Miracle-dz/UniFAR-FTUs huggingface dataset:
Gliotoxin-induced cytotoxicity proceeds via apoptosis and is mediated by caspases and reactive oxygen species in LLC-PK1 cells.

Renal failure associated with aspergillosis is caused by pathogenic fungi. Gliotoxin is a toxic epipolythiodioxopiperazine metabolite produced by the pathogens. The present study investigated the cytotoxicity and underlying mechanisms induced by gliotoxin in LLC-PK1 cells, a porcine renal proximal tubular cell line. Gliotoxin at 100 ng/ml did not show a cytotoxic effect, but unmasked a dose-dependent cell death induced by TNF-alpha. TNF-alpha-induced cell death in the presence of gliotoxin was associated with hypodiploid nuclei and activation of caspase-3-like proteases. Blockade of caspases by boc-aspartyl (OMe)-fluoromethylketone and z-DEVD.fmk inhibited TNF-alpha-induced cell death. As the concentrations of gliotoxin were increased, gliotoxin killed the cells directly in a dose-dependent manner. Further analyses of DNA fragmentation, hypodiploid nuclei, mitochondrial membrane potential, and plasma membrane integrity revealed that cell death proceeded via apoptosis. Gliotoxin-induced apoptosis was associated with dose-dependent and time-dependent activation of caspase-3-like proteases. Boc-aspartyl (OMe)-fluoromethylketone attenuated the killing effect. Gliotoxin also increased the intracellular levels of reactive oxygen species as measured by flow cytometry. N-acetylcysteine, a well-known antioxidant, completely abolished the gliotoxin-induced caspase-3-like activity, cytotoxicity, and reactive oxygen species. In conclusion, (1) gliotoxin at 100 ng/ml unmasks the ability of TNF-alpha-induced apoptosis, and the effect of TNF-alpha is mediated by caspase-3-like proteases; and (2) at higher concentrations gliotoxin itself induces cell death, which is via apoptosis and dependent on caspase-3-like activity and reactive oxygen species.
Identification of the Entamoeba histolytica Galactose-Inhibitable Lectin Epitopes Recognized by Human Immunoglobulin A Antibodies following Cure of Amebic Liver Abscess

ABSTRACT Immunity to Entamoeba species intestinal infection is associated with the presence of intestinal IgA antibodies against the parasite's galactose-inhibitable adherence lectin. We determined the epitope specificity of serum and intestinal antilectin IgA antibodies by enzyme-linked immunosorbent assay using overlapping fragments of a recombinant portion of the lectin heavy subunit, designated LC3. These findings were correlated with the effects of epitope-specific murine antilectin immunoglobulin A (IgA) monoclonal antibodies (MAbs) on amebic in vitro galactose-specific adherence. LC3 is a highly antigenic and immunogenic cysteine-rich protein (amino acids [aa] 758 to 1150) that includes the lectin's carbohydrate binding domain. The study subjects, from Durban, South Africa, were recently cured of amebic liver abscess (ALA) with or without concurrent Entamoeba histolytica intestinal infection or were infection free 1 year after cure. We also studied seropositive subjects that were infected with E. histolytica, disease free, and asymptomatic. Serum anti-LC3 IgA antibodies from all study groups exclusively recognized the third (aa 868 to 944) and the seventh (aa 1114 to 1134) LC3 epitopes regardless of clinical status; epitope 6 (aa 1070 to 1114) was also recognized by serum anti-LC3 IgG antibodies. However, IgG antibody recognition of epitope 6 but not 3 or 7 was lost 1 year following cure of ALA. We produced 14 murine anti-LC3 IgA MAbs which collectively recognized five of the seven LC3 epitopes. The majority of the murine MAbs recognized the first epitope (aa 758 to 826), which was not recognized by human IgA antibodies. Interestingly, adherence of E. histolytica trophozoites to CHO cells was inhibited by MAbs against epitopes 1, 3, 4 (aa 944 to 987), and 6 (P < 0.01). The LC3 epitopes recognized by human IgA antibodies (3 and 7) were further characterized by use of overlapping synthetic peptides. We identified four peptides (aa 891 to 903, 918 to 936, 1114 to 1134, and 1128 to 1150) that in linear or cyclized form were recognized by pooled intestinal IgA antibodies and serum IgG antibodies from subjects with ALA and asymptomatic, seropositive infected subjects. This study identifies the lectin epitopes to be studied in an amebiasis subunit vaccine designed to elicit mucosal immunity mimicking that of humans cured of ALA.
Statistical Thermodynamics Of Surfaces, Interfaces, And Membranes

* NOTE: Each Part begins with an Introduction, and ends with Problems and References. Mixtures and Interfaces * Complex Materials and Interfaces * Review of Classical Statistical Mechanics * Phase Separation in Binary Mixtures * Differential Geometry of Surfaces * Review of Hydrodynamics Interfacial Tension * Free Energy of Surfaces and Interfaces * Surface/Interfacial Tension Theory * Surface-Active Agents Fluctuations of Interfaces * Free Energy of a Fluctuating Interface * Thermal Fluctuations of Interfaces * Capillary Instabilities of Interfaces * Roughening Transition of Solid Surfaces Wetting of Interfaces * Equilibrium * Long-Range Interactions: Macroscopic Theory * Fluctuations of the Contact Line * Equilibrium: Microscopic Description * Dynamics of Wetting Interactions of Rigid Interfaces * Molecular Interactions * Van der Waals Interaction Energies * Continuum Theory of van der Waals Forces * Electrostatic Interactions * Solute-Induced Interactions Flexible Interfaces * Fluid Membranes and Surfactants * Curvature Elasticity of Fluid Membranes * Curvature Moduli * Fluctuations of Fluid Membranes * Interactions of Fluid Membranes Colloidal Dispersions * Dispersions of Interacting Particles * Colloid interactions: DLVO Theory * Long-Range Electrostatic Interactions * Steric Interactions: Polymer Adsorption * Structure of Colloidal Aggregates Self-Absorbing Interfaces * Micelles * Vesicles * Microemulsions * Spongelike and Bicontinuous Phases
RecA‐mediated SOS induction requires an extended filament conformation but no ATP hydrolysis

The Escherichia coli SOS response to DNA damage is modulated by the RecA protein, a recombinase that forms an extended filament on single‐stranded DNA and hydrolyzes ATP. The RecA K72R (recA2201) mutation eliminates the ATPase activity of RecA protein. The mutation also limits the capacity of RecA to form long filaments in the presence of ATP. Strains with this mutation do not undergo SOS induction in vivo. We have combined the K72R variant of RecA with another mutation, RecA E38K (recA730). In vitro, the double mutant RecA E38K/K72R (recA730,2201) mimics the K72R mutant protein in that it has no ATPase activity. The double mutant protein will form long extended filaments on ssDNA and facilitate LexA cleavage almost as well as wild‐type, and do so in the presence of ATP. Unlike recA K72R, the recA E38K/K72R double mutant promotes SOS induction in vivo after UV treatment. Thus, SOS induction does not require ATP hydrolysis by the RecA protein, but does require formation of extended RecA filaments. The RecA E38K/K72R protein represents an improved reagent for studies of the function of ATP hydrolysis by RecA in vivo and in vitro.
Comparison of the effects of mirror therapy and electromyography-triggered neuromuscular stimulation on hand functions in stroke patients: a pilot study

To determine the effectiveness of mirror therapy and electromyography (EMG)-triggered neuromuscular stimulation on improvement of functions of the upper extremity in patients with subacute stroke in comparison with conventional therapy as well as to evaluate the advantage of each treatment over another, we conducted a prospective, randomized, and controlled trial involving 24 patients with ischemic stroke. The mean age and mean time since stroke of the patients were 58.79±11.49 years and 5.25±2.25 months. Patients were assigned randomly to a mirror therapy group (MT group, n=9), which consisted of therapy with a mirror box 5 days/week, 30 min/day, for 3 weeks, an electrostimulation group (ES group, n=7), which consisted of therapy with EMG-triggered stimulation (EMG-stim) of similar duration and frequency of treatment as the MT group, and a control group (n=8). All the groups received conventional physiotherapy for the same period as the MT group. Patients in the MT group practiced their therapy at home after supervised sessions. The Fugl-Meyer scores of the upper extremity, grip force, wrist extension, and Box and Block Test were evaluated at baseline, after treatment, and at 3 months after the treatment. All of these measures were evaluated by a blinded researcher. We found that there was no significant improvement in wrist extension range and grip force in control group. The MT and EMG-stim were effective in increasing the Fugl-Meyer motor scale for upper extremity (MT group: P<0.01), increasing wrist extension range, grip force, and hand dexterity determined by the Box and Block Test (MT group and ES group P<0.05). Furthermore, hand skills were increased significantly in the MT group compared with the ES group at the follow-up assessment (P<0.05). This pilot study suggested that MT was more efficient in improving motor performance than physiotherapy alone. Also, MT may be more useful in improving the hand skills compared with EMG-stim. We assume that this difference might be related to the feasibility of maintenance of MT at home.
Densification and connectivity in polycrystalline MgB2 materials for improvement of critical current density

1 Thesis Organization. 5 Chapter 1: Introduction. 6 1.1 Literature Review on MgB2 Superconductor. 6 1.1.1 Background. 6 1.1.2 Crystal and Electrical Structure of MgB2. 10 1.1. 3 Two-band and Two-gap Superconductivity in MgB2. 14 1.1. 3.1 Pairing Mechanism. 14 1.1. 3.2 Superconducting Gap. 15 1.1. 3.3 The First Two-gap Superconductor. 18 1.1. 3.4 The Origin of Two Superconducting Gaps. 18 1.1. 3.5 Resistivity in the Normal State and Tc. 21 1.1. 3.6 Lattice Disorder and Tc. 22 1.1. 3.7 Bc2 Behaviour. 23 1.1. 4 Fabrication Methods of MgB2 Bulks and Wires. 27 1.1. 4.1 In Situ Powder-in-Tube Method. 27 1.1. 4.2 Ex Situ Powder-in-Tube Method. 33 1.1. 4.3 Hot Pressing Method. 34 1.1. 4.4 Diffusion Method. 34 1.1. 5 Chemical Doping. 39 1.1. 6 Existing Problems in MgB2 Application. 42 1.2 PhD Project Plan for Addressing Existing Problems. 45 Reference. 47 V Chapter 2: Experimental. 60 2.1 Sample Preparation. 60 2.2 Sample Characterization. 60 2.2.1 X-ray Diffraction Studies. 60 2.2.2 Raman Spectroscopy Studies. 65 2.2. 3 Electron Microscopy Studies. 66 2.2. 4 Measurements of Superconducting Properties. 67 2.2. 4.1 Critical Transition Temperature (Tc). 67 2.2. 4.2 Upper Critical Field (Bc2) and Irreversibility Field (Birr). 68 2.2. 4.2 Critical Current Density (Jc). 69 Reference. 71 Chapter 3: Fabrication of Highly Dense MgB2 Bulk at Ambient Pressure. 73 3.
Predictors of Bacteraemia in Patients with Suspected Community-Acquired Pneumonia

Introduction The diagnostic yield of blood cultures is limited in patients with community-acquired pneumonia (CAP). Yet, positive blood culture results provide important information for antibiotic treatment and for monitoring epidemiologic trends. We investigated the potential of clinical predictors to improve the cost-benefit ratio of obtaining blood cultures. Methods Data from two prospective cohort studies of adults with suspected CAP, admitted to non-ICU wards, were combined. Two models were created, one using readily available parameters and one additionally including laboratory parameters. Results 3,786 patients were included (2,626 (69%) with X-ray confirmed CAP). Blood cultures were obtained from 2,977 (79%) patients (and from 2,107 (80%) with X-ray confirmed CAP). 266 (8.9%) of the patients with a blood culture had bacteraemia. Clinical predictors of bacteraemia were absence of pre-admission antibiotic treatment, pleuritic pain, gastro-intestinal symptoms, tachycardia, tachypnea, hypotension and absence of hypoxia. After including laboratory results in the model, younger age, C-reactive protein, leukocytosis or leukopenia, low thrombocyte count, low sodium level, elevated urea and elevated arterial pH were added, while gastro-intestinal symptoms and hypotension were no longer significant. The area under the receiver operating characteristics curve was 0.66 (95% confidence interval 0.63–0.70) for the first model and 0.76 (95% confidence interval 0.73–0.79) for the second model. Conclusion In conclusion, in patients hospitalized with CAP, bacteraemia was moderately predictable using clinical parameters only. We recommend against the use of a risk prediction model for the decision to obtain blood cultures.
A Corpus for Studying Addressing Behavior in Multi-Party Dialogues

This paper describes a multi-modal corpus of hand-annotated meeting di-alogues that was designed for studying addressing behavior in face-to-face conversations. The corpus contains annotated dialogue acts, addressees, adjacency pairs and gaze direction. First, we describe the corpus design where we present the annotation schema, annotation tools and annotation process itself. Then, we analyze the reproducibility and stability of the annotation schema.
Finite element analysis of particle impact problems

Particle impacts are of fundamental importance in many areas and there has been a renewed interest in research on particle impact problems. A comprehensive investigation of the particle impact problems, using finite element (FE) methods, is presented in this thesis. The capability of FE procedures for modelling particle impacts is demonstrated by excellent agreements between FE analysis results and previous theoretical, experimental and numerical results. For normal impacts of elastic particles, it is found that the energy loss due to stress wave propagation is negligible if it can reflect more than three times during the impact, for which Hertz theory provides a good prediction of impact behaviour provided that the contact deformation is sufficiently small. For normal impact of plastic particles, the energy loss due to stress wave propagation is also generally negligible so that the energy loss is mainly due to plastic deformation. Finite-deformation plastic impact is addressed in this thesis so that plastic impacts can be categorised into elastic-plastic impact and finite-deformation plastic impact. Criteria for the onset of finite-deformation plastic impacts are proposed in terms of impact velocity and material properties. It is found that the coefficient of restitution depends mainly upon the ratio of impact velocity to yield Vni/Vy0 for elastic-plastic impacts, but it is proportional to [(Vni/Vy0)*(Y/E*)]-1/2, where Y /E* is the representative yield strain for finite-deformation plastic impacts. A theoretical model for elastic-plastic impacts is also developed and compares favourably with FEA and previous experimental results. The effect of work hardening is also investigated.
A preliminary controlled study to determine whether whole-plant cannabis extracts can improve intractable neurogenic symptoms

Objectives: To determine whether plant-derived cannabis medicinal extracts (CME) can alleviate neurogenic symptoms unresponsive to standard treatment, and to quantify adverse effects. Design: A consecutive series of double-blind, randomized, placebo-controlled single-patient cross-over trials with two-week treatment periods. Setting: Patients attended as outpatients, but took the CME at home. Subjects: Twenty-four patients with multiple sclerosis (18), spinal cord injury (4), brachial plexus damage (1), and limb amputation due to neurofibromatosis (1). Intervention: Whole-plant extracts of delta-9-tetrahydrocannabinol (THC), cannabidiol (CBD), 1:1 CBD:THC, or matched placebo were self-administered by sublingual spray at doses determined by titration against symptom relief or unwanted effects within the range of 2.5–120 mg/24 hours. Measures used: Patients recorded symptom, well-being and intoxication scores on a daily basis using visual analogue scales. At the end of each two-week period an observer rated severity and frequency of symptoms on numerical rating scales, administered standard measures of disability (Barthel Index), mood and cognition, and recorded adverse events. Results: Pain relief associated with both THC and CBD was significantly superior to placebo. Impaired bladder control, muscle spasms and spasticity were improved by CME in some patients with these symptoms. Three patients had transient hypotension and intoxication with rapid initial dosing of THC-containing CME. Conclusions: Cannabis medicinal extracts can improve neurogenic symptoms unresponsive to standard treatments. Unwanted effects are predictable and generally well tolerated. Larger scale studies are warranted to confirm these findings.
An Optimized Blockwise Nonlocal Means Denoising Filter for 3-D Magnetic Resonance Images

A critical issue in image restoration is the problem of noise removal while keeping the integrity of relevant image information. Denoising is a crucial step to increase image quality and to improve the performance of all the tasks needed for quantitative imaging analysis. The method proposed in this paper is based on a 3-D optimized blockwise version of the nonlocal (NL)-means filter (Buades, , 2005). The NL-means filter uses the redundancy of information in the image under study to remove the noise. The performance of the NL-means filter has been already demonstrated for 2-D images, but reducing the computational burden is a critical aspect to extend the method to 3-D images. To overcome this problem, we propose improvements to reduce the computational complexity. These different improvements allow to drastically divide the computational time while preserving the performances of the NL-means filter. A fully automated and optimized version of the NL-means filter is then presented. Our contributions to the NL-means filter are: 1) an automatic tuning of the smoothing parameter; 2) a selection of the most relevant voxels; 3) a blockwise implementation; and 4) a parallelized computation. Quantitative validation was carried out on synthetic datasets generated with BrainWeb (Collins, , 1998). The results show that our optimized NL-means filter outperforms the classical implementation of the NL-means filter, as well as two other classical denoising methods [anisotropic diffusion (Perona and Malik, 1990)] and total variation minimization process (Rudin, , 1992) in terms of accuracy (measured by the peak signal-to-noise ratio) with low computation time. Finally, qualitative results on real data are presented.
Mosquito noise in MPEG-compressed video: test patterns and metrics

Mosquito noise is a time dependent video compression impairment in which the high frequency spatial detail in video images having crisp edges is aliased intermittently. A new synthetic test pattern of moving spirals or circles is described which generates mosquito noise (MN) under Motion Pictures Expert Group (MPEG) compression. The spiral pattern is one of several NIST-developed patterns designed to stress specific features of compression based on motion estimation and quantization. The 'Spirals' pattern has several spirals or circles superimposed on a uniform background. The frames are filtered to avoid interline flicker which may be confounded with MN. Motion of the spirals and changing luminance of the background can be included to reduce the correlation between successive frames. Unexpectedly, even a static pattern of spirals can induce mosquito noise due to the stochastic character of the encoder. We consider metrics which are specific to the impairment being measured. For mosquito noise, we examine two separable detectors: each consists of a temporal (frame-to-frame) computation applied to the output of a spatial impairment detector which is applied to each frame. The two spatial detectors are: FLATS, which detects level 8 X 8 pixel image blocks; and the root-mean-square (RMS) applied to the image differences between original and compressed frames. The test patterns are encoded at low bit rates. We examine the measured mosquito noise as a function of the Group-of-Pictures (GOP) pattern in the MPEG-2 encoding and find that the GOP structure defines the periodicities of the MN.
THE D E H Y D R O X Y L A T I O N OF THE KAOLINITE CLAY MINERALS USING INFRARED EMISSION SPECTROSCOPY

Abs t rac t -The dehydroxylation of a series of the kaolinite clay minerals, kaolinite, halloysite and dickite, has been investigated by Fourier transform in situ infrared emission spectroscopy over a temperature range of 100 to 800 ~ at both 50 and 5 ~ intervals. Excellent correspondence was obtained between the high temperature emission spectra and FTIR absorption spectra of the quenched clay mineral phases. The major advantage of the technique lies in the ability to obtain vibrational spectroscopic information in situ at the elevated temperature. Dehydroxylation at a number of temperatures was determined by the loss of intensity of hydroxyl bands as indicated by intensity changes of the 3550 cm ~ to 3750 cm 1 emission spectra. As with all clay minerals, kaolinite clay mineral dehydroxylation is structure dependent. No clay phase changes occur until after dehydroxylation takes place. The kaolinite clay mineral loses the inner sheet and inner hydroxyl groups simultaneously, whereas dickite and halloysites are shown to lose the outer hydroxyls, as evidenced by the intensity loss of the -3684 cm 1 peak, before the inner hydroxyl groups as determined by the intensity loss of the 3620 cm 1 peak. Evidence for a high temperature stable hydroxyl band at 3730 cm ~ for dickite and halloysite was obtained. This band is attributed to the formation of a silanol group formed during the dehydroxylation process. It is proposed that the dehydroxylation process for kaolinite takes place homogenously and involves 2 mechanisms. The dehydroxylation of dickite and halloysite takes place in steps, with the first hydroxyl loss taking place homogenously and the second inhomogenously. Key Words----Dehydroxylation, Dickite, Emission, Halloysite, Hydroxyl, Infrared, Kandite, Kaolinite, Mechanism of dehydroxylation.
An Investigation Into Thermal Necrosis Of BoneAssociated With Surgical Procedures

We present the results of an investigation into thermal bone damage or necrosis associated with orthopaedic surgical procedures. Thermal necrosis can lead to infections and pin loosening. It is reported that the critical level at which thermal necrosis appears is when the bone is exposed to a temperature of around 56°C over a time of 10 seconds. At this temperature the denaturation point of alkaline phosphatase is reached, which means that the change in properties are directly attributed to the reorientation of collagen molecules and hydroxyapatite. We present data based on the use of pig bone. No human subjects were used in this study and ethical approval was therefore not necessary. Drilling was undertaken using an engineering instrument on which the speed may be adjusted. K-wires of varying diameters were used in this drill assembly. Bone sections through drilling points were examined in a scanning electron microscope (SEM). Results are presented in instances where K-wires of different diameters have been inserted by drilling into bone, for different drilling speeds, and for different times taken to drill the K-wire into bones. We present data that indicates that the cooling of bone during surgical procedures may significantly reduce the degree of thermal necrosis arising during orthopaedic surgical procedures.
Pharmacogenetics of the mycophenolic acid targets inosine monophosphate dehydrogenases IMPDH1 and IMPDH2: gene sequence variation and functional genomics

BACKGROUND AND PURPOSE Inosine monophosphate dehydrogenases, encoded by IMPDH1 and IMPDH2, are targets for the important immunosuppressive drug, mycophenolic acid (MPA). Variation in MPA response may result, in part, from genetic variation in IMPDH1 and IMPDH2.