Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel evolution leading to impaired biofilm formation in invasive Salmonella strains

Pathogenic Salmonella strains that cause gastroenteritis are able to colonize and replicate within the intestines of multiple host species. In general, these strains have retained an ability to form the rdar morphotype, a resistant biofilm physiology hypothesized to be important for Salmonella transmission. In contrast, Salmonella strains that are host-adapted or even host-restricted like Salmonella enterica serovar Typhi, tend to cause systemic infections and have lost the ability to form the rdar morphotype. Here, we investigated the rdar morphotype and CsgD-regulated biofilm formation in two non-typhoidal Salmonella (NTS) strains that caused invasive disease in Malawian children, S. Typhimurium D23580 and S. Enteritidis D7795, and compared them to a panel of NTS strains associated with gastroenteritis, as well as S. Typhi strains. Sequence comparisons combined with luciferase reporter technology identified key SNPs in the promoter region of csgD that either shut off biofilm formation completely (D7795) or reduced transcription of this key biofilm regulator (D23580). Phylogenetic analysis showed that these SNPs are conserved throughout the African clades of invasive isolates, dating as far back as 80 years ago. S. Typhi isolates were negative for the rdar morphotype due to truncation of eight amino acids from the C-terminus of CsgD. We present new evidence in support of parallel evolution between lineages of nontyphoidal Salmonella associated with invasive disease in Africa and the archetypal host-restricted invasive serovar; S. Typhi. We hypothesize that the African invasive isolates are becoming human-adapted and ‘niche specialized’ with less reliance on environmental survival, as compared to gastroenteritis-causing isolates.
Comparison of Segmentation Framework on Digital Microscope Images for Acute Lymphoblastic Leukemia Diagnosis Using RGB and HSV Color Spaces

Image segmentation process is considered the most essential step in image analysis especially in the medical field. In this paper, the color segmentation for acute lymphoblastic leukemia images (ALL) is applied to segment each leukemia image into two clearly defined regions: blasts and background. The ALL segmentation process is based on two different color spaces: RGB color space and HSV color space. The comparison performance between the segmentation methods based on RGB and HSV color spaces are investigated to find the best method to segment the acute lymphoblastic leukemia images. The experimental results show that the segmentation of ALL images based on HSV color space yield better accuracy than RGB color space when compared with the manual segmentation image made by medical experts. Using HSV color space, the shape of blasts in ALL blood samples is closely preserved with segmentation accuracy over 99.00%. However, segmentation based HSV color space was chosen as it produced the highest ALL segmentation rate.
Effects of Long-Term Physical Activity and Diet on Skin Glycation and Achilles Tendon Structure

Advanced glycation end-products (AGEs) accumulate with aging and have been associated with tissue modifications and metabolic disease. Regular exercise has several health benefits, and the purpose of this study was to investigate the effect of regular long-term exercise and diet on skin autofluorescence (SAF) as a measure of glycation and on Achilles tendon structure. In connection with the 2017 European Masters Athletics Championships Stadia, high-level male athletes (n = 194) that had regularly trained for more than 10 years were recruited, in addition to untrained controls (n = 34). SAF was non-invasively determined using an AGE Reader. Achilles tendon thickness and vascular Doppler activity were measured by ultrasonography, and diet was assessed by a questionnaire. There was no significant difference in SAF between the athletes and controls. However, greater duration of exercise was independently associated with lower SAF. Diet also had an effect, with a more “Western” diet in youth being associated with increased SAF. Furthermore, our data demonstrated that greater Achilles tendon thickness was associated with aging and training. Together, our data indicate that long-term exercise may yield a modest reduction in glycation and substantially increase Achilles tendon size, which may protect against injury.
Comment on: Synthesis of New Azo Compounds Based on N-(4-Hydroxyphenyl)maleimide and N-(4-Methylphenyl)maleimide. Molecules 2010, 15, 7498–7508

The synthesis of (E)-phenylazo-3-N-(4-hydroxyphenyl)maleimide (1) using a procedure previously reported in Molecules is deemed to be erroneous. A detailed re-investigation of the earlier work suggests that the spectral data for key intermediates and the final product, (1), was mis-assigned. We conclude that compound (1) was not synthesized, but rather an unusual ring opening reaction of the maleimide unit of the starting material, N-(4-hydroxyphenyl)maleimide (2) leading to the generation of (Z)-4-((4-hydroxyphenyl)amino)-4-oxobut-2-enoic acid, (3) was observed instead. Examination of the original experimental data reveals systematic errors in the reporting of all of the combustion microanalytical data. Overall, the present investigation suggests that errors in the interpretation of spectral data, falsification of analytical data and selective editing of experimental results raise questions over the veracity of the work presented in the original paper.
Anti-aging interventions affect lifespan variability in sex, strain, diet and drug dependent fashion

Decreased forkhead box O1 (FoxO1) activity induces hyperlipidemia and increased PPARγ, leading to hyperlipidemia in association with endoplasmic reticulum (ER) stress. In the liver, aging and comorbidities such as hyperlipidemia and diabetes significantly influence a wide variety of steatosis, but the underlying mechanisms are complex and remain elusive. To establish the modulatory role of FoxO1 and the functional consequences of its altered interaction with PPARγ in the present study, we utilized a cell culture system, aged rats and diabetic db/db mice. We found that, under ER stress, FoxO1 induces PPARγ-mediated lipid accumulation in aged rat livers. Our data showed that the FoxO1-induced hepatic lipid accumulation was negatively regulated by Akt signaling. PPARγ, a key lipogenesis transcription factor, was increased in aged liver, resulting in lipid accumulation via hepatic ER stress under hyperglycemic conditions. We further demonstrated that loss of FoxO1 causes a decline in PPARγ expression and reduces lipid accumulation. In addition, the interaction between FoxO1 and PPARγ was shown to induce hepatic steatosis in aging and db/db mice. We provide evidence that, in aged rats, FoxO1 interaction with PPARγ promotes hepatic steatosis, due to hyperglycemia-induced ER stress, which causes an impairment in Akt signaling, such in aging-related diabetes.
Tuning the optoelectronic properties of PEDOT:PSS-PVP core–shell electrospun nanofibers by solvent-quantum dot doping and phase inversion

In the present study core–shell PEDOT:PSS-polyvinylpirrolidone nanofibers were synthesized by coaxial electrospinning. These fibers were doped with different solvents (dimethylsulphoxide, dimethyl sulfoxide (DMSO), isopropyl alcohol (IPA), and ethylene glycol), and PbS nanoparticles at different concentrations; additionally, the coaxial electrospinning setup process was inverted in order to exchange the phases comprising the core–shell morphology. Experimental results showed that DMSO and IPA solvents produced a change in the PEDOT:PSS phase from its benzoid structure to a more conjugated (quinoid) one. The synthesized samples displayed an increment in the conductance of the composite nanofibers, based on a more conjugated structure of the PEDOT:PSS phase, and a better dispersion of the PbS nanoparticles within the nanofibers; this increment was, under certain synthesis conditions, up to three orders of magnitude higher than in the case of the nanofibers with no solvent, nor nanoparticles, added. Photoresponse also showed a clear increment in the value of the photogenerated current as the concentration of the nanoparticles increased. Inverting the arrangement of the core–shell phases in the nanofibers increased the conductance and the photogenerated current in the cases analyzed. These results show novel evidence on the capability of tuning the conductance and photoresponse of composite core–shell nanofibers, based on the doping of the PEDOT:PSS phase with different solvents and PbS nanoparticles, and the arrangement of the core–shell phases. Tailoring the optoelectronic properties of conductive, flexible nanofibers is a desirable competence in technological areas such as transparent flexible conductors, biosensors and tissue engineering.
Strand-specific affinity of host factor hnRNP C1/C2 guides positive to negative-strand ratio in Coxsackievirus B3 infection

ABSTRACT Coxsackievirus B3 is an enterovirus, with positive-sense single-stranded RNA genome containing ‘Internal Ribosome Entry Site’ (IRES) in the 5ʹUTR. Once sufficient viral proteins are synthesized in the cell from the input RNA, viral template switches from translation to replication to synthesize negative-strand RNA. Inhibition of translation is a key step in regulating this switch as the positive-strand RNA template should be free of ribosomes to enable polymerase movement. In this study, we show how a host protein hnRNP C1/C2 inhibits viral RNA translation. hnRNP C1/C2 interacts with stem-loop V in the IRES and displaces poly-pyrimidine tract binding protein, a positive regulator of translation. We further demonstrate that hnRNP C1/C2 induces translation to replication switch, independently from the already known role of the ternary complex (PCBP2-3CD-cloverleaf RNA). These results suggest a novel function of hnRNP C1/C2 in template switching of positive-strand from translation to replication by a new mechanism. Using mathematical modelling, we show that the differential affinity of hnRNP C1/C2 for positive and negative-strand RNAs guides the final ± RNA ratio, providing first insight in the regulation of the positive to negative-strand RNA ratio in enteroviruses.
Adaptation and Validation of Alternative Healthy Eating Index in Hemodialysis Patients (AHEI-HD) and Its Association with all-Cause Mortality: A Multi-Center Follow-Up Study

A valid diet quality assessment scale has not been investigated in hemodialysis patients. We aimed to adapt and validate the alternative healthy eating index in hemodialysis patients (AHEI-HD), and investigate its associations with all-cause mortality. A prospective study was conducted on 370 hemodialysis patients from seven hospital-based dialysis centers. Dietary data (using three independent 24-hour dietary records), clinical and laboratory parameters were collected. The construct and criterion validity of original AHEI-2010 with 11 items and the AHEI-HD with 16 items were examined. Both scales showed reasonable item-scale correlations and satisfactory discriminant validity. The AHEI-HD demonstrated a weaker correlation with energy intake compared with AHEI-2010. Principle component analysis yielded the plateau scree plot line in AHEI-HD but not in AHEI-2010. In comparison with patients in lowest diet quality (tertile 1), those in highest diet quality (tertile 3) had significantly lower risk for death, with a hazard ratio (HR) and 95% confidence intervals (95%CI) of HR: 0.40; 95%CI: 0.18 - 0.90; p = 0.028, as measured by AHEI-2010, and HR: 0.37; 95%CI: 0.17-0.82; p = 0.014 as measured by AHEI-HD, respectively. In conclusion, AHEI-HD was shown to have greater advantages than AHEI-2010. AHEI-HD was suggested for assessments of diet quality in hemodialysis patients.
Novel Picobirnaviruses in Respiratory and Alimentary Tracts of Cattle and Monkeys with Large Intra- and Inter-Host Diversity

Picobirnaviruses (PBVs) are mostly found in animal alimentary samples. In this study, among 576 respiratory specimens from 476 mammals and 100 chickens, genogroup I PBVs were detected in three cattle and three monkeys, and a genogroup II PBV-positive sample was collected from one cattle specimen. More than one PBV sequence type was observed in two and one genogroup I PBV-positive samples from cattle and monkeys, respectively. Twenty-four complete/near-complete segments 2 (nine from respiratory and 15 from alimentary samples) from the cattle and monkey genogroup I PBVs and one complete segment 2 from the cattle genogroup II PBV were sequenced. Similar to other studies, the cattle PBVs also showed a high diversity. In contrast, the monkey PBVs observed in this study were clustered into three distinct clades. Within each clade, all the sequences showed >99% amino acid identities. This unique phenomenon is probably due to the fact that monkeys in our locality reside in separated troops with minimal inter-troop contact.
Identification and Expression Analyses of the Nitrate Transporter Gene (NRT2) Family Among Skeletonema species (Bacillariophyceae)

High‐affinity nitrate transporters are considered to be the major transporter system for nitrate uptake in diatoms. In the diatom genus Skeletonema, three forms of genes encoding high‐affinity nitrate transporters (NRT2) were newly identified from transcriptomes generated as part of the marine microbial eukaryote transcriptome sequencing project. To examine the expression of each form of NRT2 under different nitrogen environments, laboratory experiments were conducted under nitrate‐sufficient, ammonium‐sufficient, and nitrate‐limited conditions using three ecologically important Skeletonema species: S. dohrnii, S. menzelii, and S. marinoi. Primers were developed for each NRT2 form and species and Q‐RT‐PCR was performed. For each NRT2 form, the three Skeletonema species had similar transcriptional patterns. The transcript levels of NRT2:1 were significantly elevated under nitrogen‐limited conditions, but strongly repressed in the presence of ammonium. The transcript levels of NRT2:2 were also repressed by ammonium, but increased 5‐ to 10‐fold under nitrate‐sufficient and nitrogen‐limited conditions. Finally, the transcript levels of NRT2:3 did not vary significantly under various nitrogen conditions, and behaved more like a constitutively expressed gene. Based on the observed transcript variation among NRT2 forms, we propose a revised model describing nitrate uptake kinetics regulated by multiple forms of nitrate transporter genes in response to various nitrogen conditions in Skeletonema. The differential NRT2 transcriptional responses among species suggest that species‐specific adaptive strategies exist within this genus to cope with environmental changes.
Predictive control : with constraints

1. Introduction to Predictive Control. 2. A Standard Formulation of Predictive Control. 3. Solving Predictive Control Problems. 4. Step Response and Transfer Function Formulations. 5. Tuning. 6. Stability. 7. Robust Predictive Control. 8. Perspectives. 9. Case Studies. 10. The Model Predictive Control Toolbox. References Appendices A. Some Commercial MPC Products B. MATLAB Program basicmpc C. The MPC Toolbox D. Solutions to Problems
Retired Athletes and the Intersection of Food and Body: A Systematic Literature Review Exploring Compensatory Behaviours and Body Change

Background: Retirement from elite sport is a unique transition that influences significant identity, body, and lifestyle changes. This mixed-studies systematic literature review reports on athletic retirement, maladaptive eating behaviours, and body dissatisfaction. Methods: The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed to search the following databases: Web of Science, Scopus, PubMed, EBSCO Host, Sport Discus, and CINAHL. Sixteen studies were synthesised and contrasted through thematic analysis to develop three overarching themes. Results: The three themes that arose include body dissatisfaction and grief, disordered eating and compensation, and long term influence of sporting culture. Maladaptive and compensatory behaviours can arise from sustained athletic identity, body grief, lack of education, and contradictory body ideals. Conclusion: The concept Athletic Body Transition is defined as exploring how a lack of body acceptance may lead to maladaptive behaviours related to food, exercise, and body arising in this transitory period. This review identifies the need for sporting organisations and health professionals to acknowledge this significant transition in regards to athletes’ relationship with food and body subsequent to a sporting career.
Macular Vascular Microcirculation in Eyes With Open-angle Glaucoma Using Different Visual Field Severity Classification Systems

Supplemental Digital Content is available in the text. Precis: We found significant differences in macular vascular microcirculation between normal and glaucomatous eyes using optical coherence tomography angiography (OCTA). Macular vascular microcirculation changes also showed significant correlations with visual field (VF) severity classification systems. Purpose: To correlate VF severity defined by different classification systems and macular vascular microcirculation in eyes with glaucoma using OCTA. Patients and Methods: Twenty normal and 58 open-angle glaucoma (OAG) eyes were scanned using a swept-source OCTA (Plex Elite 9000) and macular vascular microcirculation was measured by calculating the overall blood flux index (BFI) and vessel area density (VAD) over the entire 6×6 mm area excluding the big retinal vessels. Glaucomatous eyes were staged into severity groups based on 4 VF severity classifications: Hodapp-Parrish-Anderson scale, Glaucoma Severity Staging system, ICD-10 glaucoma staging definitions, and VF mean deviation. Central 10-degree VF mean sensitivity (CMS) was calculated based on 24-2 VF. One-way analysis of variance was used to analyze the differences and correlation between macular vascular microcirculation and other clinical parameters. Results: Glaucomatous eyes had significantly lower ganglion cell and inner plexiform layer BFI and VAD (P<0.0001) compared with normal eyes. In OAG patients, BFI and VAD were significantly higher in mild OAG compared with severe OAG with all VF disease severity classification systems (P<0.001). Glaucoma Severity Staging had the highest correlation with changes in macular vascular microcirculation metrics (r=0.734 for BFI; r=0.647 for VAD) and VF CMS had highest correlation with macular vascular microcirculation metrics (r=0.887 for BFI; r=0.903 for VAD). Conclusion: Macular vascular microcirculation metrics detected by OCTA correlate with disease severity in glaucomatous eyes. VF CMS, calculated from only 12 tested central 10-degree points, correlated best with macular OCTA.
An Engineered Hybrid Protein from Dermatophagoides pteronyssinus Allergens Shows Hypoallergenicity

The house dust mite (HDM) Dermatophagoides pteronyssinus is an important risk factor for asthma and rhinitis. Allergen specific immunotherapy that is based on recombinant proteins has been proposed for the safer and more efficient treatment of allergic diseases. The aim of this study was to design and obtain a hybrid protein (DPx4) containing antigenic regions of allergens Der p 1, Der p 2, Der p 7, and Der p 10 from this mite. DPx4 was produced in Escherichia coli and its folding was determined by circular dichroism. Non-denaturing dot-blot, ELISA, basophil activation test, dot blot with monoclonal antibodies, ELISA inhibition, and cysteine protease activity assays were performed. Mice that were immunized with DPx4 were also analyzed. We found that DPx4 had no cysteine protease activity and it showed significantly lower IgE reactivity than Der p 1, Der p 2, and D. pteronyssinus extract. DPx4 induced lower basophil activation than Der p 2 and the allergen extract. Immunized mice produced IgG antibodies that inhibited the binding of allergic patient’s IgE to the allergen extract and induced comparatively higher levels of IL-10 than the extract in peripheral blood mononuclear cells (PBMC) culture. These results suggest that DPx4 has immunological properties that are useful for the development of a mite allergy vaccine.
Proteasome and Autophagy-Mediated Impairment of Late Long-Term Potentiation (l-LTP) after Traumatic Brain Injury in the Somatosensory Cortex of Mice

Traumatic brain injury (TBI) can lead to impaired cognition and memory consolidation. The acute phase (24–48 h) after TBI is often characterized by neural dysfunction in the vicinity of the lesion, but also in remote areas like the contralateral hemisphere. Protein homeostasis is crucial for synaptic long-term plasticity including the protein degradation systems, proteasome and autophagy. Still, little is known about the acute effects of TBI on synaptic long-term plasticity and protein degradation. Thus, we investigated TBI in a controlled cortical impact (CCI) model in the motor and somatosensory cortex of mice ex vivo-in vitro. Late long-term potentiation (l-LTP) was induced by theta-burst stimulation in acute brain slices after survival times of 1–2 days. Protein levels for the plasticity related protein calcium/calmodulin-dependent protein kinase II (CaMKII) was quantified by Western blots, and the protein degradation activity by enzymatical assays. We observed missing maintenance of l-LTP in the ipsilateral hemisphere, however not in the contralateral hemisphere after TBI. Protein levels of CaMKII were not changed but, interestingly, the protein degradation revealed bidirectional changes with a reduced proteasome activity and an increased autophagic flux in the ipsilateral hemisphere. Finally, LTP recordings in the presence of pharmacologically modified protein degradation systems also led to an impaired synaptic plasticity: bath-applied MG132, a proteasome inhibitor, or rapamycin, an activator of autophagy, both administered during theta burst stimulation, blocked the induction of LTP. These data indicate that alterations in protein degradation pathways likely contribute to cognitive deficits in the acute phase after TBI, which could be interesting for future approaches towards neuroprotective treatments early after traumatic brain injury.
The Influence of the Duration of Breastfeeding on the Infant’s Metabolic Epigenome

Nutrition in the postnatal period is associated with metabolic programming. One of the presumed underlying mechanisms involves epigenetic modifications (e.g., DNA methylation). Breastfeeding has an unknown impact on DNA methylation at a young age. Within the Maternal Nutrition and Offspring’s Epigenome (MANOE) study, we assessed the effect of breastfeeding duration on infant growth and buccal methylation in obesity-related genes (n = 101). A significant difference was found between infant growth and buccal RXRA and LEP methylation at 12 months of breastfeeding. For RXRA CpG2 methylation, a positive association was found with duration of breastfeeding (slope = 0.217; 95% confidence interval (CI) 1.03, 0.330; p < 0.001). For RXRA CpG3 and CpG, mean methylation levels were significantly lower when children were breastfed for 4–6 months compared to non-breastfed children (only CpG3), and those breastfed for 7–9 months, 10–12 months, or 1–3 months. On the other hand, higher LEP CpG3 methylation was observed when mothers breastfed 7–9 months (6.1%) as compared to breastfeeding for 1–3 months (4.3%; p = 0.007) and 10–12 months (4.6%; p = 0.04). In addition, we observed that infant weight was significantly lower when children were breastfed for 10–12 months. Breastfeeding duration was associated with epigenetic variations in RXRA and LEP at 12 months and with infant biometry/growth. Our results support the hypothesis that breastfeeding could induce epigenetic changes in infants.