Miracle-dz/UniFAR-FTUs huggingface dataset:
Subcellular localization of Forssman glycolipid in epithelial MDCK cells by immuno-electronmicroscopy after freeze-substitution

Forssman antigen, a neutral glycosphingolipid carrying five monosaccharides, was localized in epithelial MDCK cells by the immunogold technique. Labeling with a well defined mAb and protein A- gold after freeze-substitution and low temperature embedding in Lowicryl HM20 of aldehyde-fixed and cryoprotected cells, resulted in high levels of specific labeling and excellent retention of cellular ultrastructure compared to ultra-thin cryosections. No Forssman glycolipid was lost from the cells during freeze-substitution as measured by radio-immunostaining of lipid extracts. Redistribution of the glycolipid between membranes did not occur. Forssman glycolipid, abundantly expressed on the surface of MDCK II cells, did not move to neighboring cell surfaces in cocultures with Forssman negative MDCK I cells, even though they were connected by tight junctions. The labeling density on the apical plasma membrane was 1.4-1.6 times higher than basolateral. Roughly two-thirds of the gold particles were found intracellularly. The Golgi complex was labeled for Forssman as were endosomes, identified by endocytosed albumin-gold, and lysosomes, defined by double labeling for cathepsin D. In most cases, the nuclear envelope was Forssman positive, but the labeling density was 10-fold less than on the plasma membrane. Mitochondria and peroxisomes, the latter identified by catalase, remained free of label, consistent with the notion that they do not receive transport vesicles carrying glycosphingolipids. The present method of lipid immunolabeling holds great potential for the localization of other antigenic lipids.
Seroincidence of HIV‐1 infection in African women of reproductive age: a prospective cohort study in Kigali, Rwanda, 1988–1992

Objective:To estimate the seroincidence of HIV-1 infection among women of reproductive age in Kigali, Rwanda.Design:Fixed prospective cohort followed for 36 months between November 1988 and June 1992, as part of an ongoing study of mother-to-child transmission of HIV-1.Setting:Centre Hospitalier, Kigali, Rwanda.Subjects:A total of 216 HIV-seronegative women were enrolled at delivery between November 1988 and June 1989.Methods:A blood sample was obtained at delivery to test for HIV antibodies (by enzyme-linked immunosorbent assay and Western blot). Serum was tested every 3 months during follow-up. Incidence density rates of HIV seroconversion were estimated.Results:The follow-up rate after 3 years was 89%, assessed by the maximum person-years method. The seroincidence density rate was 3.5 per 100 women-years (95% confidence interval, 1.9–5.0). It decreased linearly from 7.6 during the first 6-months postpartum to 2.5 per 100 women-years during the last 6 months of the third year of follow-up. Maternal age did not affect HIV incidence rates. We examined the role of the cohort, counselling, and the first 6-month postpartum effects on this estimate.Conclusion:This fixed cohort provided an overall estimation of the HIV infection incidence rate and its dynamics. These figures could be used for programming future HIV preventive vaccine efficacy trials in Rwanda.
Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate

Hepatitis C virus (HCV) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase. Little is known about the initial viral diversification and the viral life cycle processes that influence diversity. We studied the diversification of HCV during acute infection in 17 plasma donors, with frequent sampling early in infection. To analyze these data, we developed a new stochastic model of the HCV life cycle. We found that the accumulation of mutations is surprisingly slow: at 30 days, the viral population on average is still 46% identical to its transmitted viral genome. Fitting the model to the sequence data, we estimate the median in vivo viral mutation rate is 2.5×10−5 mutations per nucleotide per genome replication (range 1.6–6.2×10−5), about 5-fold lower than previous estimates. To confirm these results we analyzed the frequency of stop codons (N = 10) among all possible non-sense mutation targets (M = 898,335), and found a mutation rate of 2.8–3.2×10−5, consistent with the estimate from the dynamical model. The slow accumulation of mutations is consistent with slow turnover of infected cells and replication complexes within infected cells. This slow turnover is also inferred from the viral load kinetics. Our estimated mutation rate, which is similar to that of other RNA viruses (e.g., HIV and influenza), is also compatible with the accumulation of substitutions seen in HCV at the population level. Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification.
Assessment of Foetal Exposure to the Homogeneous Magnetic Field Harmonic Spectrum Generated by Electricity Transmission and Distribution Networks

During the last decades studies addressing the effects of exposure to Extremely Low Frequency Electromagnetic Fields (ELF-EMF) have pointed out a possible link between those fields emitted by power lines and childhood leukaemia. They have also stressed the importance of also including in the assessment the contribution of frequency components, namely harmonics, other than the fundamental one. Based on the spectrum of supply voltage networks allowed by the European standard for electricity quality assessment, in this study the exposure of high-resolution three-dimensional models of foetuses to the whole harmonic content of a uniform magnetic field with a fundamental frequency of 50 Hz, was assessed. The results show that the main contribution in terms of induced electric fields to the foetal exposure is given by the fundamental frequency component. The harmonic components add some contributions to the overall level of electric fields, however, due to the extremely low permitted amplitude of the harmonic components with respect to the fundamental, their amplitudes are low. The level of the induced electric field is also much lower than the limits suggested by the guidelines for general public exposure, when the amplitude of the incident magnetic field is set at the maximum permitted level.
Bmc Family Practice Somatisation: Illness Perspectives of Asylum Seeker and Refugee Patients from the Former Country of Yugoslavia

Background: Somatisation is particularly challenging in multicultural contexts where patients and physicians often differ in terms of their illness-related beliefs and practices and health care expectations. This paper reports on a exploratory study aimed at better understanding how asylum seeker and refugee patients from the former country of Yugoslavia who were identified by their physicians as somatising make sense of their suffering.
Role of soluble triggering receptor expressed on myeloid cells in inflammatory bowel disease.

AIM To investigate the probable role of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) in the pathogenesis of inflammatory bowel disease (IBD). METHODS Fifty-eight patients were enrolled; nineteen healthy volunteers served as controls; 8 patients were diagnosed with Crohn's disease, and 31 with ulcerative colitis. Clinical and endoscopic activity indexes of patients with Crohn's disease and ulcerative colitis respectively were estimated. Upon admission blood was sampled; sTREM-1 and TNFalpha were measured by an immunoassay and malondialdehyde (MDA) by the thiobarbitourate assay, after passage through an HPLC system. RESULTS Median +/- SE of TNFalpha of controls, patients with Crohn's disease and patients with ulcerative colitis were 6.02 +/- 3.94, 7.98 +/- 5.08 (P = NS vs controls), and 8.45 +/- 4.15 ng/L (P = 0.018 vs controls) respectively. Respective values of sTREM-1 were 53.31 +/- 32.93, 735.10 +/- 197.17 (P = 0.008 vs controls) and 435.82 +/- 279.71 ng/L (P = 0.049 vs controls). sTREM-1 was positively correlated with Crohn's disease activity index and clinical and endoscopic activity indexes of ulcerative colitis (P = 0.002, 0.001 and 0.009, respectively). sTREM-1 of patients with ulcerative colitis was positively correlated with TNFalpha (P = 0.001). CONCLUSION sTREM-1 seems to behave as a novel mediator in IBD in correlation with the degree of the inflammatory reaction of the intestinal mucosa.
Immunochemical analysis of respiratory-chain components of micrococcus luteus (lysodeikticus)

Membrane-bound antigens of the respiratory chain of Micrococcus luteus were analyzed by crossed immunoelectrophoresis after growth of the organism in the presence of 59Fe, the flavin adenine dinucleotide-flavin mononucleotide precursor D-[2-14C]riboflavin, or the heme precursor 5-amino-[4-(14)C]levulinic acid. Using zymograms and procedures of selective extraction in conjunction with autoradiography, it was possible to resolve and partially characterize a number of antigens. Succinate dehydrogenase (EC 1.3.99.1) was shown to possess covalently bound flavin and nonheme iron and was possibly present as a complex with cytochrome. Three other dehydrogenases, namely, NADH dehydrogenase, NAD(P)H dehydrogenase (EC 1.6.99.3), and malate dehydrogenase (EC 1.1.1.37), contained flavin in noncovalent linkage, the NAD(P)H dehydrogenase also possessing nonheme iron. Four other discrete antigens (or antigen complexes) containing both iron and heme centers also resolved, as were two minor immunogens possessing iron as the sole detectable prosthetic group.
Assessing the Impact of Differential Genotyping Errors on Rare Variant Tests of Association

Genotyping errors are well-known to impact the power and type I error rate in single marker tests of association. Genotyping errors that happen according to the same process in cases and controls are known as non-differential genotyping errors, whereas genotyping errors that occur with different processes in the cases and controls are known as differential genotype errors. For single marker tests, non-differential genotyping errors reduce power, while differential genotyping errors increase the type I error rate. However, little is known about the behavior of the new generation of rare variant tests of association in the presence of genotyping errors. In this manuscript we use a comprehensive simulation study to explore the effects of numerous factors on the type I error rate of rare variant tests of association in the presence of differential genotyping error. We find that increased sample size, decreased minor allele frequency, and an increased number of single nucleotide variants (SNVs) included in the test all increase the type I error rate in the presence of differential genotyping errors. We also find that the greater the relative difference in case-control genotyping error rates the larger the type I error rate. Lastly, as is the case for single marker tests, genotyping errors classifying the common homozygote as the heterozygote inflate the type I error rate significantly more than errors classifying the heterozygote as the common homozygote. In general, our findings are in line with results from single marker tests. To ensure that type I error inflation does not occur when analyzing next-generation sequencing data careful consideration of study design (e.g. use of randomization), caution in meta-analysis and using publicly available controls, and the use of standard quality control metrics is critical.
The Missing Waveform Information in the Orthogonal Electrocardiogram (Frank Leads): III. Computer Diagnosis of Angina Pectoris from “Maximal’ QRS Surface Waveform Information At Rest

Nine surface electrocardiograms recorded on the thoracic surface at fixed and identical locations in 412 individuals were found to account for the maximal useful waveform information available in each individual. In other words, nine waveforms were capable of resynthesizing any waveform recorded on their thoracic surface. These nine waveforms were then submitted to multivariate statistical procedures and their diagnostic performance compared to the Frank leads on which the same procedures were applied. Before the data were fed into the computer, all waveforms were time-normalized and divided into eight equal parts, yielding 72 variables and 24 variables for the nine lead system and the Frank leads, respectively, for each individual.In this paper we attempted to discriminate between normal subjects and patients with documented angina pectoris (typical history and positive coronary angiography); myocardial infarction was excluded in these patients. Only the resting QRS complex was considered. With the 9-lead system, keeping the specificity (true negatives) at 90%, the sensitivity (true positives) is 76%; with the Frank leads, the same specificity yielded a sensitivity of 49%. The repeatability of the results on new independent controls was also found very satisfactory.The discrimination between patients with angina pectoris on one hand and left ventricular hypertrophy and myocardial infarction on the other hand resulted in a performance level of 89% and 87%, respectively, for the 9-lead system. A good correlation was also found between the extent of the coronary lesions (number of coronary vessels involved) and the fraction of correctly diagnosed patients.The present study concluded that the retrieval of more complete surface information results in an evident improvement of the diagnostic performance of electrocardiography.
Multithreaded Java program test generation

We describe ConTest, a tool for detecting synchronization faults in multithreaded Java™ programs. The program under test is seeded with a sleep(), yield(), or priority() primitive at shared memory accesses and synchronization events. At run time, ConTest makes random or coverage-based decisions as to whether the seeded primitive is to be executed. Thus, the probability of finding concurrent faults is increased. A replay algorithm facilitates debugging by saving the order of shared memory accesses and synchronization events.
New lessons on the Sudd hydrology learned from remote sensing and climate modeling

Despite its local and regional importance, hydro-meteorological data on the Sudd (one of Africa's largest wetlands) is very scanty. This is due to the physical and political situation of this area of Sudan. The areal size of the wetland, the evaporation rate, and the influence on the micro and meso climate are still unresolved questions of the Sudd hydrology. The evaporation flux from the Sudd wetland has been estimated using thermal infrared remote sensing data and a parameterization of the surface energy balance (SEBAL model). It is concluded that the actual spatially averaged evaporation from the Sudd wetland over 3 years of different hydrometeorological characteristics varies between 1460 and 1935 mm/yr. This is substantially less than open water evaporation. The wetland area appears to be 70% larger than previously assumed when the Sudd was considered as an open water body. The groundwater table characterizes a distinct seasonality, confirming that substantial parts of the Sudd are seasonal swamps. The new set of spatially distributed evaporation parameters from remote sensing form an important dataset for calibrating a regional climate model enclosing the Nile Basin. The Regional Atmospheric Climate Model (RACMO) provides an insight not only into the temporal evolution of the hydro-climatological parameters, but also into the land surface climate interactions and embedded feedbacks. The impact of the flooding of the Sudd on the Nile hydroclimatology has been analysed by simulating two land surface scenarios (with and without the Sudd wetland). The paper presents some of the model results addressing the Sudd's influence on rainfall, evaporation and runoff of the river Nile, as well as the influence on the microclimate.
Usefulness of contrast-enhanced cardiac magnetic resonance in identifying the ventricular arrhythmia substrate and the approach needed for ablation.

AIMS The endocardial vs. epicardial origin of ventricular arrhythmia (VA) can be inferred from detailed electrocardiogram (ECG) analysis. However, despite its clinical usefulness, ECG has limitations. Alternatively, scarred tissue sustaining VAs can be identified by contrast-enhanced cardiac magnetic resonance (ce-CMR). The objective of this study was to determine the clinical value of analysing the presence and distribution pattern of scarred tissue in the ventricles to identify the VA site of origin and the ablation approach required. METHODS AND RESULTS A ce-CMR study was carried out before the index ablation procedure in a cohort of 80 patients with non-idiopathic VA. Hyper-enhancement (HE) in each ventricular segment was coded as absent, subendocardial, transmural, mid-myocardial, or epicardial. The endocardial or epicardial VA site of origin was also assigned according to the approach needed for ablation. The clinical VA was successfully ablated in 77 (96.3%) patients, all of them showing HE on ce-CMR. In segments with successful ablation of the clinical ventricular tachycardia, HE was absent in 3 (3.9%) patients, subendocardial in 19 (24.7%), transmural in 36 (46.7%), mid-myocardial in 8 (10.4%), and subepicardial in 11 (14.3%) patients. Epicardial ablation of the index VA was necessary in 3 (6.1%) ischaemic and 12 (42.9%) non-ischaemic patients. The presence of subepicardial HE in the successful ablation segment had 84.6% sensitivity and 100% specificity in predicting an epicardial origin of the VA. CONCLUSION Contrast-enhanced cardiac magnetic resonance is helpful to localize the target ablation substrate of non-idiopathic VA and also to plan the approach needed, especially in non-ischaemic patients.
Emergent states in transition metal oxides

Transition metal oxides adopt a wide variety of crystal structures and display a diverse range of physical phenomena from Mott insulating states to electronnematics to unconventional superconductivity. Detailed understanding of these states and how they may be manipulated by structural modi cations requires both precise structural knowledge and in-depth physical property measurements using as many techniques over as wide a range of phase space as possible. In the work described in this thesis a range of transition metal oxides were studied using high-resolution powder neutron di raction and detailed low-temperature physical property measurements. The quaternary barium orthotellurates Ba2NiTeO6, Ba2CuTeO6 and Ba2ZnTeO6 belong to an almost unstudied family of materials. The development of procedures for synthesizing large single crystals has facilitated the investigation of interesting new anisotropic magnetic states in the Cu and Ni systems and the existence of a possible structural phase transition in the Zn-based compound. YMnO3 is a multiferroic with improper ferrielectricity. The study of the high-temperature structural phases described in this thesis has led to the identi cation both of the transition path to the ferrielectric state and the identi cation of an isostructural phase transition within the ferrielectric phase. BiFe0.7Mn0. 3O3 is also a multiferroic material but with proper ferroelectricity. The investigation of the structural phases of this compound have provided con rmation of the high-temperature phases with the reassignment of the symmetry of the highest-temperature phase which is intriguingly di erent to that of the unsubstituted material. Finally, an investigation of the electronic structures of the high conductivity delafossites PdCoO2 and PdCrO2 using micro-cantilever torque magnetometry measurements of quantum oscillations is described. This has resolved the warping of the Fermi surface of PdCoO2 and given insights into the complicated Fermi surface of the itinerant antiferromagnet PdCrO2.
A prospective comparison of the selective observation and routine exploration methods for penetrating abdominal stab wounds with organ or omentum evisceration.

BACKGROUND Both routine laparotomy and selective observation methods have been used in the treatment of penetrating abdominal stab wounds with organ or omentum evisceration. There still are some conflicts about these treatment methods. METHODS Between 1998 and 2003, 61 patients treated in the authors' emergency clinic because of penetrating abdominal stab wounds with organ or omentum evisceration were evaluated prospectively. Excepting those with absolute indications for mandatory laparotomy, these patients were treated by either routine laparotomy or selective observation methods. Their prognosis, rates of unnecessary laparotomy, length of hospital stay, and complications were compared using Fisher's exact test and Student's t test. RESULTS Nine patients underwent mandatory laparotomy and were therefore excluded from the study. The overall incidence of the patients who had no significant abdominal pathology was 54.1% (33/61). The overall incidence of significant injuries among the asymptomatic patients was 36.5% (19/52). Routine laparotomy was performed for 21 patients, who experienced unnecessary laparotomy and complication rates of 33.33% and 19%, respectively. The mean length of hospital stay in this group was 137.38 +/- 53.25 hours. Of 31 patients, 24 who had been treated by selective observation methods were discharged without laparotomy. The unnecessary laparotomy and complication rates for this group were 6.45% (28.6% for the patients treated surgically) and 3.2%, respectively, whereas the mean length of hospital stay for this group was 81.22 +/- 42.46 hours. There were statistically significant differences in terms of unnecessary laparotomy rates and mean lengths of hospital stay, but no difference in terms of complication rates. CONCLUSION The selective observation method is safe and superior to routine laparotomy for the treatment of penetrating abdominal stab wounds with omentum evisceration.
The unique mutation in ace‐1 giving high insecticide resistance is easily detectable in mosquito vectors

High insecticide resistance resulting from insensitive acetylcholinesterase (AChE) has emerged in mosquitoes. A single mutation (G119S of the ace‐1 gene) explains this high resistance in Culex pipiens and in Anopheles gambiae. In order to provide better documentation of the ace‐1 gene and the effect of the G119S mutation, we present a three‐dimension structure model of AChE, showing that this unique substitution is localized in the oxyanion hole, explaining the insecticide insensitivity and its interference with the enzyme catalytic functions. As the G119S creates a restriction site, a simple PCR test was devised to detect its presence in both A. gambiae and C. pipiens, two mosquito species belonging to different subfamilies (Culicinae and Anophelinae). It is possibile that this mutation also explains the high resistance found in other mosquitoes, and the present results indicate that the PCR test detects the G119S mutation in the malaria vector A. albimanus. The G119S has thus occurred independently at least four times in mosquitoes and this PCR test is probably of broad applicability within the Culicidae family.
Genome Sequence of Amycolatopsis sp. Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete

ABSTRACT We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis sp. strain 39116, one of few bacterial species that are known to consume the lignin component of plant biomass. This genome sequence will further ongoing efforts to use microorganisms for the conversion of plant biomass into fuels and high-value chemicals.