference for global over local image processing is reversed by prior experience in honeybees

Traditional models of insect vision have assumed that insects are only capable of low-level analysis of local cues and are incapable of global, holistic perception. However, recent studies on honeybee (Apis mellifera) vision have refuted this view by showing that this insect also processes complex visual information by using spatial configurations or relational rules. In the light of these findings, we asked whether bees prioritize global configurations or local cues by setting these two levels of image analysis in competition. We trained individual free-flying honeybees to discriminate hierarchical visual stimuli within a Y-maze and tested bees with novel stimuli in which local and/or global cues were manipulated. We demonstrate that even when local information is accessible, bees prefer global information, thus relying mainly on the object's spatial configuration rather than on elemental, local information. This preference can be reversed if bees are pre-trained to discriminate isolated local cues. In this case, bees prefer the hierarchical stimuli with the local elements previously primed even if they build an incorrect global configuration. Pre-training with local cues induces a generic attentional bias towards any local elements as local information is prioritized in the test, even if the local cues used in the test are different from the pre-trained ones. Our results thus underline the plasticity of visual processing in insects and provide new insights for the comparative analysis of visual recognition in humans and animals.
Characterization of the proteasome interaction with the Sec61 channel in the endoplasmic reticulum

Biogenesis of secretory proteins requires their translocation into the endoplasmic reticulum (ER) through the Sec61 channel. Proteins that fail to fold are transported back into the cytosol and are degraded by proteasomes. For many substrates this retrograde transport is affected by mutations in the Sec61 channel, and can be promoted by ATP and the 19S regulatory particle of the proteasome, which binds directly to the Sec61 channel via its base. Here, we identify mutations in SEC61 which reduce proteasome binding to the channel, and demonstrate that proteasomes and ribosomes bind differently to cytosolic domains of the channel. We found that Sec63p and BiP coprecipitate with ER-associated proteasomes, but Sec63p does not contribute to proteasome binding to the ER. The 19S base contains six AAA-ATPase subunits (Rpt proteins) that have non-equivalent functions in proteasome-mediated protein turnover and form a hetero-hexamer. Mutations in the ATP-binding sites of individual Rpt proteins all reduced the affinity of 19S complexes for the ER, suggesting that the 19S base in the ATP-bound conformation docks at the Sec61 channel.
The effects of efficacy beliefs on training outcomes : looking beyond self-efficacy

Previous research has shown that self-efficacy has an important influence on the effects of training. The present research broadens the view on efficacy beliefs by taking into account the role of collective efficacy and response efficacy on training outcomes. Additionally it explores the influence of supervisors on follower efficacy beliefs. To investigate these proposed relations, in the first study a survey was distributed to police officers before and after participation in a group training, in the second study follow up interviews were conducted. Although the results of the first study do not confirm the proposed relations, there are signs that response efficacy and collective efficacy may play a role, but more research is necessary to further explore the exact role of these efficacy beliefs. The second study showed that supervisors did influence the efficacy beliefs, the influence of vicarious experience was however much stronger. These findings can be attributed to the specific type of training, since most participants knew the training from national television. Future research should focus on further exploring the influence of response and collective efficacy and measuring the influence of supervisors on efficacy beliefs in a direct manner.
Single-Cell Analysis of Innate Cytokine Responses to Pattern Recognition Receptor Stimulation in Children across Four Continents

Innate immunity instructs adaptive immunity, and suppression of innate immunity is associated with an increased risk for infection. We showed previously that whole-blood cellular components from a cohort of South African children secreted significantly lower levels of most cytokines following stimulation of pattern recognition receptors compared with whole blood from cohorts of Ecuadorian, Belgian, or Canadian children. To begin dissecting the responsible molecular mechanisms, we set out to identify the relevant cellular source of these differences. Across the four cohorts represented in our study, we identified significant variation in the cellular composition of whole blood; however, a significant reduction in the intracellular cytokine production on the single-cell level was only detected in South African children’s monocytes, conventional dendritic cells, and plasmacytoid dendritic cells. We also uncovered a marked reduction in polyfunctionality for each of these cellular compartments in South African children compared with children from the other continents. Together, our data identify differences in cell composition, as well as profoundly lower functional responses of innate cells, in our cohort of South African children. A possible link between altered innate immunity and increased risk for infection or lower response to vaccines in South African infants needs to be explored.