Miracle-dz/UniFAR-FTUs huggingface dataset:
Histopathologic and Microbiologic Aspects of Ventilator-associated Pneumonia

Background The relationship between microbiology and histology in patients with ventilator-associated pneumonia has been sparsely described. Methods Twenty-five patients who died in the intensive care unit after their lungs had been mechanically ventilated for 72 h were studied. Twenty of the 25 died with clinical suspicion of pulmonary infection. A total of 375 immediate postmortem pulmonary biopsies were obtained after death and processed for quantitative microbiology and histology. Four evolutionary stages of pneumonia were defined: early, intermediate, advanced, and resolution. Results At least one specimen with histologic evidence of pneumonia was found in all but two patients (92%). Histologic pneumonia was a widespread and frequent process (46% of biopsies examined) involving predominantly the lower lobes (55% of all biopsies with pneumonia) and showing different histopathologic stages of progression coexisting in the same lung lobes. Lung cultures were frequently polymicrobial (149 of 375, 40% of the pulmonary biopsy cultures, and 20 of 25, 80% of the cases) and not always yielding the same pathogen (19 microorganisms) when comparing one lung to the other. Histopathology and microbiologic biopsy cultures showed a weak relationship (28% and 49% of species had counts greater or equal to 103 cfu/g in samples without pneumonia from patients with and without prior antibiotic treatment, respectively). Histopathologic evolutionary stages were not associated with any differences in quantitative culture results of pulmonary biopsies, independently of prior administration of antibiotics. Higher bacterial concentrations of biopsy cultures were associated with the absence of prior antibiotic treatment. Conclusions Ventilator-associated pneumonia is a frequent diffuse and polymicrobial process showing different coexisting degrees of evolution and involving preferentially the lower lobes. Microbiology and histology can be dissociated even in the absence of prior antibiotic treatment. Lung histology appears more reliable than bacteriology as a diagnostic reference test.
Mycobacterium ulcerans low infectious dose and mechanical transmission support insect bites and puncturing injuries in the spread of Buruli ulcer

Addressing the transmission enigma of the neglected disease Buruli ulcer (BU) is a World Health Organization priority. In Australia, we have observed an association between mosquitoes harboring the causative agent, Mycobacterium ulcerans, and BU. Here we tested a contaminated skin model of BU transmission by dipping the tails from healthy mice in cultures of the causative agent, Mycobacterium ulcerans. Tails were exposed to mosquito (Aedes notoscriptus and Aedes aegypti) blood feeding or punctured with sterile needles. Two of 12 of mice with M. ulcerans contaminated tails exposed to feeding A. notoscriptus mosquitoes developed BU. There were no mice exposed to A. aegypti that developed BU. Eighty-eight percent of mice (21/24) subjected to contaminated tail needle puncture developed BU. Mouse tails coated only in bacteria did not develop disease. A median incubation time of 12 weeks, consistent with data from human infections, was noted. We then specifically tested the M. ulcerans infectious dose-50 (ID50) in this contaminated skin surface infection model with needle puncture and observed an ID50 of 2.6 colony-forming units. We have uncovered a biologically plausible mechanical transmission mode of BU via natural or anthropogenic skin punctures.
Effect of ropinirole on sleep onset: A randomized, placebo-controlled study in healthy volunteers

Abstract—Somnolence and “sleep attacks” have been reported as an adverse effect of several antiparkinsonian drugs. The authors document, in a placebo-controlled, randomized, double-blind, crossover study performed in 20 healthy volunteers, using the Multiple System Latency Test (MSLT) as primary outcome, that ropinirole reduces time to sleep onset in humans. Ropinirole therapy was not associated with daytime episodes of rapid eyes movement (REM) sleep.
Effects of Melagatran, a New Low-molecular-weight Thrombin Inhibitor, on Thrombin and Fibrinolytic Enzymes

Summary Melagatran, a new, competitive and rapid inhibitor of thrombin with a molecular mass of 429 Da is described. Melagatran is well tolerated when administered in very high doses, and the oral bioavailability in the dog is relatively high. The aim of the study was to determine, in the preclinical setting, the degree of selectivity against the fibrinolytic system required for entering the clinical development phase. Melagatran was compared with two structurally similar thrombin inhibitors, inogatran and H 317/86. The potent inhibition of thrombin by melagatran was demonstrated by a low inhibition constant (Ki) for thrombin (0.002 μmol/l) and prolongation of clotting time to twice the control value in coagulation assays at low concentrations (0.010, 0.59 and 2.2 μmol/l for thrombin time, activated partial thromboplastin time and prothrombin time, respectively). Furthermore, thrombin-induced platelet aggregation was inhibited at the same concentration (IC50-value 0.002 μmol/l) as the Ki-value for thrombin. In two assays of global fibrinolysis, inhibition was observed at a concentration of 1.1 μmol/l in a euglobulin plasma fraction model, while no inhibition was observed at a concentration of ≤10 μmol/l in a plasma model. In an in vivo model of endogenous fibrinolysis in the rat, inhibition of fibrinolysis was observed at ≥1.0 μmol/l. In all assays, except the Ki-ratio determinations, the compounds could be graded with regard to selectivity against the fibrinolytic system: inogatran > melagatran > H 317/86. For melagatran, inhibition of fibrinolysis was not observed at concentrations below the upper limit of the proposed therapeutic plasma concentration interval (<0.5 μmol/l). Thus, melagatran seems to have a sufficient selectivity against the fibrinolytic system, while H 317/86 was considered to be insufficient for clinical development.
Commentary: the value of the ECG in the preparticipation sports physical examination: the Italian experience.

1. Renato Vitiello, MD 1. Unita Operativa Complessa di Pediatria e Neonatologia Ospedal Civile Torre Annunziata Torre Annunziata, Italy Editor’s note: This commentary by Dr Vitiello addresses cardiovascular preparticipation sports screening by describing the extensive Italian protocol aimed at preventing cardiovascular deaths in athletes. Presented data indicate the value of the protocol, and extending the practice across Europe has been proposed. Readers not only will find this information to be educational but also will appreciate the value of viewpoints and experiences from other countries. We hope to present more of these contributions from outside of North America in the near future. —LFN In 1982, the Italian Ministry of Health mandated required screening for everyone who participates in competitive sports. (1) The law states that every 1 to 2 years, all competitive athletes must be certified for participation. The definition of …
Water Deprivation: A New Migraine Precipitant

Fifty migraineurs were asked if insufficient fluid intake could provoke their migraine attacks. Twenty replied “yes,” 7 were doubtfully positive, and 23 said “no.” In addition 14 of 45 migraineurs at a meeting of the British Migraine association (UK) also recognized fluid deprivation as one of their migraine triggers. Thus a total of 34 of 95 migraineurs knew that dehydration could provoke their attacks, a precipitant not recognized by the medical profession. This indicates that we can add fluid deprivation to our list of migraine precipitants. It would be interesting to know the extent to which it applies in other climates. Further research is needed into the mechanism of this precipitant.
Designing PRIMA: A Precise Visual Language for Modeling with Agents, in a Physical environment

In this paper we introduce PRIMA: A PRecise vIsual language for Modeling with Agents, in a physical environment. Our objective is to design an expressive Domain Specific Visual Language for building agent-based models. Models in PRIMA are diagrams, which describe the agent structure (i.e. actuators and sensors), behavior, instances and environment topology. We show the use of metamodeling techniques to describe the multi-view language PRIMA, its definition in the AToM tool, and the generation of a customized modeling environment for it.
Recent accumulation variability in northwest Greenland from ground-penetrating radar and shallow cores along the Greenland Inland Traverse

Abstract Accumulation is a key parameter governing the mass balance of the Greenland ice sheet. Several studies have documented the spatial variability of accumulation over wide spatial scales, primarily using point data, remote sensing or modeling. Direct measurements of spatially extensive, detailed profiles of accumulation in Greenland, however, are rare. We used 400 MHz ground-penetrating radar along the 1009 km route of the Greenland Inland Traverse from Thule to Summit during April and May of 2011, to image continuous internal reflecting horizons. We dated these horizons using ice-core chemistry at each end of the traverse. Using density profiles measured along the traverse, we determined the depth to the horizons and the corresponding water-equivalent accumulation rates. The measured accumulation rates vary from ~0.1 m w.e. a–1 in the interior to ~0.7 m w.e. a–1 near the coast, and correspond broadly with existing published model results, though there are some excursions. Comparison of our recent accumulation rates with those collected along a similar route in the 1950s shows a ~10% increase in accumulation rates over the past 52 years along most of the traverse route. This implies that the increased water vapor capacity of warmer air is increasing accumulation in the interior of Greenland.
Memory for emotional words: The role of semantic relatedness, encoding task and affective valence

Emotional stimuli have been repeatedly demonstrated to be better remembered than neutral ones. The aim of the present study was to test whether this advantage in memory is mainly produced by the affective content of the stimuli or it can be rather accounted for by factors such as semantic relatedness or type of encoding task. The valence of the stimuli (positive, negative and neutral words that could be either semantically related or unrelated) as well as the type of encoding task (focused on either familiarity or emotionality) was manipulated. The results revealed an advantage in memory for emotional words (either positive or negative) regardless of semantic relatedness. Importantly, this advantage was modulated by the encoding task, as it was reliable only in the task which focused on emotionality. These findings suggest that congruity with the dimension attended at encoding might contribute to the superiority in memory for emotional words, thus offering us a more complex picture of the underlying mechanisms behind the advantage for emotional information in memory.
Effect of cytomegalovirus on an experimental model of chronic renal allograft rejection under triple-drug treatment in the rat.

BACKGROUND Cytomegalovirus (CMV) infection is thought to be a risk factor of chronic rejection. In clinical studies and animal models, mainly concerning graft vasculopathy, CMV has been demonstrated to enhance allograft arteriosclerosis. In this study we have investigated the effect of CMV on the early inflammatory response and graft histology in an experimental model of renal transplantation in a rat strain combination that develops chronic rejection under triple-drug immunosuppression. METHODS Renal transplantations were performed in a rat strain combination of DA-->BN receiving triple-drug treatment (2 mg/kg methylprednisolone, 2 mg/kg azathioprine, 5 mg/kg cyclosporine daily subcutaneously). One group of immunosuppressed animals was infected with rat CMV, the Maastricht strain (10(5) plaque-forming units intraperitoneally), and the other group was left uninfected. As a positive control for alloresponse, one group of recipients received neither immunosuppression nor virus. Syngenic transplantations with triple-drug treatment and CMV were used as negative controls. The grafts were monitored by frequent ultrasound-guided fine-needle aspiration biopsies, and the intragraft inflammation was quantified in detail by the increment method and expressed in corrected increment units (CIU). Graft histology was performed in parallel. RESULTS Nonimmunosuppressed animals developed acute rejection with a high peak of inflammation (7.9+/-3.2 CIU), a typical blast response, and lymphocytosis followed by infiltration of macrophages and necrosis within 7 days. Triple drug-treated animals had a short, mild inflammatory response (3.3+/-1.4 CIU at the peak) in the graft 3-5 days after transplantation but ended up with histological changes characteristic of chronic rejection with vasculopathy and fibrosis 40-60 days later. Triple drug-treated animals with CMV demonstrated a significantly stronger inflammation (4.5+/-1.8 CIU, P<0.01) than those without, and lymphoid activation continued longer and was followed by infiltration of macrophages in the graft. CMV infection of the graft was demonstrated by viral culture and antigen detection. In histology, chronic rejection with intimal thickening of arteries and arterioles and medial necrosis of large arteries was seen at 14 days, ending up with remarkable graft fibrosis within 20 days after transplantation. CONCLUSION CMV prolonged and increased graft inflammation and accelerated chronic rejection of renal allografts under triple-drug treatment.
Management of acute respiratory infections by community health volunteers: experience of Bangladesh Rural Advancement Committee (BRAC).

OBJECTIVE To assess the role of management practices for acute respiratory infections (ARIs) in improving the competency of community health volunteers in diagnosing and treating acute respiratory infections among children. METHODS Data were collected by a group of research physicians who observed the performance of a sample of 120 health volunteers in 10 sub-districts in Bangladesh in which Bangladesh Rural Advancement Committee (BRAC) had run a community-based ARI control programme since mid-1992. Standardized tests were conducted until the 95% interphysician reliability on the observation of clinical examination was achieved. FINDINGS The sensitivity, specificity, and overall agreement rates in diagnosing and treating ARIs were significantly higher among the health volunteers who had basic training and were supervised routinely than among those who had not. CONCLUSION Diagnosis and treatment of ARIs at the household level in developing countries are possible if intensive basic training and the close supervision of service providers are ensured.
Nutrient Leaching When Soil Is Part of Plant Growth Media

Soils can serve as sorbents for phosphorus (P), negating the need for artificial sorbents. The purpose of this study was to compare soils with different properties for their effect on nutrient levels in effluent. Four soils were mixed with sand and packed into columns 0.5 m long, with or without compost on the surface. Infiltration and effluent concentrations were measured before and after growing plants [Buffalograss (Buchloe dactyloides (Nutt.) Engelm. ) and bluegrama grasses (Bouteloua gracilis H.B.K.) and red clover (Trifolium pratense L.)]. The growth media with compost at the surface had higher nutrient levels than the media without the compost, but the final effluent nitrate concentrations post-harvest were significantly lower for columns with the compost blanket (59 vs. 86 mg L−1). All of the nitrate concentrations were high (many >100 mg L−1) due to mineralization and nitrogen fixation. The final effluent P concentrations before planting were significantly higher in the soil with the most sand (0.71 mg L−1), and after harvest in the mixture that contained the high soil P levels (0.58 mg L−1). Some soils (high in aluminum or calcium) were adequate sorbents for P without additions of other sorbents, but soils often generated too much nitrate in effluent.
BB rat lyp mutation and Type 1 diabetes

Summary: BioBreeding (BB) rats spontaneously develop an autoimmune diabetic syndrome similar to that observed in humans and NOD mice. One of the diabetes susceptibility loci maps to the lyp locus on chromosome 4. In this article we describe the consequences of the BB rat lyp mutation on T‐cell homeostasis, repertoire and function, as well as its role in the pathogenesis of type I diabetes.
Biodegradation of Chlorpyrifos, Malathion, and Dimethoate by Three Strains of Bacteria Isolated from Pesticide-Polluted Soils in Sudan.

This study was done to identify pesticide-biodegrading microorganisms and to characterize degradation rates. Bacillus safensis strain FO-36bT, Bacillus subtilis subsp. inaquosorum strain KCTC13429T, and Bacillus cereus strain ATCC14579T were isolated from pesticide-polluted soil in Sudan, separately incubated with each pesticide with periodic samples drawn for GC and GC-MS. Pesticide biodegradation followed a biphasic model. α and β half-lives (days) of chlorpyrifos, malathion, and dimethoate in B. safensis culture were 2.13, 4.76; 2.59, 5.66; and 9.5, 11.0, respectively. Values in B. subtilis and B. cereus cultures were 4.09, 9.45 and 4.33, 9.99 for chlorpyrifos; 2.99, 5.36 and 2.43, 4.71 for malathion; and 9.53, 15.11 and 4.16, 9.27 for dimethoate. No metabolite was detected in B. subtilis cultures, whereas a few were detected from B. safensis and B. cereus cultures. Bacterial efficiency can be ordered as B. safensis > B. subtilis > B. cereus for chlorpyrifos and B. cereus > B. subtilis > B. safensis for malathion and dimethoate.
Biophysical mechanisms of phase contrast in gradient echo MRI

Recently reported contrast in phase images of human and animal brains obtained with gradient-recalled echo MRI holds great promise for the in vivo study of biological tissue structure with substantially improved resolution. Herein we investigate the origins of this contrast and demonstrate that it depends on the tissue “magnetic architecture” at the subcellular and cellular levels. This architecture is mostly determined by the structural arrangements of proteins, lipids, non-heme tissue iron, deoxyhemoglobin, and their magnetic susceptibilities. Such magnetic environment affects/shifts magnetic resonance (MR) frequencies of the water molecules moving/diffusing in the tissue. A theoretical framework allowing quantitative evaluation of the corresponding frequency shifts is developed based on the introduced concept of a generalized Lorentzian approximation. It takes into account both tissue architecture and its orientation with respect to the external magnetic field. Theoretical results quantitatively explain frequency contrast between GM, WM, and CSF previously reported in motor cortex area, including the absence of the contrast between WM and CSF. Comparison of theory and experiment also suggests that in a normal human brain, proteins, lipids, and non-heme iron provide comparable contributions to tissue phase contrast; however, the sign of iron and lipid contributions is opposite to the sign of contribution from proteins. These effects of cellular composition and architecture are important for quantification of tissue microstructure based on MRI phase measurements. Also theory predicts the dependence of the signal phase on the orientation of WM fibers, holding promise as additional information for fiber tracking applications.
Recent Advances in the Design, Modeling, and Control of Multiphase Machines—Part I

Multiphase machines are well recognized as an attractive alternative to conventional three-phase machines in a number of applications where high overall system reliability and reduction in total power per phase are required. The pace of developments in the field has accelerated in the last few years, and substantial knowledge has been recently generated. The main objective of the two-part survey named ‘Recent Advances in the Design, Modeling, and Control of Multiphase Machines’ is to present relevant contributions to encourage and guide new advances and developments in the field. More specifically, part 1 of the work analyzes the recent progress in the design, modeling, and control, including healthy operation, of multiphase motor drives, and discusses open challenges and future research directions in the area.
Neural crest specification: tissues, signals, and transcription factors

The neural crest is a transient population of multipotent and migratory cells unique to vertebrate embryos. Initially derived from the borders of the neural plate, these cells undergo an epithelial to mesenchymal transition to leave the central nervous system, migrate extensively in the periphery, and differentiate into numerous diverse derivatives. These include but are not limited to craniofacial cartilage, pigment cells, and peripheral neurons and glia. Attractive for their similarities to stem cells and metastatic cancer cells, neural crest cells are a popular model system for studying cell/tissue interactions and signaling factors that influence cell fate decisions and lineage transitions. In this review, we discuss the mechanisms required for neural crest formation in various vertebrate species, focusing on the importance of signaling factors from adjacent tissues and conserved gene regulatory interactions, which are required for induction and specification of the ectodermal tissue that will become neural crest. WIREs Dev Biol 2012, 1:52–68. doi: 10.1002/wdev.8
Utility Based Data Gathering in Mobile Sensor Network

Abstract Traditional data gathering approaches cannot be applied to Mobile Sensor Network (MSN) due to sparse network density and sensor node mobility. In this paper, we propose a utility based data gathering protocol (UDG). The distance utility is used to indicate the closeness between sensor nodes and the sink node, and the activity utility is used to evaluate the ability of sensor nodes acting as relays. UDG combines the distance utility with the activity utility to make routing decisions. It also presents a buffer management scheme based on the utility. Experimental results show that UDG achieves desirable performance with low delivery overhead.
Age‐related effects of the neuromodulator d‐serine on neurotransmission and synaptic potentiation in the CA1 hippocampal area of the rat

The effects of the co‐agonist of the N‐methyl‐d‐aspartate receptor (NMDAr) d‐serine on glutamatergic neurotransmission and synaptic potentiation were studied in the CA1 hippocampal field of young (3–5 months old) and aged (25–27 months old) Sprague–Dawley rats using ex vivo extracellular electrophysiological recording techniques. Exogenous d‐serine depressed fast neurotransmission mediated by the α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid/kainate subtype of glutamate receptors in young but not in aged rats by acting on inhibitory glycinergic interneurons. In contrast, d‐serine dose‐dependently enhanced NMDAr‐mediated synaptic responses in both groups of animals, but with a larger magnitude in aged rats, thus preventing the age‐related decrease in NMDAr activation. d‐serine also increased the magnitude of long‐term potentiation in aged but not in young rats. Finally, d‐serine levels were dramatically reduced in hippocampal tissues of aged rats. Taken together, these results indicate a weaker activation of the NMDAr glycine modulatory site by endogenous d‐serine in aged animals, which accounts for a reduced NMDAr contribution to synaptic plasticity in ageing.