Miracle-dz/UniFAR-FTUs huggingface dataset:
Palatability and Predator Avoidance Behavior of Salamanders in Response to the Virginia Opossum (Didelphis Virginiana)

Abstract. Our understanding of mammalian predation on salamanders is primarily restricted to small carnivorous species (i.e., shrews). We conducted a series of investigations to determine whether the Virginia opossum (Didelphis virginiana) is a predator of various salamander species [Desmognathus fuscus, Plethodon dorsalis, and Notophthalmus viridescens (adult and eft)] from the eastern United States. All species, including toxic newt efts, were palatable to opossums. These results suggest opossums could be an active predator of salamanders. In a second study, each terrestrial salamander species exhibited avoidance responses to kairomones from opossums indicating that despite a significant risk of mortality each salamander has evolved mechanisms to minimize predation risk. Combined with overlapping habitat preferences, foraging behavior that places them in contact, and a dietary preference for animal matter, these data suggest opossums may be an important predator on terrestrial salamanders.
Role of Interleukin-4 (IL-4), IL-12, and Gamma Interferon in Primary and Vaccine-Primed Immune Responses to Friend Retrovirus Infection

ABSTRACT The immunological resistance of a host to viral infections may be strongly influenced by cytokines such as interleukin-12 (IL-12) and gamma interferon (IFN-γ), which promote T helper type 1 responses, and IL-4, which promotes T helper type 2 responses. We studied the role of these cytokines during primary and secondary immune responses against Friend retrovirus infections in mice. IL-4- and IL-12-deficient mice were comparable to wild-type B6 mice in the ability to control acute and persistent Friend virus infections. In contrast, more than one-third of the IFN-γ-deficient mice were unable to maintain long-term control of Friend virus and developed gross splenomegaly with high virus loads. Immunization with a live attenuated vaccine virus prior to challenge protected all three types of cytokine-deficient mice from viremia and high levels of spleen virus despite the finding that the vaccinated IFN-γ-deficient mice were unable to class switch from immunoglobulin M (IgM) to IgG virus-neutralizing antibodies. The results indicate that IFN-γ plays an important role during primary immune responses against Friend virus but is dispensable during vaccine-primed secondary responses.
Environmental Mastitis

Mastitis is the more economically important disease in dairy herds. Costs originated by this disease are not only those related to lost of milk production, treatment of sick animals or culled cows, but also those related with the prevention of this disease. Intramammary infections (IMI) are most of the times caused by infection with bacterial pathogens that could be divided into contagious or environmental pathogens. The first of these are characterize to cause cow to cow infections mainly through contaminated milking equipment, milker hands, or cloths used to clean and wipe udders. In this group, Staphylococcus aureus, Streptococcus agalactiae and Mycoplasmas spp. are the main organisms. Environmental pathogens are those that live in the cow's environment and include environmental streptococci (Streptococcus uberis and S. dysgalactiae) and coliforms (Escherichia coli). These two bacterial groups account for more than the 80% of environmental mastitis.
Validation study of a diffusion MRI derived vessel density biomarker for detecting viral hepatitis-b induced liver fibrosis

Aim Liver vessel density can be evaluated by an imaging biomarker DDVD (diffusion derived vessel density): DDVD/area(b0b2) = Sb0/ROIarea0 – Sb2/ROIarea2, where Sb0 and Sb2 refer to the liver signal when b is 0 or 2 (s/mm2); ROIarea0 and ROIarea2 refer to the region-of-interest on b= 0 or 2 images; and Sb2 may be replaced by Sb15 (b=15). This concept was validated in this study. Materials and Methods Liver diffusion images were acquired at 1.5T. For a scan-rescan repeatability study of 6 subjects, b-values of 0 and 2 were used. The validation study composed of 26 healthy volunteers and 19 consecutive suspected chronic viral hepatitis-b patients, and diffusion images with 16 b-values of 0, 2, 4, 7, 10, 15, 20, 30, 46, 60, 72, 100, 150, 200, 400, 600 were acquired. Four patients did not have liver fibrosis, and the rest were four stage-1, three stage-2, four stage 3, and one stage-4 patients respectively. Results Intraclass correlation coefficient for repeatability was 0.994 for DDVD/area(Sb0Sb2), and 0.978 for DDVD/area(Sb0Sb15). In the validation study, DDVD/area(Sb0Sb2) and area(Sb0Sb15) were 14.80±3.06 and 26.58±3.97 for healthy volunteers, 10.51±1.51 and 20.15±2.21 for stage 1-2 fibrosis patients, and 9.42±0.87 and 19.42±1.89 for stage 3-4 fibrosis patients. For 16 patients where IVIM analysis was performed, a combination of DDVD/area, PF, and Dfast achieved the best differentiation for non-fibrotic livers and fibrotic livers. DDVD/area were weakly correlated with PF or Dfast. Conclusion Both DDVD/area(Sb0Sb2) and area(Sb0Sb15) are useful imaging biomarker to separate fibrotic and non-fibrotic livers, with fibrotic livers had lower measurements.
Effect of cra gene mutation on the metabolism of Escherichia coli for a mixture of multiple carbon sources

The major player for catabolite repression is the phosphotransferase systems (PTSs) and cAMP-Crp. Moreover, Cra controls the carbon flow in the metabolic network. In the present research, the effect of modulating cra gene (Δcra) on the consumption of multiple carbon sources such as glucose and fructose (as well as xylose) was investigated under both aerobic and anaerobic conditions. It was shown that glucose and fructose could be co-metabolized with fructose consumed faster than glucose in cra mutant under both aerobic and anaerobic conditions. It was also implied that cra mutant consumed higher amount of total carbon sources, which contributed to the highest metabolite production as compared to the wild type strain. Thus, cra mutant can be a good candidate for the efficient utilization of multiple carbon sources such as glucose and fructose, where xylose consumption was repressed by catabolite repression. The overall regulation mechanisms were clarified based on fermentation data and gene transcript analysis.
Interlinking Periodontitis and Type 2 Diabetes Mellitus by Assessment of Crevicular Visfatin Levels in Health and in Disease Before and After Initial Periodontal Therapy.

INTRODUCTION Visfatin is a new adipocytokine associated with both chronic periodontitis and type 2 diabetes mellitus independently. AIM We aimed to estimate and compare the changes in the levels of visfatin in the Gingival Crevicular Fluid (GCF) of healthy subjects and in subjects with periodontitis with or without controlled Type 2 Diabetes Mellitus (T2DM) after administration of non-surgical periodontal therapy. MATERIALS AND METHODS Forty two subjects were equally divided into Group 1 (healthy), Group 2 (systemically healthy with chronic periodontitis), Group 3 (subjects with chronic periodontitis having controlled T2DM). Defined clinical parameters were recorded at baseline and at one month follow-up period. Visfatin was assessed using enzyme linked immunosorbent assay. One way ANOVA and Tukey's multiple post hoc procedures were used. Pearson's correlation coefficient was used for correlation. RESULTS Significant increase in the visfatin levels was seen with the highest values observed in diabetes with periodontal disease. Visfatin responded to non-surgical periodontal therapy as observed by significant decrease in levels after one month but even at this period diabetics showed the highest levels. CONCLUSION Visfatin levels are highest in individuals with both periodontal disease and diabetes even after periodontal therapy. Individuals with T2DM may be at higher risk of developing periodontal disease.
Microcantilever equipped with nanowire template electrodes for multiprobe measurement on fragile nanostructures

We present a technique for fabricating nanoelectrode extensions to microcantilevers for multiprobe electrical characterization. For electrical measurements of fragile samples, such as thin films and nanostructures, it is advantageous to combine a small contact force with a small contact area, which can be done by reducing the dimensions of the electrodes to nanoscale dimensions. Here we report a fabrication method of a nanoscale four-point probe utilizing silicon nanowires as templates for metal electrodes. Using nanomanipulation, we attach 200–300 nm wide silicon nanowires to microfabricated cantilevers. By subsequently covering these nanowires with a metallic coating, they are made conducting and at the same time fixed to the cantilevers. These silicon nanowire four-point probes were tested on 7 and 35 nm thick Au films as well as poorly adhering 16 nm thin Au nanowires deposited on a silicon surface through a nanofabricated shadow mask. It was found that the nanowire extensions dramatically reduce the .
The use of stents for duct-to-duct anastomoses of biliary reconstruction in orthotopic liver transplantation.

BACKGROUND/AIMS Biliary anastomotic complications remain a major cause of morbidity in liver transplant recipients. The objective of this retrospective study is to reassess the use of anastomotic stents for biliary reconstruction while focusing on an end-to-end choledochocholedochostomy (EECC) in orthotopic liver transplantation (OLT). METHODOLOGY EECC for the biliary reconstruction in OLT was performed in 115 patients. Sixty-three had their bile duct reconstructed over a T-tube stent (S group) while the remaining 52 patients underwent the same procedure without the stent (non-S group). The two groups were compared in terms of biliary complications and the conversion rate to a hepaticojejunostomy (HJS). RESULTS Twenty-three biliary complications were observed in the OLT patients. In the S group, the incidence of a biliary leak was 12.7%, 8 of 63 patients in which 5 patients showed a bile leak when T tubes were removed. The rate of biliary stricture in the S group was 25.4%, or 16 patients. This stricture rate was not significantly different from the 13.5% rate observed in the non-S group (p=0.086). In the non-S group, 7 patients showed a biliary stricture. Four of 7 patients also developed a bile leak identified to be an anastomotic leak, which consequently resulted in HJS. A total of 6 patients, 5.2% of all OLT patients, underwent a subsequent revision of their primary anastomoses. The incidence of conversion from EECC to HJS in the non-S group, 57.1% was significantly higher than that in the S group, 12.5% (p=0.046). CONCLUSIONS EECC (i.e. with or without a T-tube stent) is both a safe and effective technique for biliary reconstruction in OLT. However, the conversion rate from EECC to HJS in the non-S group was significantly higher than that in the S group. An indwelling T-tube stent is therefore considered to be useful for both achieving the lowest possible rate of severe anastomotic stricture and to prevent any subsequent intervention.
Phylogeography and Molecular Species Delimitation Reveal Cryptic and Incipient Speciation in Synchronous Flashing Fireflies (Coleoptera: Lampyridae) of Southeast Asia

Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet, knowledge on its biodiversity and evolutionary history remains lacking. Recent studies have revealed notable population-level phylogeographic structure within the P. tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Additionally, the close morphological and genetic affinity of the recently described species P. balingiana to P. malaccae has raised questions about its validity. In this study, we assembled the most densely sampled genetic dataset on Pteroptyx to-date to estimate a comprehensive phylogeny using mitochondrial and nuclear DNA and subsequently implemented a suite of distance-, phylogeny-, and coalescent-based species delimitation methods to characterize species boundaries within the P. tener, P. bearni, and P. balingiana/P. malaccae groups. Using a total evidence approach from multiple lines of evidence, we showed that populations of P. tener along the west coast of Peninsular Malaysia are sufficiently divergent from populations from the east coast and Borneo to warrant specific recognition, despite the absence of morphological differentiation. Conversely, divergence of P. bearni from Borneo and eastern Peninsular Malaysia, as well as P. balingiana from P. malaccae were modest and their distinction as separate species were ambiguous; consistent with incipient species in the gray zone of speciation. Overall, this study contributes to the limited but growing body of genetic work on Southeast Asian fireflies and underscores the urgent need to increase the breadth and depth of geographic, taxonomic, and genetic sampling to provide a deeper understanding of their biodiversity and evolutionary history.
EGFR-Ligand Signaling in Breast Cancer Metastasis: Recurring Developmental Themes

Nicole K. Nickerson1, Jennifer L. Gilmore1, Kah Tan Allen1, David J. Riese II2, Kenneth P. Nephew1,3 and John Foley1,3,4 1Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 2Harrison School of Pharmacy, Auburn University, Auburn, AL 3Indiana University Cancer Center Indiana University School of Medicine, Indianapolis, IN 4Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN United States of America
Estimation of Serum Copper and Zinc Levels in Patients with Oral Submucous Fibrosis

Background and objectives: The present study was conducted to estimate the serum levels of zinc, copper and copper/zinc ratio in patients with OSF, compare these values among patients with OSF and normal subjects, and to correlate the values among clinical and histological grades in OSF. Methods: The study consisted of 30 OSF patients and 30 normal subjects. Diagnosis of OSF patients was based on clinical and histopathologic findings. Khanna and Andrade grouping both clinically and histopathologically were followed for OSF patients. Serum levels of zinc and copper were estimated using semiautoanalyzer and data was statistically analyzed. Results: The mean serum levels of zinc and copper were decreased in patients with OSF, compared to normal subjects. The mean serum levels of copper and Cu/Zn ratio were increased in OSF patients compared to normal subjects. The mean serum levels of zinc showed no change through clinical and histological stages of OSF. The mean serum levels of copper and Cu/Zn ratio showed a gradual increase from clinical and histological grade I to IV in OSF patients. Interpretation and conclusion: Serum levels of these trace elements may be taken as prognostic markers of the disease progression in OSF patients.
Pitch targets anchor Chinese tone and intonation patterns

This paper presents a study on the role of pitch targets in the manifestation of Chinese tone and intonation. Pitch targets are particularly measured as (fundamental frequency) peaks and valleys over time. Analysis and perceptual experiments were conducted on 72 sentences, each with almost identical tone mapping, uttered two times by a female native in statements or questions. The tone and intonation patterns observed from the contours were quantitatively analyzed using a functional model and then re-synthesized using the model parameters predicted from the pitch targets measured. Two perceptual experiments were done. One rates the similarity between the resynthesized tone and intonation patterns from the pitch targets and the original; the other tests human perception of tone and intonation when systematically varying the pitch targets of the final tone (Tone 2 and Tone 4) in two statements. Experimental results consistently indicate that the pitch targets are prominent for anchoring Chinese tone and intonation patterns; the exact shape of an contour is predictable, given the pitch targets.
Kinetic characteristics of propofol-induced inhibition of electron-transfer chain and fatty acid oxidation in human and rodent skeletal and cardiac muscles

Introduction Propofol causes a profound inhibition of fatty acid oxidation (FAO) and reduces spare electron transfer chain (ETC) capacity in a range of human and rodent cells and tissues – a feature that might be related to the pathogenesis of Propofol Infusion Syndrome. We aimed to explore the mechanism of propofol-induced alteration of bioenergetic pathways by describing its kinetic characteristics. Methods We obtained samples of skeletal and cardiac muscle from Wistar rat (n=3) and human subjects: vastus lateralis from hip surgery patients (n=11) and myocardium from brain-dead organ donors (n=10). We assessed mitochondrial functional indices using standard SUIT protocol and high resolution respirometry in fresh tissue homogenates with or without short-term exposure to a range of propofol concentration (2.5-100 μg/ml). After finding concentrations of propofol causing partial inhibition of a particular pathways, we used that concentration to construct kinetic curves by plotting oxygen flux against substrate concentration during its stepwise titration in the presence or absence of propofol. By spectrophotometry we also measured the influence of the same propofol concentrations on the activity of isolated respiratory complexes. Results We found that human muscle and cardiac tissues are more sensitive to propofol-mediated inhibition of bioenergetic pathways than rats tissue. In human homogenates, palmitoyl carnitine-driven respiration was inhibited at much lower concentrations of propofol than that required for a reduction of ETC capacity, suggesting FAO inhibition mechanism different from downstream limitation or carnitine-palmitoyl transferase-1 inhibition. Inhibition of Complex I was characterised by more marked reduction of Vmax, in keeping with non-competitive nature of the inhibition and the pattern was similar to the inhibition of Complex II or ETC capacity. There was no inhibition of Complex IV nor increased leak through inner mitochondrial membrane with up to 100 μg/ml of propofol. If measured in isolation by spectrophotometry, propofol 10 μg/ml did not affect the activity of any respiratory complexes. Conclusion In human skeletal and heart muscle homogenates, propofol in concentrations that are achieved in propofol-anaesthetized patients, causes a direct inhibition of fatty acid oxidation, in addition to inhibiting flux of electrons through inner mitochondrial membrane. The inhibition is more marked in human as compared to rodent tissues.
Effect of storytelling on hopefulness in girl students

BACKGROUND AND AIM: One of the methods that help students in learning critical thinking and decision-making skills is storytelling. Story helps the students to place themselves in the same situation as the main protagonist and try different ways and finally select and implement the best possible method. The goal of this study is to investigate the effect of storytelling on hopefulness of students, age 8–11 in Isfahan's 2nd educational district. METHODS: This is an applied, quasi-experimental study. The study population comprised of 34 randomly selected students attending one of the schools in Isfahan's 2nd educational district. The data gathering tool was the standard Kazdin hopefulness scale (α = 0.72) and data were gathered before and after 8 storytelling sessions for the intervention group. The gathered data were analyzed using descriptive and analytical (paired and independent t-test) with the help of SPSS Version 18 software. RESULTS: The study's findings showed a significant difference in the average hopefulness score of students in study group in pre- and posttest (P = 0.04). Furthermore, independent t-test results showed a significant difference in hopefulness score of intervention and control (P = 0.001). The average hopefulness score of the control group after storytelling sessions was higher than that of the intervention and control. CONCLUSION: The results show the effectiveness of storytelling as a method for improving hopefulness in students.
Advances in biomolecular simulations: methodology and recent applications

1. Introduction 258 2. Set-up of MD simulations 260 2.1 Constant-pressure dynamics 260 2.2 Grand-canonical dynamics 261 2.3 Boundary conditions 261 3. Force fields 262 3.1 Proteins 262 3.2 Nucleic acids 265 3.3 Carbohydrates 266 3.4 Phospholipids 266 3.5 Polarization 267 4. Electrostatics 267 4.1 Spherical truncation methods 268 4.2 Ewald summation methods 269 4.3 Fast multipole (FM) methods 271 4.4 Reaction-field methods 271 5. Implicit solvation models 271 6. Speeding-up the simulation 273 6.1 SHAKE and its relatives 273 6.2 Multiple time-step algorithms 274 6.3 Other algorithms 275 7. Conformational space sampling 275 7.1 Multiple copy simultaneous search (MCSS) and locally enhanced sampling (LES) 275 7.2 Steered or targeted MD 276 7.3 Self-guided MD 276 7.4 Leaving the standard 3D Cartesian coordinate system: 4D MD and internal coordinate MD 277 7.5 Temperature variations 277 8. Thermodynamic calculations 278 8.1 Lambda (λ) dynamics 278 8.2 Extracting thermodynamic information from simulations 279 8.3 Non-Boltzmann thermodynamic integration (NBTI) 279 8.4 Other methods 279 9. QM/MM calculations 282 10. MD simulations of protein folding and unfolding 283 10.1 High-temperature effects 284 10.2 Co-solvent and polarization effects 288 10.3 External force effects 288 11. On the horizon 291 12. Acknowledgements 292 13. References 292 Molecular dynamics simulations are widely used today to tackle problems in biochemistry and molecular biology. In the 25 years since the first simulation of a protein computers have become faster by many orders of magnitude, algorithms and force fields have been improved, and simulations can now be applied to very large systems, such as protein–nucleic acid complexes and multimeric proteins in aqueous solution. In this review we give a general background about molecular dynamics simulations, and then focus on some recent technical advances, with applications to biologically relevant problems.
Rearing Temperature and Fatty Acid Supplementation Jointly Affect Lipid Fluorescence Polarization and Heat Tolerance in Daphnia

The homeoviscous adaptation hypothesis states that the relative abundance of polyunsaturated fatty acids (PUFAs) in membrane phospholipids of ectothermic organisms decreases with increasing temperatures to maintain vital membrane properties. We reared Daphnia magna at 15°, 20°, and 25°C and increasing dietary concentrations of the long-chain PUFA eicosapentaenoic acid (EPA) to test the hypothesis that the well-documented increase in heat tolerance of high-temperature-reared Daphnia is due to a reduction in body PUFA concentrations. Heat tolerance was assessed by measuring the time to immobility at a lethally high temperature (T imm at 37°C), and whole body lipid fluorescence polarization (FP) was used as an estimate of membrane fluidity. At all rearing temperatures, EPA supplementation resulted in an increase in the relative abundance of EPA in body tissues, but only at 15° and 25°C did this result in a decrease in heat tolerance, and only at 20°C was this associated with an increase in membrane fluidity (i.e., decrease in FP). Overall, however, the degree of tissue fatty acid unsaturation correlated well with heat tolerance and FP. Our results support the homeoviscous adaptation hypothesis by showing that cold-reared Daphnia accumulate PUFAs within their body tissues and thus are more susceptible to heat than hot-reared Daphnia accumulating fewer PUFAs. However, our data also point out that further studies are required that elucidate the complex relationships between PUFA supply, membrane fluidity, and heat tolerance in ectotherms.