Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time PCR assays for diagnosing brucellar spondylitis using formalin-fixed paraffin-embedded tissues

Abstract It is difficult to diagnose brucellar spondylitis because of its nonspecific clinical, radiological, and histological characteristics. This study aimed to determine whether real-time polymerase chain reaction (PCR) using formalin-fixed paraffin-embedded (FFPE) tissues was superior to conventional serum-based methods for diagnosing brucellar spondylitis. This retrospective study included 31 patients with brucellosis and a control group of 20 people with no history of brucellosis or exposure to Brucella spp. Samples from all patients with brucellar spondylitis were evaluated using Giemsa staining, the standard tube agglutination (STA) test, blood culture, and real-time PCR. The brucellar spondylitis was acute in 7 patients (22.6%), subacute in 15 patients (48.4%), and chronic in 9 patients (29%). Serological assays provided positive results for 25 patients (80.1%), real-time PCR provided positive results for 29 patients (93.5%), and blood cultures provided positive results for 11 patients (35.5%). The real-time PCR provided sensitivity of 93.5%, specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 100%. The corresponding values for the STA test were 80.1%, 100%, 100%, and 76.9%, respectively. Real-time PCR provided better sensitivity than Giemsa staining, the STA test, and blood culture, although the difference between PCR and STA was not statistically significant (P = .22). B melitensis was the only pathogen that was detected in patient with brucellar spondylitis using real-time PCR. These results suggest that real-time PCR provides a high sensitivity for diagnosing brucellar spondylitis. Furthermore, the real-time PCR results indicate that B melitensis was the causative pathogen in these cases.
Reliability and validity of the script concordance test for postgraduate students of general practice

Abstract Background: The script concordance test (SCT) is a validated method of examining students’ clinical reasoning. Medical students’ professional skills are assessed during their postgraduate years as they study for a specialist qualification in general practice. However, no specific provision is made for assessing their clinical reasoning during their postgraduate study. Objective: The aim was to demonstrate the reliability and validity of the SCT in general practice and to determine if this tool could be used to assess medical students’ progress in acquiring clinical reasoning. Methods: A 135-question SCT was administered to postgraduate medical students at the beginning of their first year of specialized training in general practice, and then every six months throughout their three-year training, as well as to a reference panel of 20 expert general practitioners. For score calculation, we used the combined scoring method as the calculator made available by the University of Montreal’s School of Medicine in Canada. For the validity, student’ scores were compared with experts, p <. 05 was considered statistically significant. Results: Ninety students completed all six assessments. The experts’ mean score (76.7/100) was significantly higher than the students’ score across all assessments (p <.001), with a Cronbach’s alpha value of over 0.65 for all assessments. Conclusion: The SCT was found to be reliable and capable of discriminating between students and experts, demonstrating that this test is a valid tool for assessing clinical reasoning skills in general practice.
Rescue of Pompe disease in mice by AAV-mediated liver delivery of secretable acid α-glucosidase

Liver delivery of engineered GAA transgenes to mice with Pompe disease rescued glycogen accumulation in multiple tissues. Revealing a secretable GAA for Pompe disease Pompe disease is a genetic disorder caused by mutations in the acid α-glucosidase (GAA) gene, leading to glycogen accumulation in all cells of the body. This accumulation leads to severe neuromuscular disabilities that can be life-threatening. Puzzo et al. used bioinformatic analysis, protein engineering, and gene therapy to develop and deliver a GAA transgene encoding a secretable GAA. Liver-specific, adeno-associated virus (AAV) vector–mediated GAA delivery rescued the Pompe disease phenotype in a mouse model and increased GAA expression in healthy monkeys, opening possibilities for future translation of this approach for treating Pompe disease. Glycogen storage disease type II or Pompe disease is a severe neuromuscular disorder caused by mutations in the lysosomal enzyme, acid α-glucosidase (GAA), which result in pathological accumulation of glycogen throughout the body. Enzyme replacement therapy is available for Pompe disease; however, it has limited efficacy, has high immunogenicity, and fails to correct pathological glycogen accumulation in nervous tissue and skeletal muscle. Using bioinformatics analysis and protein engineering, we developed transgenes encoding GAA that could be expressed and secreted by hepatocytes. Then, we used adeno-associated virus (AAV) vectors optimized for hepatic expression to deliver the GAA transgenes to Gaa knockout (Gaa−/−) mice, a model of Pompe disease. Therapeutic gene transfer to the liver rescued glycogen accumulation in muscle and the central nervous system, and ameliorated cardiac hypertrophy as well as muscle and respiratory dysfunction in the Gaa−/− mice; mouse survival was also increased. Secretable GAA showed improved therapeutic efficacy and lower immunogenicity compared to nonengineered GAA. Scale-up to nonhuman primates, and modeling of GAA expression in primary human hepatocytes using hepatotropic AAV vectors, demonstrated the therapeutic potential of AAV vector–mediated liver expression of secretable GAA for treating pathological glycogen accumulation in multiple tissues in Pompe disease.
Factorial estimation of energy requirement for egg production.

Based on balance and respiration measurements with 60 White Leghorns during the laying period from 27 to 48 wk of age, a factorial method for estimating the energy requirement for egg production is proposed. The present experiment showed that the deposition of fat and energy increased during the laying period, but protein deposition slightly decreased. It has been shown that the efficiency of ME utilization for fat energy deposition is higher than for protein energy deposition in the egg. Because the proportions of protein and fat differ during the laying period, and because energy utilization is different between protein and fat, the ME requirement was calculated as the sum of ME for maintenance and the partial requirements for protein, fat, and carbohydrate deposition. For practical applications, functions for prediction of protein (OP), fat (OF), and energy (OE) in eggs during the laying period have been established according to the following model: OP, OF, or OE = a + b1 x egg (grams per day) + b2 x age (weeks). The average ME requirement [calculated with either measured or predicted chemical composition, and by applying a constant maintenance requirement of 98 kcal/kg BW.75 and partial efficiencies for energy retention in protein (Kop = .50), fat (Kof = .79), and carbohydrates (Koc = .79)] increased from . 26 Mcal at 27 wk of age to . 29 Mcal at 48 wk, corresponding to 5.93 and 6.07 Mcal/kg egg.
Evaluation of Peripheral Blood and Cord Blood Platelet Lysates in Isolation and Expansion of Multipotent Mesenchymal Stromal Cells

Background: Multipotent Mesenchymal Stromal Cells (MSCs) are used in tissue engineering and regenerative medicine. The in vitro isolation and expansion of MSCs involve the use of foetal bovine serum (FBS). However, many concerns have been raised regarding the safety of this product. In this study, alternative additives derived either from peripheral or cord blood were tested as an FBS replacement. Methods: Platelet lysates (PL) from peripheral and cord blood were used for the expansion of MSCs. The levels of growth factors in peripheral blood (PB) and cord blood (CB) PLs were determined using the Multiple Reaction Monitoring (MRM). Finally, the cell doubling time (CDT), tri-lineage differentiation and phenotypic characterization of the MSCs expanded with FBS and PLs were determined. Results: MSCs treated with culture media containing FBS and PB-PL, were successfully isolated and expanded, whereas MSCs treated with CB-PL could not be maintained in culture. Furthermore, the MRM analysis yielded differences in growth factor levels between PB-PL and CB-PL. In addition, the MSCs were successfully expanded with FBS and PB-PL and exhibited tri-lineage differentiation and stable phenotypic characteristics. Conclusion: PB-PL could be used as an alternative additive for the production of MSCs culture medium applied to xenogeneic-free expansion and maintenance of MSCs in large scale clinical studies.
Boolean modeling techniques for protein co-expression networks in systems medicine

ABSTRACT Introduction: Application of systems biology/systems medicine approaches is promising for proteomics/biomedical research, but requires selection of an adequate modeling type. Areas covered: This article reviews the existing Boolean network modeling approaches, which provide in comparison with alternative modeling techniques several advantages for the processing of proteomics data. Application of methods for inference, reduction and validation of protein co-expression networks that are derived from quantitative high-throughput proteomics measurements is presented. It’s also shown how Boolean models can be used to derive system-theoretic characteristics that describe both the dynamical behavior of such networks as a whole and the properties of different cell states (e.g. healthy or diseased cell states). Furthermore, application of methods derived from control theory is proposed in order to simulate the effects of therapeutic interventions on such networks, which is a promising approach for the computer-assisted discovery of biomarkers and drug targets. Finally, the clinical application of Boolean modeling analyses is discussed. Expert commentary: Boolean modeling of proteomics data is still in its infancy. Progress in this field strongly depends on provision of a repository with public access to relevant reference models. Also required are community supported standards that facilitate input of both proteomics and patient related data (e.g. age, gender, laboratory results, etc.).
Processing the problematic fine fraction of incinerator bottom ash into a raw material for manufacturing ceramics

The aim of this research was to develop a novel thermal treatment technology able to transform the problematic fine fraction of incinerator bottom ash (IBA) into an inert material suitable for the production of ceramics. In this project two different problematic fractions of fine IBA have been used. The less than 1mm fraction of processed fine IBA dust was obtained from the dry discharge system for IBA used in the Energy from Waste (EfW) plant at Monthey, Zurich. The dry discharged fine IBA dust from the Monthey plant is currently disposed of to landfill at high cost. The second fine IBA fraction was supplied by Day Group who process wet discharge IBA from the Lakeside and the Newhaven EfW facilities in the South of England. There are currently no beneficial uses for the fine fraction which is either blended back into coarser fractions or disposed of to landfill. The conclusion from the research is that the fine fractions of IBA generated from both discharge techniques can be transformed into an inert material suitable for the production of hard, dense ceramics. Processing involves the addition of glass, wet ball milling and calcining, pressing and sintering. The addition of glass aids liquid phase sintering and improves the appearance of the ceramic body formed, milling increases sintering reactivity and calcining limits the loss of volatiles and shrinkage during firing. This transforms the major crystalline phases present in the fine IBA fraction from quartz (SiO2), calcite (CaCO3), gehlenite (Ca2Al2SiO7) and hematite (Fe2O3), to the pyroxene group minerals diopside (CaMgSi2O6) and clinoenstatite (MgSi2O6), together with some andradite (Ca3Fe2Si3O12). Processed calcined powders can be pressed and sintered to form dense (>2.5 g/cm), hard ceramics that exhibit low firing shrinkage (<7%), zero water absorption and minimal leaching. Calcining the IBA: glass powders before processing was able to minimize the linear shrinkage observed compared to samples produced using uncalcined powders. Calcining also had the effect of reducing the leaching of metals of environmental concern present in the fine IBA fraction by over 95%. These are encapsulated within the glassy phases present in the calcined and sintered materials.
New insights for mesospheric OH: multi-quantum vibrational relaxation as a driver for non-local thermodynamic equilibrium

The question of whether mesospheric OH(υ) rotational population distributions are in equilibrium with the local kinetic temperature has been debated over several decades. Despite several indications for the existence of non-equilibrium effects, the general consensus has been that emissions originating from low rotational levels are thermalized. Sky spectra simultaneously observing several vibrational levels demonstrated reproducible trends in the extracted OH(υ) rotational temperatures as a function of vibrational excitation. Laboratory experiments provided information on rotational energy transfer and direct evidence for fast multi-quantum OH(high-υ) vibrational relaxation by O atoms. We examine the relationship of the new relaxation pathways with the behavior exhibited by OH(υ) rotational population distributions. Rapid OH(high-υ) + O multi-quantum vibrational relaxation connects high and low vibrational levels and enhances the hot tail of the OH(low-υ) rotational distributions. The effective rotational temperatures of mesospheric OH(υ) are found to deviate from local thermodynamic equilibrium for all observed vibrational levels.
Estimating Source Carbon from Crop Residues, Roots and Rhizodeposits Using the National Grain-Yield Database

Crop residue management receivedlittle attention until about 1970. Records of crop residue production are limited, but crop yield databases have been available since 1865. Carbon sequestration and other conservation benefits require a detailed knowledge of crop residue production and management. Our objectives are to: (i) review grain and biomass yield, harvest index (HI), and root C/shoot C ratios (k) of major grain crops in the USA; (ii) discuss historical agriculturalpractice impacts on soil organic C (SOC); and (iii) compare estimates of total (above- and belowground) source C production (ESC) relative to minimum source C inputs required to maintain SOC (MSC). Aboveground MSC input averaged 2.5 6 1.0 Mg C ha 21 yr 21 (n 5 13) based on moldboard plow sites and 1.8 6 0.44 Mg C ha 21 yr 21 (n 5 5) based on no-till and chisel plow sites. These MSC values included only aboveground source C, thus underestimate the total MSC. When ESC is estimated from k, including rhizodeposition (krec), the true magnitude of the C cycle is at least twice that when ESC is estimated using k excluding rhizodeposition (khis). Neglecting rhizodeposition C underestimates the net production of C in cropland. Current yields and measured MSC predict continued SOC loss associated with soybean [Glycine max (L.) Merr. ] and some wheat (Triticum aestivum L.) production management unless conservation tillage is used and ESC is increased. The adequacies of ESC to maintain SOC has direct implications for estimating the amount of crop residue that can be harvested and yet maintain SOC.
Microbiological Evaluation of Ozone on Dentinal Lesions in Young Permanent Molars using the Stepwise Excavation.

AIM To assess the microbial effect of ozone gas on dentinal lesions in young permanent molars using the stepwise excavation. STUDY DESIGN An experimental, controlled clinical trial was performed. The sample included 80 immature first permanent molars, showing deep occlusal carious cavities that were indicated for stepwise excavation. Following first step of dentin excavation, the sample was divided into test (ozone gas) and control (calcium hydroxide (Ca(OH)2) base material) groups. One half of the cases in each group were evaluated for microbiological changes after 6 months, and the other half after 12 months. RESULTS Mutans streptococci (MS), Lactobacilli, and Candida counts were significantly reduced immediately after ozone application in the test group (P ≤0.05). At the final assessment period, MS and Lactobacilli were significantly reduced in the test group (P ≤0.05). Meanwhile, the Candida counts were significantly reduced only in the test group of the 6 and 12 month-cases (P ≤0.05). Regarding the control group, the significant reduction in microbial count was observed with MS after 6 and 12 months (P ≤0.05). No significant differences were observed between test and control groups at different evaluation periods (P >0.05). CONCLUSIONS Ozone gas had a significant antimicrobial effect in deep class I carious lesions.
Two zinc-binding domains in the transporter AdcA from Streptococcus pyogenes facilitate high-affinity binding and fast transport of zinc

Zinc is an essential metal in bacteria. One important bacterial zinc transporter is AdcA, and most bacteria possess AdcA homologs that are single-domain small proteins due to better efficiency of protein biogenesis. However, a double-domain AdcA with two zinc-binding sites is significantly overrepresented in Streptococcus species, many of which are major human pathogens. Using molecular simulation and experimental validations of AdcA from Streptococcus pyogenes, we found here that the two AdcA domains sequentially stabilize the structure upon zinc binding, indicating an organization required for both increased zinc affinity and transfer speed. This structural organization appears to endow Streptococcus species with distinct advantages in zinc-depleted environments, which would not be achieved by each single AdcA domain alone. This enhanced zinc transport mechanism sheds light on the significance of the evolution of the AdcA domain fusion, provides new insights into double-domain transporter proteins with two binding sites for the same ion, and indicates a potential target of antimicrobial drugs against pathogenic Streptococcus species.
Validation of the Short Self-Regulation Questionnaire for Taiwanese College Students (TSSRQ)

While self-regulation has long been recognized as an important characteristic of an individual, instruments assessing the general aptitude of self-regulation remain limited especially in Asian countries. This study re-validated Carey et al.'s (2004) Short Self-Regulation Questionnaire based on a national sample of Taiwanese college students (N = 1,988). Item analysis, exploratory factor analysis, and confirmatory factor analysis (CFA) yielded 22 items in five internally consistent factors. Descriptive findings showed that, a lack of proactiveness and volitional control, and a decrease of self-regulation throughout the college span appeared to be an overarching problem among Taiwanese college students. Furthermore, male students achieved lower self-regulation scores than female ones, and students in Services and STEM-related majors are in the need of self-regulation enhancement. Due to the generic measurement of individual's self-regulation traits, the Taiwanese Short Self-regulation Questionnaire (TSSRQ) can be flexibly applied to various contexts and used to deal with different issues beyond learning such as college students' Internet or smartphone addiction. Through this study, we hope the validated TSSRQ can promote studies on self-regulation and associated antecedents and outcomes, in turn leveraging college students' life adjustment and well-being.
The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa

ABSTRACT Developing a comprehensive and reliable taxonomy for the Colletotrichum gloeosporioides species complex will require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogenetic inference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichum species associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogenetically informative sites. Similarly, the choice of phylogenetic marker affects the delimitation of species boundaries, particularly if low phylogenetic signal is confounded with strong discordance, and inference of the species tree from multiple-gene trees. According to both phylogenetic informativeness profiling and Bayesian concordance analyses, the most informative loci are DNA lyase (APN2), intergenic spacer (IGS) between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glutamine synthetase (GS), β-tubulin (TUB2), and a new marker, the intergenic spacer between GAPDH and an hypothetical protein (GAP2-IGS). Cornmeal agar minimizes the variance in conidial dimensions compared with potato dextrose agar and synthetic nutrient-poor agar, such that species are more readily distinguishable based on phenotypic differences. We apply these insights to investigate the diversity of Colletotrichum species associated with banana anthracnose in Brazil and report C. musae, C. tropicale, C. theobromicola, and C. siamense in association with banana anthracnose. One lineage did not cluster with any previously described species and is described here as C. chrysophilum.