Miracle-dz/UniFAR-FTUs huggingface dataset:
An Exported Heat Shock Protein 40 Associates with Pathogenesis-Related Knobs in Plasmodium falciparum Infected Erythrocytes

Cell surface structures termed knobs are one of the most important pathogenesis related protein complexes deployed by the malaria parasite Plasmodium falciparum at the surface of the infected erythrocyte. Despite their relevance to the disease, their structure, mechanisms of traffic and their process of assembly remain poorly understood. In this study, we have explored the possible role of a parasite-encoded Hsp40 class of chaperone, namely PFB0090c/PF3D7_0201800 (KAHsp40) in protein trafficking in the infected erythrocyte. We found the gene coding for PF3D7_0201800 to be located in a chromosomal cluster together with knob components KAHRP and PfEMP3. Like the knob components, KAHsp40 too showed the presence of PEXEL motif required for transport to the erythrocyte compartment. Indeed, sub-cellular fractionation and immunofluorescence analysis (IFA) showed KAHsp40 to be exported in the erythrocyte cytoplasm in a stage dependent manner localizing as punctuate spots in the erythrocyte periphery, distinctly from Maurer’s cleft, in structures which could be the reminiscent of knobs. Double IFA analysis revealed co-localization of PF3D7_0201800 with the markers of knobs (KAHRP, PfEMP1 and PfEMP3) and components of the PEXEL translocon (Hsp101, PTEX150). KAHsp40 was also found to be in a complex with KAHRP, PfEMP3 and Hsp101 as confirmed by co-immunoprecipitation assay. Our results suggest potential involvement of a parasite encoded Hsp40 in chaperoning knob assembly in the erythrocyte compartment.
Nerve sheath tumors in an isolated goldfish population.

Approximately 8–10 per cent of the goldfish in an urban lagoon exhibit nerve-sheath tumors. Of 53 tumor-bearing fish, 31 had two or more tumors. These were classified as neurilemomas and neurofibromas; seven were histologically malignant. Melanophores were present in several of the neoplasms; the question of the neural crest origin of both the pigment cells and the Schwann cells was considered. All the tumors were subcutaneous with two exceptions: in one fish two large neurilemomas occupied the abdominal cavity, in another a neurilemoma arose from the second right gill arch. Growth in tissue culture was often abundant. Acquisition of the morphological characteristics of a macrophage by nerve sheath cells growing in vitro as reported by Weiss is also suggested in cultures of the neoplastic Schwann cells of the goldfish. The auto-, homoio-, and heterologous transplants of this tumor failed to grow, with the exception of a single autotransplant to the anterior chamber of the eye. Attempts to determine the presence of a carcinogenic agent by transmission experiments, including infestation with a parasitic copepod, were likewise negative. Congenital anomalies including polycystic kidneys, keratoconus, and buphthalmos occurred in some of the tumor-bearing fish as well as in otherwise normal goldfish from the same pond. The frequency of congenital lesions served to emphasize the fact that the fish were an isolated population probably subjected to considerable inbreeding and therefore had some genetic homogeneity. Although 2-year-old offspring of a pair of tumor-bearing fish are still free of tumors, a possible genetic background for both the tumors and the anomalies should be considered and a comparison drawn with von Recklinghausen's neurofibromatosis in man.
Rapid Analysis of Vessel Elements (RAVE): A Tool for Studying Physiologic, Pathologic and Tumor Angiogenesis

Quantification of microvascular network structure is important in a myriad of emerging research fields including microvessel remodeling in response to ischemia and drug therapy, tumor angiogenesis, and retinopathy. To mitigate analyst-specific variation in measurements and to ensure that measurements represent actual changes in vessel network structure and morphology, a reliable and automatic tool for quantifying microvascular network architecture is needed. Moreover, an analysis tool capable of acquiring and processing large data sets will facilitate advanced computational analysis and simulation of microvascular growth and remodeling processes and enable more high throughput discovery. To this end, we have produced an automatic and rapid vessel detection and quantification system using a MATLAB graphical user interface (GUI) that vastly reduces time spent on analysis and greatly increases repeatability. Analysis yields numerical measures of vessel volume fraction, vessel length density, fractal dimension (a measure of tortuosity), and radii of murine vascular networks. Because our GUI is open sourced to all, it can be easily modified to measure parameters such as percent coverage of non-endothelial cells, number of loops in a vascular bed, amount of perfusion and two-dimensional branch angle. Importantly, the GUI is compatible with standard fluorescent staining and imaging protocols, but also has utility analyzing brightfield vascular images, obtained, for example, in dorsal skinfold chambers. A manually measured image can be typically completed in 20 minutes to 1 hour. In stark comparison, using our GUI, image analysis time is reduced to around 1 minute. This drastic reduction in analysis time coupled with increased repeatability makes this tool valuable for all vessel research especially those requiring rapid and reproducible results, such as anti-angiogenic drug screening.
Genetic polymorphisms in the renin-angiotensin-aldosterone system associated with expression of left ventricular hypertrophy in hypertrophic cardiomyopathy: a study of five polymorphic genes in a family with a disease causing mutation in the myosin binding protein C gene

Background: Hypertrophic cardiomyopathy (HCM) is an inherited disease of the sarcomere characterised clinically by myocardial hypertrophy and its consequences. Phenotypic expression is heterogeneous even within families with the same aetiological mutation and may be influenced by additional genetic factors. Objective: To determine the influence of genetic polymorphisms of the renin-angiotensin-aldosterone system (RAAS) on ECG and two dimensional echocardiographic left ventricular hypertrophy (LVH) in genetically identical patients with HCM. Patients and methods: Polymorphisms of five RAAS components were determined in 26 gene carriers from a single family with HCM caused by a previously identified myosin binding protein C mutation. Genotypes associated with a higher activation status of the RAAS were labelled “pro-LVH genotypes”. Results: There was a non-biased distribution of pro-LVH genotypes in the gene carriers. Those without pro-LVH genotypes did not manifest cardiac hypertrophy whereas gene carriers with pro-LVH genotypes did (mean (SD) left ventricular muscle mass 190 (48) v 320 (113), p = 0.002; interventricular septal thickness 11.5 (2.0) v 16.4 (6.7), p = 0.01; pathological ECG 0% (0 of 10) v 63% (10 of 16), respectively). Multivariate analysis controlling for age, sex, and hypertension confirmed an independent association between the presence of pro-LVH polymorphisms and left ventricular mass. When each polymorphism was assessed individually, carriers of each pro-LVH genotype had a significantly greater left ventricular mass than those with no pro-LVH mutation; these associations, with the exception of cardiac chymase A AA polymorphism (p = 0.06), remained significant in multivariate analysis. Conclusion: Genetic polymorphisms of the RAAS influence penetrance and degree of LVH in 26 gene carriers from one family with HCM caused by a myosin binding protein C mutation.
Benefits and feasibility of the partial loading approach in cellular mobile radio systems

This paper analyzes the feasibility and potential benefits of following a novel design strategy for cellular systems known as partial loading. This strategy seeks low channel occupancy per cell at the capacity limit, as opposed to the high channel occupancy per cell of more conventional design strategies. By doing so, a considerable flexibility for the radio resource management is obtained, which can be exploited both to increase system capacity and to ease the accommodation of highly fluctuating traffic. A comprehensive system capacity analysis has been performed, based on an analytical model, and it is shown that the introduction of flexibility through partial loading has a capacity cost associated with it. However, it is shown that when that flexibility is properly exploited by adaptive radio link control techniques, such as link adaptation, frequency hopping, or call admission control policies, that cost is more than compensated for, making the partial loading approach a very attractive strategy for the evolution of current TDMA systems and the design of future ones.
Deleterious Effects of Mild Hypothermia in Septic Rats Are Ameliorated by Granulocyte Colony-stimulating Factor

Background The authors studied the effects of mild hypothermia on the outcome in a rat model of intraabdominal sepsis and tested whether granulocyte colony-stimulating factor (G-CSF) augments the host response and improves outcome during mild hypothermia. Methods A rat model of peritoneal contamination and infection with human stool bacteria was used to simulate clinical trials that included increasing complexity. In trial 1, postoperative hypothermia (32°C) was compared with normothermia (38°C), without supportive treatment (10 rats per group). In trial 2, with a more severe infection, rats were given antibiotic prophylaxis. Using 20 rats per group, the authors compared postoperative hypothermia (32°C), normothermia, and postoperative hypothermia (32°C) with 20 &mgr;g/kg G-CSF prophylaxis given 12 h before surgery and 12 h and 36 h after surgery. The primary endpoint was death at 120 h. Secondary endpoints were systemic cytokine concentrations, leukocyte counts, and the phagocytic activity of granulocytes and monocytes. Results In trial 1, 50% of the normothermia group and 10% of the postoperative hypothermia group survived. In trial 2, 50% of the normothermia group, 20% of the hypothermia group, and 60% of the hypothermia plus G-CSF group survived. Postoperative hypothermia plus G-CSF reduced plasma concentrations of interleukin-6 (hypothermia group, 511 ± 104 pg/ml; hypothermia plus G-CSF group, 247 ± 51 pg/ml) and macrophage inflammatory protein-2 (hypothermia group, 239 ± 43 pg/ml; hypothermia plus G-CSF group, 178 ± 21 pg/ml). Conclusions In this rat model of intraabdominal sepsis, postoperative hypothermia was deleterious. However, G-CSF treatment, initiated before contamination, reduced the mortality rate, increased the neutrophil count, and downgraded the systemic cytokine response.
Applications of Bayesian model selection to cosmological parameters

Bayesian model selection is a tool to decide whether the introduction of a new parameter is warranted by data. I argue that the usual sampling statistic significance tests for a null hypothesis can be misleading, since they do not take into account the information gained through the data, when updating the prior distribution to the posterior. On the contrary, Bayesian model selection offers a quantitative implementation of Occam’s razor. I introduce the Savage–Dickey density ratio, a computationally quick method to determine the Bayes factor of two nested models and hence perform model selection. As an illustration, I consider three key parameters for our understanding of the cosmological concordance model. By using WMAP 3–year data complemented by other cosmological measurements, I show that a non–scale invariant spectral index of perturbations is favoured for any sensible choice of prior. It is also found that a flat Universe is favoured with odds of 29 : 1 over non–flat models, and that there is strong evidence against a CDM isocurvature component to the initial conditions which is totally (anti)correlated with the adiabatic mode (odds of about 2000 : 1), but that this is strongly dependent on the prior adopted. These results are contrasted with the analysis of WMAP 1–year data, which were not informative enough to allow a conclusion as to the status of the spectral index. In a companion paper, a new technique to forecast the Bayes factor of a future observation is presented.
Tailoring the Electrochemical and Mechanical Properties of PEDOT:PSS Films for Bioelectronics

The effect of 3-glycidoxypropyltrimethoxysilane (GOPS) content in poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) dispersions on the properties of films spun cast from these formulations is investigated. It has been found out that the concentration of GOPS has a tremendous, yet gradual impact on the electrical, electrochemical, and mechanical properties of the PEDOT:PSS/GOPS films and that there is an optimum concentration which maximizes a particular feature of the film such as its water uptake or elasticity. The benefits of aqueous stability and mechanical strength with GOPS are to be compensated by an increase in the electrochemical impedance. GOPS aids obtaining excellent mechanical integrity in aqueous media with still highly conducting properties. Moreover, active devices like organic electrochemical transistors that contain 1 wt% GOPS, which is a concentration that leads to film with high electrical conductivity with sufficient mechanical stability and softness, exhibit steady performance over three weeks. These results suggest that variations in the concentration of such an additive like GOPS can enable a facile co-optimization of electrical and mechanical properties of a conducting polymer film for in vivo bioelectronics application.
Predictors of body dissatisfaction in boys and girls with asthma.

BACKGROUND Body satisfaction is an important issue for youth. Youth with more severe asthma may have experiences and emotions associated with less body satisfaction; however, this has not been studied. OBJECTIVE To identify correlates of body dissatisfaction in youth with asthma. METHODS Sixty-three females and 60 males, ages 8-18 years with asthma, completed measures of body dissatisfaction, anxiety, depression, asthma symptoms, and behaviors. Parents completed measures of asthma limitations; clinicians rated asthma severity. RESULTS Anxiety, depression, and body mass index (BMI) accounted for 21 and 15% of the variance in body dissatisfaction for females and males, respectively. Physical activity added 13% variance to the above model for females. Asthma symptoms added 14% for males. Of note, neither parent ratings of asthma limitations nor clinician ratings of asthma severity contributed additional variance. CONCLUSION This study increases our understanding of youth with asthma and provides future research directions.
Functional &mgr; Opioid Receptors Are Reduced in the Spinal Cord Dorsal Horn of Diabetic Rats

Background The mechanisms of decreased spinal analgesic potency of morphine in neuropathic pain are not fully known. Agonist-stimulated [35S]GTP&ggr;S receptor autoradiography has been used to measure receptor activation of G proteins in vitro. Using this technique, we determined changes in the functional &mgr; opioid receptors in the spinal dorsal horn in diabetic rats. Methods Rats were rendered diabetic with an intraperitoneal injection of streptozotocin. The lumbar spinal cord was obtained from age-matched normal and diabetic rats 4 weeks after streptozotocin treatment. [D-Ala2,N-MePhe4,Gly5-ol]-enkephalin (DAMGO, 10 &mgr;m)-stimulated [35S]GTP&ggr;S binding was performed in both tissue sections and isolated membranes. Results The DAMGO-stimulated [35S]GTP&ggr;S binding in the spinal dorsal horn was significantly reduced (approximately 37%) in diabetic rats compared with normal rats. However, [35S]GTP&ggr;S bindings in the spinal dorsal horn stimulated by other G protein-coupled receptor agonists, including [D-Pen2,D-Pen5]-enkephalin, R (−)N6-(2-phenylisopropyl)-adenosine, and WIN-55212, were not significantly altered in diabetic rats. The basal [35S]GTP&ggr;S binding in the spinal dorsal horn was slightly (approximately 13%) but significantly increased in diabetic rats. Western blot analysis revealed no significant difference in the expression of the &agr; subunits of Gi and Go proteins in the dorsal spinal cord between normal and diabetic rats. Conclusions These data suggest that the functional &mgr; opioid receptors in the spinal cord dorsal horn of diabetic rats are reduced. The impaired functional &mgr; opioid receptors in the spinal cord may constitute one of the mechanisms underlying the reduced spinal analgesic effect of &mgr; opioids in diabetic neuropathic pain.
Incentive spirometry with expiratory positive airway pressure brings benefits after myocardial revascularization

BACKGROUND Patients undergoing coronary artery bypass graft (CABG) surgery have higher risk to develop pulmonary complications (PCs) such as atelectasis, pneumonia and pleural effusion. These complications could increase the length of hospital stay, resources utilization and also are associated with reduced quality of life and functional capacity a long term. OBJECTIVE To test if the use of incentive spirometry (IS) associated with expiratory positive airway pressure (EPAP), after CABG surgery improves dyspnea, effort perceived and quality of life 18 months after CABG. METHODS Sixteen patients submitted to a CABG, were randomized to a control group (n=8) or IS+EPAP group (n=8). The protocol of IS+EPAP was applied in the immediate postoperative period and following for more 4 weeks in the patient's home. Eighteen months after CABG, the strength of the respiratory muscle, the functional capacity, the lung function, the quality of life and the level of physical activity were evaluated. RESULTS After six minute walk test (6-MWT), the score of the dyspnea (1.6+/-0.6 vs 0.6+/-0.3, P<0.05) and the perceived effort (13.4+/-1.2 vs 9.1+/-0.7, P<0.05) were higher in the control group, when compared with the IS+EPAP group. In quality of life evaluation, the domain related to the physical aspects limitations was better in IS+EPAP group (93.7+/-4.1 vs 50+/-17, P<0.02). CONCLUSION Patients that were submitted to IS+EPAP present reduction of dyspnea and lower effort sensation after the 6-MWT, and also a better quality of life 18 months after CABG.
Biological synthesis of gold and silver chloride nanoparticles by Glycyrrhiza uralensis and in vitro applications

Abstract The current study highlights the rapid biosynthesis of gold nanoparticles (Gu–AuNps) and silver chloride nanoparticles (Gu–AgClNps) by aqueous root extract of Glycyrrhiza uralensis, a medicinal plant. G. uralensis has been reported for anticancer and hepatoprotective effects. The reduction of chloroauric acid and silver nitrate by the Glycyrrhiza root extract prompted the formation of Gu–AuNps and Gu–AgClNps within 4 and 40 min at 80 °C, respectively. The complete reaction did not require supplemental reducing and stabilizing agents, which demonstrated green synthesis. Field emission transmission electron microscopy (FE-TEM) revealed the spherical shape of Gu–AuNps and Gu–AgClNps. X-ray diffraction (XRD) showed face-centred cubic structure of Gu–AuNps and Gu–AgClNps with average crystallite size 12.25 nm and 8.01 nm, respectively. The biosynthesized Gu–AgClNps served as competent antimicrobial agent against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella enterica. Additionally, Gu–AuNps and Gu–AgClNps were analyzed for their catalytic ability to reduce methylene blue as model test pollutant. Likewise, both nanoparticles possessed free radical scavenging activity against 2,2-diphenyl-1-picrylhydrzyl (DPPH). Moreover, in vitro cytotoxicity in murine macrophage (RAW264.7) and human breast cancer (MCF7) cells were evaluated. Thus, the study proposes a green synthesis of Gu–AuNps and Gu–AgClNps by G. uralensis extract and in vitro biological applications.
T4-Related Bacteriophage LIMEstone Isolates for the Control of Soft Rot on Potato Caused by ‘Dickeya solani’

The bacterium ‘Dickeya solani’, an aggressive biovar 3 variant of Dickeya dianthicola, causes rotting and blackleg in potato. To control this pathogen using bacteriophage therapy, we isolated and characterized two closely related and specific bacteriophages, vB_DsoM_LIMEstone1 and vB_DsoM_LIMEstone2. The LIMEstone phages have a T4-related genome organization and share DNA similarity with Salmonella phage ViI. Microbiological and molecular characterization of the phages deemed them suitable and promising for use in phage therapy. The phages reduced disease incidence and severity on potato tubers in laboratory assays. In addition, in a field trial of potato tubers, when infected with ‘Dickeya solani’, the experimental phage treatment resulted in a higher yield. These results form the basis for the development of a bacteriophage-based biocontrol of potato plants and tubers as an alternative for the use of antibiotics.
The successful culture and autologous transplantation of rabbit oral mucosal epithelial cells on amniotic membrane.

PURPOSE To determine the feasibility of using human amniotic membrane (AM) as a substrate for culturing oral epithelial cells and to investigate the possibility of using autologous cultivated oral epithelial cells in ocular surface reconstruction. METHODS An ocular surface injury was created in one eye of each of eight adult albino rabbits by a lamellar keratectomy, and a conjunctival excision was performed, including and extending 5 mm outside the limbus. Oral mucosal biopsy specimens were obtained from these eight adult albino rabbits and cultivated for 3 weeks on a denuded AM carrier. The cultivated epithelium was examined by electron microscopy (EM) and immunohistochemically labeled for several keratins. At 3 to 4 weeks after the ocular surface injury, the conjunctivalized corneal surfaces of the eight rabbits were surgically reconstructed by transplanting the autologous cultivated oral epithelial cells on the AM carrier. RESULTS The cultivated oral epithelial sheet had four to five layers of stratified, well-differentiated cells. EM revealed that the epithelial cells were very similar in appearance to those of normal corneal epithelium, had numerous desmosomal junctions, and were attached to a basement membrane with hemidesmosomes. Immunohistochemistry confirmed the presence of the keratin pair 4 and 13 and keratin-3 in the cultivated oral epithelial cells. Corneas that were grafted with the cultivated oral epithelial cells on an AM carrier were clear and were all epithelialized 10 days after surgery. CONCLUSIONS Cultures of oral epithelial cells can be generated to confluence on AM expanded ex vivo from biopsy-derived oral mucosal tissue. Autologous transplantation was performed with these cultivated oral epithelial cells onto the ocular surfaces of keratectomized rabbit eyes. Autologous transplantation of cultivated oral epithelium is a feasible method for ocular surface reconstruction. The long-term outcome of such transplantation is not yet clear, and its feasibility in clinical use should be evaluated further.
PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt

A mapping between chains in the Protein Databank and Enzyme Classification numbers is invaluable for research into structure-function relationships. Mapping at the chain level is a non-trivial problem and we present an automatically updated Web-server, which provides this link in a queryable form and as a downloadable XML or flat file.