Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and immunochemical studies of teichoic acid of Listeria monocytogenes.

An immunologically active teichoic acid component was isolated from the cell wall of Listeria monocytogenes strain EGD. The teichoic acid component, accounting for about 20% of the weight of cell wall, contained N-acetylglucosamine, rhamnose, ribitol, and phosphorus in a molar ratio of 0.95 : 1.0 : 0.97 : 0.98. The molecular weight of the teichoic acid chain was about 120,000 as analyzed by gel filtration. The probable structure was deduced from the results of methylation analysis, Smith degradation, and proton magnetic resonance spectrometry of the teichoic acid, together with the characterization of fragments obtained by treatment with hydrofluoric acid, as follows: (formula; see text) Inhibition testing with monosaccharide and fragments obtained from HF treatment of Listeria teichoic acid in the quantitative precipitin reaction suggested that the rhamnose residue is a major antigenic determinant.
Adrenal insufficiency during septic shock*

ObjectiveTo determine whether a baseline (random) cortisol concentration <25 &mgr;g/dL in patients with septic shock was a better discriminator of adrenal insufficiency than the standard (250 &mgr;g) and the low-dose (1 &mgr;g) corticotropin stimulation tests as assessed by the hemodynamic response to steroid replacement. SettingIntensive care unit. PatientsFifty-nine patients with septic shock. Their mean age was 57 ± 16.7 yrs; 29 were male. InterventionsA baseline cortisol concentration was obtained. Patients then received an intravenous injection of 1 &mgr;g of corticotropin (low-dose test) followed 60 mins later by an injection of 249 &mgr;g of corticotropin (high-dose test). Cortisol concentrations were obtained 30 and 60 mins after low- and high-dose corticotropin. All patients were administered hydrocortisone (100 mg every 8 hrs) for the first 24 hrs while awaiting results of cortisol assessment. Patients were considered steroid responsive if the pressor agent could be discontinued within 24 hrs of the first dose of hydrocortisone. Measurements and Main ResultsForty-seven percent of patients died. Twenty-two percent of patients met the diagnostic criteria of adrenal insufficiency by the low-dose test and 8% by the high-dose test. However, 61% of patients met the criteria of adrenal insufficiency when we used a baseline cortisol concentration of <25 &mgr;g/dL. Twenty-two patients (37%) were steroid responsive; the baseline serum cortisol was 14.1 ± 5.2 &mgr;g/dL in the steroid-responsive patients compared with 33.3 ± 18 &mgr;g/dL in the steroid-nonresponsive patients (p < .0001). Ninety-five percent of steroid-responsive patients had a baseline cortisol concentration <25 &mgr;g/dL. Fifty-four percent of steroid responders had a diagnostic low-dose test and 22% a diagnostic high-dose test. Receiver operating characteristic curve analysis revealed that a stress cortisol concentration of 23.7 &mgr;g/dL was the most accurate diagnostic threshold for determination of the hemodynamic response to glucocorticoid therapy. ConclusionsAdrenal insufficiency is common in patients with septic shock, the incidence depending largely on the diagnostic test and criteria used to make the diagnosis. There is clearly no absolute serum cortisol concentration that distinguishes an adequate from an insufficient adrenal response. However, we believe that a random cortisol concentration of <25 &mgr;g/dL in a highly stressed patient is a useful diagnostic threshold for the diagnosis of adrenal insufficiency.
Characterization of municipal waste in Kampala, Uganda

In Kampala, Uganda, about 28,000 tons of waste is collected and delivered to a landfill every month. Kampala Capital City Authority (KCCA) records show that this represents approximately 40% of the waste generated in the city. The remaining uncollected waste is normally dumped in unauthorized sites, causing health and environmental problems. However, the organic fraction of domestic waste can provide an opportunity to improve livelihoods and incomes through fertilizer and energy production. This study characterized the municipal waste generated in Kampala and delivered to Kiteezi landfill between July 2011 and June 2012, that is, covering the dry and wet months. On each sampling day, waste was randomly selected from five trucks, sorted and weighed into different physical fractions. Samples of the organic waste from each truck were analyzed for total solids, major nutrients, and energy content. During the wet months, the waste consisted of 88.5% organics, 3.8% soft plastics, 2.8% hard plastics, 2.2% paper, 0.9% glass, 0.7% textiles and leather, 0.2% metals, and 1.0% others. During the dry months, the waste consisted of 94.8% organics, 2.4% soft plastics, 1.0% hard plastics, 0.7% papers, 0.3% glass, 0.3% textile and leather, 0.1% metals, and 0.3% others. The organic waste on average had a moisture content of 71.1% and contained 1.89% nitrogen, 0.27% phosphorus, and 1.95% potassium. The waste had an average gross energy content of 17.3 MJ/kg. It was concluded that the organic waste generated can be a suitable source of some plant nutrients that are useful especially in urban agriculture. Implications: The result of the waste characterization in Kampala was found to be significantly different from that obtained for other Sub-Saharan African (SSA) cities, showing that studies assuming average values for the waste fractions are likely to result in erroneous results. Furthermore, no reduction in organic fraction of the waste was noticed when compared with a study done two decades ago in spite of greatly improved economic status of Kampala city, a finding that is not in agreement with several other similar studies done for other SSA cities.
Influence of stocking rate and grazing system on plant basal cover and botanical composition of veld in the northern cape 1

Abstract Changes in basal cover and botanical composition were recorded at four stocking rates, both under continuous and rotational grazing in the Northern Cape. The experiment was conducted with cattle. Results suggested that heavier stocking rates could be applied under rotational grazing than under continuous grazing without veld deterioration occuring. After four seasons, botanical composition deteriorated only under continuous grazing. Plant basal cover decreased significantly at the heavy stocking rates, both under rotational and continuous grazing. This result illustrates the danger of grazing strategies based on an injudicious increase in stock numbers. Basal cover was found to be a better indicator of trends in veld condition than botanical composition, despite annual fluctuations resulting from rainfall variability. Changes in the botanical composition apparently occur only where veld deterioration is more advanced.
Effect of Various Antibacterial Preparations on the Pathogenic Oral Flora in Elderly Patients Fed via Nasogastric Tube

ABSTRACT Oropharyngeal colonization by pathogenic gram-negative bacilli (GNB) and Staphylococcus aureus is associated with aspiration pneumonia. Decolonization in high-risk populations may be important. We prospectively evaluated six antiseptic compounds in nasogastric tube-fed frail elderly patients; only polymixine reduced oropharyngeal colonization with GNB. None had an effect on S. aureus colonization.
Histopathology and immunohistochemistry of bats infected by Australian bat lyssavirus.

OBJECTIVE To describe the lesions and distribution of viral antigens in bats infected by Australian bat lyssavirus. DESIGN A retrospective histopathological and immunohistochemical study of bats naturally infected with the virus. PROCEDURE Tissues from 37 infected bats were examined. Nineteen flying foxes (fruit bats) and two insectivorous bats were examined in detail. Brains of another 16 flying foxes were poorly fixed and were examined less fully. RESULT Lesions varied considerably between individuals and, where present, were mostly those of nonsuppurative meningoencephalomyelitis and ganglioneuritis similar to lesions seen in rabies and rabies-like diseases. The number of cells with intracytoplasmic inclusion bodies (Negri bodies) was variable; none were seen in some bats. Intracytoplasmic vacuolation of neurons was a common finding. Lesions occurred throughout the central nervous system but were most frequent and severe in the hippocampus, thalamus and midbrain, and medulla oblongata and pons. Indirect immunoperoxidase tests for lyssavirus antigen reactions varied in intensity and distribution, but also occurred mostly in the hippocampus, thalamus and midbrain, and medulla oblongata and pons. In peripheral tissues, reactions were seen in autonomic ganglia, in nerve plexuses of the gastrointestinal tract, in nervous tissues within muscles and immediately adjacent to individual muscle fibres, in an adrenal medulla, and in epithelial tissues in one of eight salivary glands examined. CONCLUSION The main lesion in Australian bat lyssavirus infection is nonsuppurative inflammation similar to that seen in rabies and other rabies-like diseases, except that the number of Negri bodies is more variable. Reactions to immunoperoxidase tests for lyssavirus vary in intensity and distribution and may occur in both central and peripheral nervous systems. These reactions do not always occur in the salivary glands, even if brain infection is present.
Optimizing visual attention models for predicting human fixations using Genetic Algorithms

Predicting where humans look in a scene is crucial in tasks like human-computer interaction, design, graphics, image and video compression, and gaze animation. This work proposes the use of a mixed-integer constraint Genetic Algorithm (GA) for searching the optimal parameters of a bio-inspired visual saliency model for accurate prediction of human eye fixations. Bioinspired visual saliency models are complex models, mimicking the primate visual system with a vast choice of design parameters that can be tuned to achieve optimal performance. The bottom-up visual attention model used in this study was trained on three challenging image datasets from the ImgSal database using a standard performance metric (area under Receiver Operating Characteristic curve) as the fitness. To compensate for any bias of the optimized model towards the standard metric, we use two other scoring metrics to assess performance. Performance comparisons with eight state-of-the-art models have been presented for all three scoring metrics. Results show that the proposed GA optimized visual attention model provides better prediction performance than several state-of-the-art models of visual attention.
Associations of Objectively Measured Physical Activity and Sedentary Time With Arterial Stiffness in Pre-Pubertal Children.

PURPOSE To investigate the relationships of objectively measured physical activity (PA) and sedentary time (ST) to arterial stiffness in prepubertal children. METHOD Altogether 136 children (57 boys, 79 girls) aged 6-8-years participated in the study. Stiffness index (SI) was assessed by pulse contour analysis based on photoplethysmography. ST, light PA, moderate PA, and vigorous PA were assessed using combined acceleration and heart rate monitoring. We investigated the associations of ST (<1.5METs) and time spent in intensity level of PA above 2-7METs in min/d with SI using linear regression analysis. We studied the optimal duration and intensity of PA to identify children being in the highest quarter of SI using Receiver Operating Characteristics curves. RESULTS Moderate PA, vigorous PA, and cumulative time spent in PA above 3 (β=-0.279, p = .002), 4 (β =-0.341, P<0.001), 5 (β =-0.349, P<0.001), 6 (β =-0.312, P<0.001), and 7 (β =-0.254, p = .005) METs were inversely associated with SI after adjustment for age, sex, and monitor wear time. The cutoffs for identifying children being in the highest quarter of SI <68 min/d for PA exceeding 5 METs and <26 min/d for PA exceeding 6 METs. CONCLUSION Lower levels of PA exceeding 3-6 METs were related to higher arterial stiffness in children.
Characteristics of population with normal serum creatinine impaired renal function and: the validation of a MDRD formula in a healthy general population.

BACKGROUND AND AIMS Glomerular filtration rate (GFR) provides the most accurate estimation of renal function. This study investigated the clinical characteristics of patients with impaired renal function having a normal serum creatinine level. We also validated whether the new Modification of Diet in Renal Disease (MDRD) formula can be applied in a healthy general population. MATERIAL AND METHODS A total 393 participants who had serum creatinine concentration below 132.6 micromol/L without underlying diseases were randomly selected on an address basis in Ansan City. According to the level of GFR, they were divided into 3 groups and we analyzed their clinical characteristics. In 75 subjects, who were randomly selected 25 cases in each group based on GFR estimated by Cockcroft-Gault (C-G) formula, true GFR was measured using the 99mTc-DTPA renal clearance method. RESULTS A total 393 (male: 106, female: 287) participants were as follows: GFR < 60 ml/min/1.73 m2; 4% (n = 25); 60 < or = GFR < 90 ml/min/1.73 m2; 26.2% (n = 103); GFR > or = 90 ml/min/1.73 m2; 67.4% (n = 265). In the group of decreased GFR, the mean age was older (67.4+/-10.7 vs. 48.7+/-12.8 vs. 39.4+/-8.2 years, p < 0.001), the gender was male (90.33+/-28.77 vs. 110.55+/-31.64, p < 0.001), and amount of proteinuria more increased (0.61 (0.56) vs. 0.33 (0.34) vs. 0.38 (0.33) gm/day, p = 0.007). The accuracy and precision of each formula were assessed by the difference in GFR measured by the 99mTc-DTPA renal clearance method--estimated GFR by each formula (deltaGFR), and the coefficient of determination (r2) of different predictive equations. The results were as follows: deltaGFR = -14.78+/-46.03, r2 = 0.79 (24-hour urinary creatinine clearance), deltaGFR=-16.79+/-57.32, r2 = 0.66 (100/serum creatinine), deltaGFR = 9.54+/-39.18, r2 = 0.87 (C-G formula), deltaGFR = -12.30+/-54.31, r2 = 0.66 (AASK formula), deltaGFR = 8.70+/-37.62, r2 = 0.79 (MDRD formula). Multiple linear regression analysis and logistic regression analysis showed that age, serum creatinine, total cholesterol and 24-hour urinary protein excretion were independently related to GFR and associated with a significant increase in the risk of decrement of GFR. CONCLUSIONS From these results, a more accurate assessment of renal function should be required in a population characterized by older age, male gender and more proteinuria. The MDRD study formula and Cockcroft-Gault formula have greater accuracy and precision with true GFR, and this equation can be applied in subjects with healthy general population.
Phylomark, a Tool To Identify Conserved Phylogenetic Markers from Whole-Genome Alignments

ABSTRACT The sequencing and analysis of multiple housekeeping genes has been routinely used to phylogenetically compare closely related bacterial isolates. Recent studies using whole-genome alignment (WGA) and phylogenetics from >100 Escherichia coli genomes has demonstrated that tree topologies from WGA and multilocus sequence typing (MLST) markers differ significantly. A nonrepresentative phylogeny can lead to incorrect conclusions regarding important evolutionary relationships. In this study, the Phylomark algorithm was developed to identify a minimal number of useful phylogenetic markers that recapitulate the WGA phylogeny. To test the algorithm, we used a set of diverse draft and complete E. coli genomes. The algorithm identified more than 100,000 potential markers of different fragment lengths (500 to 900 nucleotides). Three molecular markers were ultimately chosen to determine the phylogeny based on a low Robinson-Foulds (RF) distance compared to the WGA phylogeny. A phylogenetic analysis demonstrated that a more representative phylogeny was inferred for a concatenation of these markers compared to all other MLST schemes for E. coli. As a functional test of the algorithm, the three markers (genomic guided E. coli markers, or GIG-EM) were amplified and sequenced from a set of environmental E. coli strains (ECOR collection) and informatically extracted from a set of 78 diarrheagenic E. coli strains (DECA collection). In the instances of the 40-genome test set and the DECA collection, the GIG-EM system outperformed other E. coli MLST systems in terms of recapitulating the WGA phylogeny. This algorithm can be employed to determine the minimal marker set for any organism that has sufficient genome sequencing.
Submitted to the Annals of Statistics ANALYSIS OF BOOSTING ALGORITHMS USING THE SMOOTH MARGIN FUNCTION ∗ By

Columbia University and Princeton University We introduce a useful tool for analyzing boosting algorithms called the “smooth margin function”, a differentiable approximation of the usual margin for boosting algorithms. We present two boosting algorithms based on this smooth margin, “Coordinate Ascent Boosting” and “Approximate Coordinate Ascent Boosting”, which are similar to Freund and Schapire’s AdaBoost algorithm and Breiman’s arc-gv algorithm. We give convergence rates to the maximum margin solution for both of our algorithms and for arc-gv. We then study AdaBoost’s convergence properties using the smooth margin function. We precisely bound the margin attained by AdaBoost when the ∗This material is based upon work supported by the National Science Foundation under Grant Numbers 0434636, CCR-0325463, IIS-0325500 and DMS-9810783; and by AFOSR award F49620-01-1-0099. This work was done while CR’s affiliations were Program in Applied and Computational Mathematics and Department of Computer Science, Princeton University, and Center for Neural Science, Courant Institute, and Howard Hughes Medical Institute, New York University. AMS 2000 subject classifications: Primary 68W40,68Q25; secondary 68Q32
Femoral head diameter in the Malaysian population.

INTRODUCTION Hip arthroplasty is commonly performed worldwide. The objective of this study was to determine the diameter of the femoral head in the Malaysian population in relation to gender and race (i.e. among Malay, Chinese and Indian patients). METHODS This was a retrospective cross-sectional study performed between January 1995 and December 2006, evaluating the femoral head diameters of all patients aged 50 years and above who underwent hemiarthroplasty at two major hospitals in Malaysia. RESULTS A total of 945 femoral heads (663 women, 282 men) were evaluated. The mean age of the patients in our cohort was 75.2 ± 9.4 (range 50-101) years. The mean femoral head diameter (with intact articular cartilage) was 44.9 ± 3.2 (range 38-54) mm. In our study, men had a significantly larger mean femoral head diameter than women (47.7 ± 2.8 mm vs. 43.7 ± 2.4 mm; p < 0.05). Patients of Chinese ethnicity were also found to have significantly larger femoral head diameters, when compared among the three races studied (p < 0.05). CONCLUSION Malaysians have a mean femoral head diameter of 44.9 ± 3.2 mm. Among our patients, Chinese patients had a significantly larger femoral head size than Malay and Indian patients. We also found that, in our cohort, men had significantly larger femoral head diameters than women.
Collagen‐Induced Arthritis

The mouse model collagen‐induced arthritis (CIA) is a widely studied autoimmune model of rheumatoid arthritis. In this model, autoimmune arthritis is induced by immunization with type II collagen (CII) emulsified in complete Freund's adjuvant. This unit describes the steps necessary for the acquisition, handling, and preparation of CII, in addition to the selection of mouse strains, proper immunization technique, and methods for evaluation of the incidence and severity of arthritis. In this model, the first signs of arthritis appear approximately 21 to 28 days after immunization. The protocols in this unit should provide the investigator with all the necessary information required to reproducibly induce a high incidence of CIA in genetically susceptible strains of mice, and to critically evaluate the pathology of the disease. Curr. Protoc. Immunol. 89:15.5. 1‐15.5. 25. © 2010 by John Wiley & Sons, Inc.
Energy Abundance, Trade and Industry Location

We study the effect of countries’ energy abundance on trade and sector activity, conditional on sector’s energy intensity, using an unbalanced panel with 14 high-income countries from Europe, America and Asia, 10 broad sectors, and years 1970-1997. We find that (i) countries with large energy endowments have low energy prices, and are thus energy abundant both on micro and macro level. (ii) Energy abundant countries have a high level of energy embodied in exports relative to imports. (iii) Energy intensive sectors export from and (iv) have higher economic activity in energy abundant countries. (v) The trade and location effects increase with a sector’s exposure to international trade. In short, energy is a major driver for sector location through specialisation. We show that capital and energy are complements in the production function and use various controls in our analysis. The results give insights into delocalisation effects that may take place among rich countries with heterogeneous energy policy.
Costs of dialysis for elderly people in the UK.

BACKGROUND Growing acceptance rates of elderly patients for dialysis requires a careful planning of renal services expansion. As little is known about the actual resource use in patients 70 years and over, we evaluated the entire range of costs related to treatment, hospitalization, medication and other health and social service use, and assessed the impact of socio-demographic and clinical factors on costs. METHODS Service use and costs were assessed in a 12-month prospective cohort study of 171 dialysis patients, 70 years of age and over, from four hospital-based renal units in London, UK. RESULTS Total costs ranged between 14,940 pounds and 58,250 pounds per annum. The average annual cost was 22,740 pounds [95% confidence interval (CI), 21,470-24,020 pounds]. The majority of costs were allocated to dialysis treatment and transport (70%), hospitalizations (12%) and medication (12%). Other health and social services accounted for only 6% of total costs. Dialysis and hospitalization costs were pound 68.4 per day on average. Univariate subgroup analyses showed no significant difference between patients on peritoneal dialysis (64.5 pounds) and haemodialysis (71.5 pounds, P = 0.13). Age 80 years and over and presence of peripheral vascular disease (PVD) were associated with higher daily costs of 73.3 pounds compared with 63.2 pounds in the 70-74 age group (P = 0.033) and 76.9 pounds vs 63.8 pounds in patients without PVD (P = 0.022), respectively. Proximity to death was associated with a nearly pound 40 increase in daily costs (96.8 vs 59.7 pounds; P < 0.001). Multiple linear regression analyses confirmed these findings and showed that age 80 years and over and presence of peripheral and cerebrovascular disease were significant predictors of costs. There was a large but marginally significant difference in costs in patients with cancer. We found no evidence that diabetes was associated with higher dialysis and hospitalization costs. CONCLUSIONS The costs of providing dialysis for patients 70 years and over are largely shaped by the treatment costs rather than by use of community health and social services. Though age above 80 and co-morbidity are associated with increased resource use, average treatment costs are not higher than estimates for dialysis patients in general. This suggests that there is no case for providing treatment to younger patients and denying it to elderly patients on grounds of cost.