Miracle-dz/UniFAR-FTUs huggingface dataset:
Grouped Cases of Pulmonary Pneumocystosis After Solid Organ Transplantation: Advantages of Coordination by an Infectious Diseases Unit for Overall Management and Epidemiological Monitoring

OBJECTIVE To determine the origin of grouped cases of Pneumocystis pneumonia in solid-organ transplant recipients at our institution. DESIGN A case series with clinical examinations, genotyping, and an epidemiological survey. SETTING A university hospital in France. PATIENTS We report 12 solid-organ transplant recipients with successive cases of Pneumocystis pneumonia that occurred over 3 years; 10 of these cases occurred in a single year. METHODS We used molecular typing of P. jirovecii strains by multilocus sequence typing and clinical epidemiological survey to determine potential dates and places of transmission. RESULTS Between May 2014 and March 2015, 10 solid-organ transplant recipients (5 kidney transplants, 4 heart transplants, and 1 lung transplant) presented with Pneumocystis pneumonia. Molecular genotyping revealed the same P. jirovecii strain in at least 6 patients. This Pneumocystis strain was not identified in control patients (ie, nontransplant patients presenting with pulmonary pneumocystosis) during this period. The epidemiological survey guided by sequencing results provided information on the probable or possible dates and places of contamination for 5 of these patients. The mobile infectious diseases unit played a coordination role in the clinical management (adaptation of the local guidelines) and epidemiological survey. CONCLUSION Our cardiac and kidney transplant units experienced grouped cases of pulmonary pneumocystosis. Genotyping and epidemiological surveying results suggested interhuman contamination, which was quickly eliminated thanks to multidisciplinary coordination. Infect Control Hosp Epidemiol 2017;38:179–185
Reference Values for Body Composition and Anthropometric Measurements in Athletes

Background Despite the importance of body composition in athletes, reference sex- and sport-specific body composition data are lacking. We aim to develop reference values for body composition and anthropometric measurements in athletes. Methods Body weight and height were measured in 898 athletes (264 female, 634 male), anthropometric variables were assessed in 798 athletes (240 female and 558 male), and in 481 athletes (142 female and 339 male) with dual-energy X-ray absorptiometry (DXA). A total of 21 different sports were represented. Reference percentiles (5th, 25th, 50th, 75th, and 95th) were calculated for each measured value, stratified by sex and sport. Because sample sizes within a sport were often very low for some outcomes, the percentiles were estimated using a parametric, empirical Bayesian framework that allowed sharing information across sports. Results We derived sex- and sport-specific reference percentiles for the following DXA outcomes: total (whole body scan) and regional (subtotal, trunk, and appendicular) bone mineral content, bone mineral density, absolute and percentage fat mass, fat-free mass, and lean soft tissue. Additionally, we derived reference percentiles for height-normalized indexes by dividing fat mass, fat-free mass, and appendicular lean soft tissue by height squared. We also derived sex- and sport-specific reference percentiles for the following anthropometry outcomes: weight, height, body mass index, sum of skinfold thicknesses (7 skinfolds, appendicular skinfolds, trunk skinfolds, arm skinfolds, and leg skinfolds), circumferences (hip, arm, midthigh, calf, and abdominal circumferences), and muscle circumferences (arm, thigh, and calf muscle circumferences). Conclusions These reference percentiles will be a helpful tool for sports professionals, in both clinical and field settings, for body composition assessment in athletes.
Urban Environments and Obesity in Southeast Asia: A Systematic Review, Meta-Analysis and Meta-Regression

Many environmental factors contribute to the rise in prevalence of obesity in populations but one key driver is urbanization. Countries in Southeast (SE) Asia have undergone rapid changes in urbanization in recent decades. The aim of this study is to provide a systematic review of studies exploring the relationship between living in an urban or rural environment (urbanicity) and obesity in Southeast Asia. In particular, the review will investigate whether the associations are uniform across countries and ages, and by sex. The literature search was conducted up to June 2014 using five databases: EMBASE, PubMed, GlobalHealth, DigitalJournal and Open Grey. Forty-five articles representing eight of the eleven countries in SE Asia were included in the review. The review found a consistent positive association between urbanicity and obesity in countries of Southeast Asia, in all age groups and both genders. Regional differences between the associations are partly explained by gross national income (GNI). In countries with lower GNI per capita, the association between urbanicity and obesity was greater. Such findings have implications for policy makers. They imply that population level interventions need to be country or region specific, tailored to suit the current stage of economic development. In addition, less developed countries might be more vulnerable to the negative health impact of urbanization than more developed countries.
Automatic design of fiber-reinforced soft actuators for trajectory matching

Significance Fluid-powered elastomeric soft robots have been shown to be able to generate complex output motion using a simple control input such as pressurization of a working fluid. This capability, which mimics similar functions often found in biology, results from variations in mechanical properties of the soft robotic body that cause it to strain to different degrees when stress is applied with the fluid. In this work, we outline a mechanics- and optimization-based approach that enables the automatic selection of mechanical properties of a fiber-reinforced soft actuator to match the kinematic trajectory of the fingers or thumb during a grasping operation. This methodology can be readily extended to other applications that require mimicking or assisting biological motions. Soft actuators are the components responsible for producing motion in soft robots. Although soft actuators have allowed for a variety of innovative applications, there is a need for design tools that can help to efficiently and systematically design actuators for particular functions. Mathematical modeling of soft actuators is an area that is still in its infancy but has the potential to provide quantitative insights into the response of the actuators. These insights can be used to guide actuator design, thus accelerating the design process. Here, we study fluid-powered fiber-reinforced actuators, because these have previously been shown to be capable of producing a wide range of motions. We present a design strategy that takes a kinematic trajectory as its input and uses analytical modeling based on nonlinear elasticity and optimization to identify the optimal design parameters for an actuator that will follow this trajectory upon pressurization. We experimentally verify our modeling approach, and finally we demonstrate how the strategy works, by designing actuators that replicate the motion of the index finger and thumb.
Oral vitamin B12 versus intramuscular vitamin B12 for vitamin B12 deficiency.

BACKGROUND Vitamin B12 deficiency is common and rises with age. Most people with vitamin B12 deficiency are treated in primary care with intramuscular vitamin B12 which is a considerable source of work for health care professionals. Several case control and case series studies have reported equal efficacy of oral administration of vitamin B12 but it is rarely prescribed in this form, other than in Sweden and Canada. Doctors may not be prescribing oral formulations because they are unaware of this option or have concerns regarding effectiveness. OBJECTIVES To assess the effectiveness of oral vitamin B12 versus intramuscular vitamin B12 for vitamin B12 deficiency. SEARCH STRATEGY Searches were undertaken of The Cochrane Library, MEDLINE, EMBASE and Lilacs in early 2005. The bibliographies of all relevant papers identified using this strategy were searched. In addition we contacted authors of relevant identified studies and Vitamin B12 research and pharmaceutical companies to enquire about other published or unpublished studies and ongoing trials. SELECTION CRITERIA Randomised controlled trials (RCTs) examining the use of oral or intramuscular vitamin B12 to treat vitamin B12 deficiency. DATA COLLECTION AND ANALYSIS All abstracts or titles identified by the electronic searches were independently scrutinised by two reviewers. When a difference between reviewers arose, we obtained and reviewed a hard copy of the papers and made decisions by consensus. We obtained a copy of all pre-selected papers and two researchers independently extracted the data from these studies using piloted data extraction forms. The whole group checked whether inclusion and exclusion criteria were met, and disagreement was decided by consensus. The methodological quality of the included studies was independently assessed by two researchers and disagreements were brought back to the whole group and resolved by consensus. MAIN RESULTS Two RCT's comparing oral with intramuscular administration of vitamin B12 met our inclusion criteria. The trials recruited a total of 108 participants and followed up 93 of these from 90 days to four months. High oral doses of B12 (1000 mcg and 2000 mcg) were as effective as intramuscular administration in achieving haematological and neurological responses. AUTHORS' CONCLUSIONS The evidence derived from these limited studies suggests that 2000 mcg doses of oral vitamin B12 daily and 1000 mcg doses initially daily and thereafter weekly and then monthly may be as effective as intramuscular administration in obtaining short term haematological and neurological responses in vitamin B12 deficient patients.
Joint Effects of Habitat Heterogeneity and Species’ Life-History Traits on Population Dynamics in Spatially Structured Landscapes

Both habitat heterogeneity and species’ life-history traits play important roles in driving population dynamics, yet there is little scientific consensus around the combined effect of these two factors on populations in complex landscapes. Using a spatially explicit agent-based model, we explored how interactions between habitat spatial structure (defined here as the scale of spatial autocorrelation in habitat quality) and species life-history strategies (defined here by species environmental tolerance and movement capacity) affect population dynamics in spatially heterogeneous landscapes. We compared the responses of four hypothetical species with different life-history traits to four landscape scenarios differing in the scale of spatial autocorrelation in habitat quality. The results showed that the population size of all hypothetical species exhibited a substantial increase as the scale of spatial autocorrelation in habitat quality increased, yet the pattern of population increase was shaped by species’ movement capacity. The increasing scale of spatial autocorrelation in habitat quality promoted the resource share of individuals, but had little effect on the mean mortality rate of individuals. Species’ movement capacity also determined the proportion of individuals in high-quality cells as well as the proportion of individuals experiencing competition in response to increased spatial autocorrelation in habitat quality. Positive correlations between the resource share of individuals and the proportion of individuals experiencing competition indicate that large-scale spatial autocorrelation in habitat quality may mask the density-dependent effect on populations through increasing the resource share of individuals, especially for species with low mobility. These findings suggest that low-mobility species may be more sensitive to habitat spatial heterogeneity in spatially structured landscapes. In addition, localized movement in combination with spatial autocorrelation may increase the population size, despite increased density effects.
Age-Related Changes in Corneal Astigmatism.

PURPOSE To analyze the changes in corneal astigmatism as a function of age and develop a novel model to estimate corneal astigmatic change according to age. METHODS This was a cross-sectional study of right eyes of 3,769 individuals. Total corneal astigmatism, keratometric astigmatism, anterior corneal astigmatism, and posterior corneal astigmatism were measured by a Scheimpflug tomographer. Smoothing fitting curves of polar values of corneal astigmatism as a function of age were drawn and average changes in corneal astigmatism at different ages were calculated. RESULTS Two turning points of age on total corneal astigmatism were 36 and 69 years. The average change of total corneal astigmatism toward against-the-rule astigmatism was 0.13 diopters (D)/10 years from 18 to 35 years, 0.45 D/10 years from 36 to 68 years, and decreased after 69 years, mainly caused by anterior corneal astigmatism. The mean magnitude of posterior corneal astigmatism was -0.33 D and exceeded 0.50 D in 14.27% of eyes. The vectorial difference between total corneal astigmatism and keratometric astigmatism was correlated with posterior corneal astigmatism, polar value of anterior corneal astigmatism, age, and corneal higher order aberrations (r = 0.636; standard partial regression coefficients were 0.479, -0.466, 0.282, and 0.196, respectively; all P < .001). Based on the non-linear model to estimate corneal astigmatic change with age, a formula was developed to calculate recommended correction of astigmatism according to age and astigmatic type. CONCLUSIONS The rate of change of total corneal astigmatism showed a non-linear trend toward against-the-rule astigmatism, which was low at young and old age, high at middle age, and should be taken into account when performing surgery to correct astigmatism. [J Refract Surg. 2017;33(10):696-703. ].
Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach

Granulomas are complex lung lesions that are the hallmark of tuberculosis (TB). Understanding antibiotic dynamics within lung granulomas will be vital to improving and shortening the long course of TB treatment. Three fluoroquinolones (FQs) are commonly prescribed as part of multi-drug resistant TB therapy: moxifloxacin (MXF), levofloxacin (LVX) or gatifloxacin (GFX). To date, insufficient data are available to support selection of one FQ over another, or to show that these drugs are clinically equivalent. To predict the efficacy of MXF, LVX and GFX at a single granuloma level, we integrate computational modeling with experimental datasets into a single mechanistic framework, GranSim. GranSim is a hybrid agent-based computational model that simulates granuloma formation and function, FQ plasma and tissue pharmacokinetics and pharmacodynamics and is based on extensive in vitro and in vivo data. We treat in silico granulomas with recommended daily doses of each FQ and compare efficacy by multiple metrics: bacterial load, sterilization rates, early bactericidal activity and efficacy under non-compliance and treatment interruption. GranSim reproduces in vivo plasma pharmacokinetics, spatial and temporal tissue pharmacokinetics and in vitro pharmacodynamics of these FQs. We predict that MXF kills intracellular bacteria more quickly than LVX and GFX due in part to a higher cellular accumulation ratio. We also show that all three FQs struggle to sterilize non-replicating bacteria residing in caseum. This is due to modest drug concentrations inside caseum and high inhibitory concentrations for this bacterial subpopulation. MXF and LVX have higher granuloma sterilization rates compared to GFX; and MXF performs better in a simulated non-compliance or treatment interruption scenario. We conclude that MXF has a small but potentially clinically significant advantage over LVX, as well as LVX over GFX. We illustrate how a systems pharmacology approach combining experimental and computational methods can guide antibiotic selection for TB.
HIF-1α Is Essential for Effective PMN Bacterial Killing, Antimicrobial Peptide Production and Apoptosis in Pseudomonas aeruginosa Keratitis

Hypoxia-inducible factor (HIF)-1α, is a transcription factor that controls energy metabolism and angiogenesis under hypoxic conditions, and a potent regulator of innate immunity. The studies described herein examined the role of HIF-1α in disease resolution in BALB/c (resistant, cornea heals) mice after ocular infection with Pseudomonas (P.) aeruginosa. Furthermore, the current studies focused on the neutrophil (PMN), the predominant cell infiltrate in keratitis. Using both siRNA and an antagonist (17-DMAG), the role of HIF-1α was assessed in P. aeruginosa-infected BALB/c mice. Clinical score and slit lamp photography indicated HIF-1α inhibition exacerbated disease and corneal destruction. Real time RT-PCR, immunohistochemistry, ELISA, Greiss and MPO assays, bacterial load, intracellular killing, phagocytosis and apoptosis assays further tested the regulatory role of HIF-1α. Despite increased pro-inflammatory cytokine expression and increased MPO levels after knocking down HIF-1α expression, in vivo studies revealed a decrease in NO production and higher bacterial load. In vitro studies using PMN provided evidence that although inhibition of HIF-1α did not affect phagocytosis, both bacterial killing and apoptosis were significantly affected, as was production of antimicrobial peptides. Overall, data provide evidence that inhibition of HIF-1α converts a normally resistant disease response to susceptible (corneal thinning and perforation) after induction of bacterial keratitis. Although this inhibition does not appear to affect PMN transmigration or phagocytosis, both in vivo and in vitro approaches indicate that the transcriptional factor is essential for effective bacterial killing, apoptosis and antimicrobial peptide production.
Early Response of Soil Properties and Function to Riparian Rainforest Restoration

Reforestation of riparian zones is increasingly practiced in many regions for purposes of biodiversity conservation, bank stabilisation, and improvement in water quality. This is in spite of the actual benefits of reforestation for recovering underlying soil properties and function remaining poorly understood. Here we compare remnant riparian rainforest, pasture and reforestation plantings aged 2–20 years in an Australian subtropical catchment on ferrosols to determine the extent to which reforestation restores key soil properties. Of the nine soil attributes measured (total nitrogen, nitrate and ammonium concentrations, net nitrification and ammonification rates, organic carbon, bulk density, fine root biomass and water infiltration rates), only infiltration rates were significantly lower in pasture than remnant riparian rainforest. Within reforestation plantings, bulk density decreased up to 1.4-fold and infiltration rates increased up to 60-fold with time post-reforestation. Our results suggest that the main outcome of belowground processes of early reforestation is the recovery of the soils' physical structure, with potential beneficial ecosystem services including reduced runoff, erosion and associated sediment and nutrient loads in waterways. We also demonstrate differential impacts of two commonly planted tree species on a subset of soil properties suggesting that preferential planting of select species could accelerate progress on specific restoration objectives.
Distribution of Giardia duodenalis Assemblages A and B among Children Living in a Remote Indigenous Community of the Northern Territory, Australia

Giardiasis is a communicable gastrointestinal disease caused by Giardia duodenalis and two genetic assemblages, A and B, cause human infection. In remote Indigenous communities of Australia, giardiasis is highly prevalent among children but disease transmission is poorly understood. This study investigated the prevalence of Giardia and genetic subtypes contributing to human disease in a remote Indigenous community, in the Northern Territory of Australia. Eighty-seven faecal samples were collected from 74 children (<15 years) over an 18 month period, and the distribution of positive cases relative to participant age and gender were examined. Screening by microscopy and 18S rRNA PCR amplification showed 66.7% (58/87) of faecal samples were positive for Giardia. Both males and females were equally affected and high detection rates were obtained for participants aged 0–<5 years and 5–<10 years (66.0 and 60.0% respectively). For 58.6% of the positive samples, Giardia was only detected by 18S rRNA PCR. Approximately 75% of cases were assemblage B, and subassemblage analyses using terminal restriction fragment length polymorphism of the glutamate dehydrogenase gene demonstrated that a variety of genetic variants were present. The high proportion of positive cases that were not detectable by microscopy, and dominance of assemblage B cases highlights the need for further research in this community, to assess the contribution of Giardia to chronic gastrointestinal disease among children, and to understand conditions conductive to assemblage B transmission.
ComQXPA Quorum Sensing Systems May Not Be Unique to Bacillus subtilis: A Census in Prokaryotic Genomes

The comQXPA locus of Bacillus subtilis encodes a quorum sensing (QS) system typical of Gram positive bacteria. It encodes four proteins, the ComQ isoprenyl transferase, the ComX pre-peptide signal, the ComP histidine kinase, and the ComA response regulator. These are encoded by four adjacent genes all situated on the same chromosome strand. Here we present results of a comprehensive census of comQXPA-like gene arrangements in 2620 complete and 6970 draft prokaryotic genomes (sequenced by the end of 2013). After manually checking the data for false-positive and false-negative hits, we found 39 novel com-like predictions. The census data show that in addition to B. subtilis and close relatives, 20 comQXPA-like loci are predicted to occur outside the B. subtilis clade. These include some species of Clostridiales order, but none outside the phylum Firmicutes. Characteristic gene-overlap patterns were observed in comQXPA loci, which were different for the B. subtilis-like and non-B. subtilis-like clades. Pronounced sequence variability associated with the ComX peptide in B. subtilis clade is evident also in the non-B. subtilis clade suggesting grossly similar evolutionary constraints in the underlying quorum sensing systems.
Magnetic resonance molecular imaging of metastatic breast cancer by targeting extradomain‐B fibronectin in the tumor microenvironment

Non‐invasive early accurate detection of malignant breast cancer is paramount to the clinical management of the life‐threatening disease. Here, we aim to test a small peptide targeted MRI contrast agent, ZD2‐Gd(HP‐DO3A), specific to an oncoprotein, extradomain‐B fibronectin (EDB‐FN), in the tumor microenvironment for MR molecular imaging of breast cancer.