Miracle-dz/UniFAR-FTUs huggingface dataset:
On Identifying Significant Edges in Graphical Models

Graphical models, and in particular Bayesian networks, have been widely used to investigate data in the biological and healthcare domains. This can be attributed to the recent explosion of high-throughput data across these domains and the importance of understanding the causal relationships between the variables of interest. However, classic model validation techniques for identifying significant edges rely on the choice of an ad-hoc threshold, which is non-trivial and can have a pronounced impact on the conclusions of the analysis. In this paper, we overcome this limitation by proposing simple, statistically-motivated approach based on L1 approximation for identifying significant edges. The effectiveness of the proposed approach is demonstrated on gene expression data sets across two published experimental studies.
The Novel Cerato-Platanin-Like Protein FocCP1 from Fusarium oxysporum Triggers an Immune Response in Plants

Panama disease, or Fusarium wilt, the most serious disease in banana cultivation, is caused by Fusarium oxysporum f. sp. cubense (FOC) and has led to great economic losses worldwide. One effective way to combat this disease is by enhancing host plant resistance. The cerato-platanin protein (CPP) family is a group of small secreted cysteine-rich proteins in filamentous fungi. CPPs as elicitors can trigger the immune system resulting in defense responses in plants. In this study, we characterized a novel cerato-platanin-like protein in the secretome of Fusarium oxysporum f. sp. cubense race 4 (FOC4), named FocCP1. In tobacco, the purified recombinant FocCP1 protein caused accumulation of reactive oxygen species (ROS), formation of necrotic reaction, deposition of callose, expression of defense-related genes, and accumulation of salicylic acid (SA) and jasmonic acid (JA) in tobacco. These results indicated that FocCP1 triggered a hypersensitive response (HR) and systemic acquired resistance (SAR) in tobacco. Furthermore, FocCP1 enhanced resistance tobacco mosaic virus (TMV) disease and Pseudomonas syringae pv. tabaci 6605 (Pst. 6605) infection in tobacco and improved banana seedling resistance to FOC4. All results provide the possibility of further research on immune mechanisms of plant and pathogen interactions, and lay a foundation for a new biological strategy of banana wilt control in the future.
Physicochemical Parameters of Real Wastewater Originating from a Plant Protection Products Factory and Modification of the QuEChERS Method for Determination of Captan

The aim of this study was the modification and application of the QuEChERS method for the preparation and purification of samples in order to determine the level of captan in real wastewater originating from a plant protection products factory which was characterized by a significant content of organic substances [Chemical Oxygen Demand (COD) = 856 ± 128 mg O2/L and Total Organic Carbon (TOC) = 62 ± 9 mg/L]. The optimization of the method consisted of the selection of solvents used for the extraction of captan from wastewater and also sorbents used to purify the extracts by the dispersion of a solid phase extraction technique (dSPE). Two steps were used: extraction and clean-up. In the extraction step, acetonitrile was replaced by anacetonitrile:acetone mixture. In the clean-up step by the dSPE, five sorbents were tested: Florisil®, aluminum oxide (Al2O3), zirconium oxide (ZrO2), silicon oxide (SiO2) and PSA (primary and secondary amine). Concentrations of captan in wastewater extracts were determined by gas chromatography (GC) combined with electron capture detection (μECD). The best recovery parameters and precision of the method were obtained for samples purified using ZrO2 (recovery 98% and precision expressed as relative standard deviation RSD 8%) and Florisil® (recovery 96%, RSD 9%). Limits of detection (LOD) and quantification (LOQ) for determination of captan in diluted extract of wastewater were 0.003 and 0.01 mg/L, respectively. Matrix effects were in the range of −69% to −44% for samples purified by ZrO2 and Florisil®, respectively. The modified and optimized method was applied for fast and simple determination of captan levels in real industrial wastewater samples, in which the concentration of captan in diluted extract was determined to be 4.0 ± 0.3 mg/L.
Transient Intraocular Pressure Fluctuations: Source, Magnitude, Frequency, and Associated Mechanical Energy

Purpose To characterize intraocular pressure (IOP) dynamics by identifying the sources of transient IOP fluctuations and quantifying the frequency, magnitude, associated cumulative IOP-related mechanical energy, and temporal distribution. Methods IOP was monitored at 500 Hz for periods of 16 to 451 days in nine normal eyes of six conscious, unrestrained nonhuman primates using a validated, fully implanted wireless telemetry system. IOP transducers were calibrated every two weeks via anterior chamber cannulation manometry. Analysis of time-synchronized, high-definition video was used to identify the sources of transient IOP fluctuations. Results The distribution of IOP in individual eyes is broad, and changes at multiple timescales, from second-to-second to day-to-day. Transient IOP fluctuations arise from blinks, saccades, and ocular pulse amplitude and were as high as 14 mm Hg (>100%) above momentary baseline. Transient IOP fluctuations occur ∼10,000 times per waking hour, with ∼2000 to 5000 fluctuations per hour greater than 5 mm Hg (∼40%) above baseline. Transient IOP fluctuations account for up to 17% (mean of 12%) of the total cumulative IOP-related mechanical energy that the eye must withstand during waking hours. Conclusions Transient IOP fluctuations occur frequently and comprise a large and significant portion of the total IOP loading in the eye and should, therefore, be considered in future studies of cell mechanotransduction, ocular biomechanics, and/or clinical outcomes where transient IOP fluctuations may be important. If IOP dynamics are similar in humans, clinical snapshot IOP measurements are insufficient to capture true IOP.
IMAGE ANALYSIS OF SOYBEAN LEAF DISEASES USING METADATA

The aim of this paper was to create an integrated environment with routines in C Language to image analysis of foliar diseases of soybean and extraction of metadata to describe aspects of the image and also verify if the leaf is sick or not. For this we have defined one standard of metadata, it was utilized the Canny Algorithm to analyze the image and created a prototype interface to see the results. It was possible to detect the edge of images submitted to the algorithm, however there was a necessity to better filtering of noise.
A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees

Significance Phenotypic trait variation can be linked to genomic sequence variation. These differences range from a single nucleotide to larger insertion and deletion (indel) of chromosomal segments. Indels can change the copy number of affected genes, which can create complex phenotypic trait variation through effects on gene expression. For example, gene dosage variation has been associated with various human chronic diseases. Here we systematically explored the effect of induced gene dosage variation on quantitative trait variation in Populus. We show that gene dosage variation at specific chromosomal locations and also gene dosage balance at a global genomic scale are both major determinants of quantitative trait variation in a plant species. Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.
Antecedents of attachment states of mind in normative-risk and high-risk caregiving: cross-race and cross-sex generalizability in two longitudinal studies.

BACKGROUND Longitudinal investigations of relatively large typical-risk (e.g., Booth-LaForce & Roisman, 2014) and higher-risk samples (e.g., Raby et al., 2017; Roisman et al., 2017) have produced evidence consistent with the claim that attachment states of mind in adolescence and young adulthood, as measured by the Adult Attachment Interview (AAI), are associated with the quality of caregiving experienced during childhood. None of these studies, however, has examined whether such associations are consistent across sex and/or race, as would be expected in light of the sensitivity hypothesis of attachment theory. METHODS We examine whether sex or race moderates previously reported links between caregiving and AAI states of mind in two longitudinal studies (pooled N = 1,058) in which caregiving was measured either within (i.e., observed [in]sensitive care) or outside (i.e., childhood maltreatment) of the normative range of caregiving experiences. RESULTS Hierarchical moderated regression analyses in both longitudinal cohorts provided evidence that maternal insensitivity and experiences of maltreatment were prospectively associated with dismissing and preoccupied states of mind in adolescence, as hypothesized. Moreover, these associations were generally comparable in magnitude for African American and White/non-Hispanic participants and were not conditional on participants' biological sex. CONCLUSIONS Both maternal insensitivity and the experience of maltreatment increased risk for insecure attachment states of mind in adolescence. Moreover, our analyses provided little evidence that either participant race or participant sex assigned at birth moderated these nontrivial associations between measures of the quality of experienced caregiving and insecure attachment states of mind in adolescence. These findings provide support for the sensitivity hypothesis of attachment theory and inform the cultural universality hypothesis of attachment processes.
Effects of utterance rate and length on the spatiotemporal index in Parkinson’s disease

Abstract Purpose: To characterise labial articulatory pattern variability using the spatiotemporal index (STI) in speakers with idiopathic Parkinson’s disease (PD) across different speaking rates and syllable-sentence conditions compared to age- and sex-matched healthy controls. Method: Ten speakers with mild–severe idiopathic PD and 10 controls produced “pa” and the Rainbow Passage at slow, typical and fast speech rates. Upper lip and lower lip kinematics were digitised during a motion capture system. Data were analysed using linear mixed modelling. Result: Regardless of the participant group, a high STI value was observed in the fast speech rate for the “pa” syllable condition, particularly for movements of the lower lip. As utterance rate increased, the control group showed the highest variability, followed by PD OFF and PD ON conditions. Syllable “pa” showed a greater STI value compared to both the first and second utterance of Rainbow Passage. Conclusion: PD manifests sufficient residual capacity to achieve near-normal motor compensation to preserve the consistency of lower lip movements during speech production. The lack of a significant difference in lip STI values between ON-OFF medication states suggests that dopaminergic treatment does not influence stability of speech for individuals with mild-moderate stage PD.
Relationship between Individual Social Capital and Cognitive Function among Older Adults by Gender: A Cross-Sectional Study

As it is not easy to modify lifestyle, it is important to examine the effect of social capital (SC), which does not require behavior modifications, on dementia prevention. This study aimed to clarify gender differences in the relationship between cognitive function and individual SC among people living in a rural area in Japan. We used the Shimane Center for Community-based Healthcare Research and Education (CoHRE) study data from 2011 to conduct a cross-sectional analysis. The analysis included 491 participants, aged 40 years or older, who had undergone medical examinations in two rural towns in Japan. Both cognitive SC and structural SC were measured. Multivariate logistic regression analysis was conducted to estimate the odds ratios (OR) and 95% confidence interval (CI) for cognitive function levels as binary outcomes. We found a significant association between cognitive function and individual cognitive SC in men (OR: 3.11, 95% CI: 1.43–6.78), and found that cognitive function was associated with structural SC in women (OR: 1.89, 95% CI: 1.08–3.31). This study showed that the relationship between cognitive function and individual SC differed by gender. These results suggest that it is important to approach dementia prevention differently in men and women.
Structure and ligand binding of the glutamine-II riboswitch

Abstract We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.
Strategy synthesis : resolving strategy paradoxes to create competitive advantage : text and readings

This is the highly anticipated new edition of the market-leading introduction to strategic management from Bob de Wit (Maastricht School of Management) and Ron Meyer (TiasNimbas Business School). Widely acclaimed for its ability to foster creative, non-prescriptive and global strategic thinking amongst students, "Strategy 4e" builds on the major international success of the prior edition. Developed from wide-ranging market feedback, all of the short and long cases have been replaced or wholly updated with dozens of new cases crafted by the authors and several international contributors. From Google to KPMG, ING Direct to the Metropolitan Opera, the text now features an unparalleled range of organizations with rich settings for students to develop key strategy skills and understanding. New readings, including coverage of hot topics like Blue Ocean Strategy, ensure the theory remains cutting-edge, while a boosted set of lecturer resources makes this the complete package for 21st century strategy courses.
Luminescence- and Fluorescence-Based Complementation Assays to Screen for GPCR Oligomerization: Current State of the Art

G protein-coupled receptors (GPCRs) have the propensity to form homo- and heterodimers. Dysfunction of these dimers has been associated with multiple diseases, e.g., pre-eclampsia, schizophrenia, and depression, among others. Over the past two decades, considerable efforts have been made towards the development of screening assays for studying these GPCR dimer complexes in living cells. As a first step, a robust in vitro assay in an overexpression system is essential to identify and characterize specific GPCR–GPCR interactions, followed by methodologies to demonstrate association at endogenous levels and eventually in vivo. This review focuses on protein complementation assays (PCAs) which have been utilized to study GPCR oligomerization. These approaches are typically fluorescence- and luminescence-based, making identification and localization of protein–protein interactions feasible. The GPCRs of interest are fused to complementary fluorescent or luminescent fragments that, upon GPCR di- or oligomerization, may reconstitute to a functional reporter, of which the activity can be measured. Various protein complementation assays have the disadvantage that the interaction between the reconstituted split fragments is irreversible, which can lead to false positive read-outs. Reversible systems offer several advantages, as they do not only allow to follow the kinetics of GPCR–GPCR interactions, but also allow evaluation of receptor complex modulation by ligands (either agonists or antagonists). Protein complementation assays may be used for high throughput screenings as well, which is highly relevant given the growing interest and effort to identify small molecule drugs that could potentially target disease-relevant dimers. In addition to providing an overview on how PCAs have allowed to gain better insights into GPCR–GPCR interactions, this review also aims at providing practical guidance on how to perform PCA-based assays.
Infection‐induced endothelial amyloids impair memory

Patients with nosocomial pneumonia exhibit elevated levels of neurotoxic amyloid and tau proteins in the cerebrospinal fluid (CSF). In vitro studies indicate that pulmonary endothelium infected with clinical isolates of either Pseudomonas aeruginosa, Klebsiella pneumoniae, or Staphylococcus aureus produces and releases cytotoxic amyloid and tau proteins. However, the effects of the pulmonary endothelium‐derived amyloid and tau proteins on brain function have not been elucidated. Here, we show that P. aeruginosa infection elicits accumulation of detergent insoluble tau protein in the mouse brain and inhibits synaptic plasticity. Mice receiving endothelium‐derived amyloid and tau proteins via intracerebroventricular injection exhibit a learning and memory deficit in object recognition, fear conditioning, and Morris water maze studies. We compared endothelial supernatants obtained after the endothelia were infected with P. aeruginosa possessing an intact [P. aeruginosa isolated from patient 103 (PA103) supernatant] or defective [mutant strain of P. aeruginosa lacking a functional type 3 secretion system needle tip complex (ΔPcrV) supernatant] type 3 secretion system. Whereas the PA103 supernatant impaired working memory, the ΔPcrV supernatant had no effect. Immunodepleting amyloid or tau proteins from the PA103 supernatant with the A11 or T22 antibodies, respectively, overtly rescued working memory. Recordings from hippocampal slices treated with endothelial supernatants or CSF from patients with or without nosocomial pneumonia indicated that endothelium‐derived neurotoxins disrupted the postsynaptic synaptic response. Taken together, these results establish a plausible mechanism for the neurologic sequelae consequent to nosocomial bacterial pneumonia. —Balczon, R. , Pittet, J.‐F. , Wagener, B. M. , Moser, S. A. , Voth, S. , Vorhees, C. V. , Williams, M. T. , Bridges, J. P., Alvarez, D. F. , Koloteva, A. , Xu, Y. , Zha, X. ‐M. , Audia, J. P., Stevens, T. , Lin, M. T. Infection‐induced endothelial amyloids impair memory. FASEB J. 33, 10300–10314 (2019). www.fasebj. org
Improved Two-Party ID-Based Authenticated Key Agreement Protocol

공개된 네트워크 상에서 통신하는 두 참여자를 위한 안전한 인증된 키 동의 프로토콜(AKA)을 고안하는 것은 중요한 연구이다. McCullagh등은 단일 도메인과 두 개의 도메인을 위해 사용될 수 있는 제 3자 키 기탁(escrow)과 제 3자 키기탁이 필요없는 두가지 속성을 지원하는 두 참여자간 식별자 기반 인증된 키동의 프로토콜을 제안하였다. 본 논문은 McCullagh등의 두 개의 도메인을 위한 프토토콜이 가장 공격(masquerading attack)에 취약함으로서 주장하는 보안을 만족하지 않음을 보인다. McCullag등의 기법에 존재하는 가장 공격은 충분한 개체 인증과 무결성 보증의 부족 때문에 발생한다. McCullagh등의 프로토콜 문제점을 해결하기 위해서 인증절차에 서명 원리가 포함된 효율적인 검증가능한 키 동의 프로토콜을 제안한다.
Prevalence of underweight in children and adolescents (aged 3–18 years) from Kraków (Poland) in 1983 and 2010

Abstract Objective: To estimate the changes in the prevalence of underweight among girls and boys living in Kraków that occurred between 1983 and 2010. Design: The study was based on two cross-sectional surveys conducted in 1983 and 2010. The prevalence of underweight was estimated based on the International Obesity Task Force (IOTF) and Centers for Disease Control and Prevention (CDC) cut-off points. Setting: The study was conducted in Kraków, Poland. Participants: Children aged 3–18 years (n 5245). Results: Between 1983 and 2010 the prevalence of underweight decreased in both sexes. Using the IOTF criteria, the prevalence of underweight decreased from 10·5 to 10·3 % in girls and from 8·9 to 7·5 % in boys, but it was still higher in girls than in boys. According to the CDC criteria, this prevalence decreased from 5·1 to 4·4 % and from 5·9 to 4·6 %, respectively, and was slightly lower in girls. According to the IOTF criteria, underweight prevalence increased slightly during childhood in both sexes while according to the CDC criteria it decreased in boys and did not change in girls. Among juveniles and adolescents, it decreased regardless of the method used. Conclusions: The frequency of underweight in the population of children and adolescents from Kraków changed slightly in 1983 and 2010 despite economic and social changes. Depending on the cut-off points used, not only the magnitude but also the direction of changes between series could be different. In order to aid global monitoring, the prevalence of underweight as well as overweight should always be evaluated by several methods.
SOME PROBLEMS OF VIRTUAL OBJECT MODELING FOR VIRTUAL REALITY APPLICATIONS

The aim of this paper is to dedicate some information about specific problem with modeling virtual reality worlds and to show some problem solutions. The first part describes basic problems of subtraction of polygon object. In the next part are described used formulas and mathematic laws implemented by modeling of virtual objects for virtual reality system PROLAND, which is developed on DCI FEI TU Kosice.
Biofabrication of phenotypic pulmonary fibrosis assays

Biofabrication techniques have enabled the formation of complex models of many biological tissues. We present a framework to contextualize biofabrication techniques within a disease modeling application. Fibrosis is a progressive disease interfering with tissue structure and function, which stems from an aberrant wound healing response. Epithelial injury and clot formation lead to fibroblast invasion and activation, followed by contraction and remodeling of the extracellular matrix. These stages have healthy wound healing variants in addition to the pathogenic analogs that are seen in fibrosis. This review evaluates biofabrication of a variety of phenotypic cell-based fibrosis assays. By recapitulating different contributors to fibrosis, these assays are able to evaluate biochemical pathways and therapeutic candidates for specific stages of fibrosis pathogenesis. Biofabrication of these culture models may enable phenotypic screening for improved understanding of fibrosis biology as well as improved screening of anti-fibrotic therapeutics.