Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Capsule and O Antigen in the Virulence of Uropathogenic Escherichia coli

Urinary tract infection (UTI) is one of the most common bacterial infections in humans, with uropathogenic Escherichia coli (UPEC) the leading causative organism. UPEC has a number of virulence factors that enable it to overcome host defenses within the urinary tract and establish infection. The O antigen and the capsular polysaccharide are two such factors that provide a survival advantage to UPEC. Here we describe the application of the rpsL counter selection system to construct capsule (kpsD) and O antigen (waaL) mutants and complemented derivatives of three reference UPEC strains: CFT073 (O6:K2:H1), RS218 (O18:K1:H7) and 1177 (O1:K1:H7). We observed that while the O1, O6 and O18 antigens were required for survival in human serum, the role of the capsule was less clear and linked to O antigen type. In contrast, both the K1 and K2 capsular antigens provided a survival advantage to UPEC in whole blood. In the mouse urinary tract, mutation of the O6 antigen significantly attenuated CFT073 bladder colonization. Overall, this study contrasts the role of capsule and O antigen in three common UPEC serotypes using defined mutant and complemented strains. The combined mutagenesis-complementation strategy can be applied to study other virulence factors with complex functions both in vitro and in vivo.
Injury Risk Assessment of Non-Lethal Projectile Head Impacts

Kinetic energy non-lethal projectiles are used to impart sufficient effect onto a person in order to deter uncivil or hazardous behavior with a low probability of permanent injury. Since their first use, real cases indicate that the injuries inflicted by such projectiles may be irreversible and sometimes lead to death, especially for the head impacts. Given the high velocities and the low masses involved in such impacts, the assessment approaches proposed in automotive crash tests and sports may not be appropriate. Therefore, there is a need of a specific approach to assess the lethality of these projectiles. In this framework, some recent research data referred in this article as “force wall approach” suggest the use of three lesional thresholds (unconsciousness, meningeal damages and bone damages) that depend on the intracranial pressure. Three corresponding critical impact forces are determined for a reference projectile. Based on the principle that equal rigid wall maximal impact forces will produce equal damage on the head, these limits can be determined for any other projectile. In order to validate the consistence of this innovative method, it is necessary to compare the results with other existing assessment methods. This paper proposes a comparison between the “force wall approach” and two different head models. The first one is a numerical model (Strasbourg University Finite Element Head Model-SUFEHM) from Strasbourg University; the second one is a mechanical surrogate (Ballistics Load Sensing Headform-BLSH) from Biokinetics.
Gas balance and fuel retention in fusion devices

The evaluation of hydrogenic retention in present tokamaks is of crucial importance to estimate the expected tritium (T) vessel inventory in ITER, limited from safety considerations to 350 g. In the framework of the European Task Force on Plasma Wall Interaction (EU TF on PWI) efforts are underway to investigate gas balance and fuel retention during discharges, and to compare the data obtained with those from post-mortem analysis of in-vessel components exposed over whole experimental campaigns. This paper summarizes the principal findings from coordinated studies on gas balance and fuel retention from a number of European tokamaks, namely, ASDEX-Upgrade (AUG), JET, TEXTOR and Tore Supra (TS). For most devices, the long-term retention fraction deduced from integrated particle balance is ∼10–20%. This is larger than the ∼3–4% deduced from post-mortem analysis of plasma facing components (PFCs). However, from the database available for tokamaks with their main PFCs made of carbon, the important conclusion is that the T inventory limit (set by the working guideline for operations) could be reached in ITER within fewer than 100 discharges. This, therefore, would seriously impact on operation of the device unless efficient T removal processes are developed.
Decrease of Plasma Glucose by Hibiscus taiwanensis in Type-1-Like Diabetic Rats

Hibiscus taiwanensis (Malvaceae) is widely used as an alternative herb to treat disorders in Taiwan. In the present study, it is used to screen the effect on diabetic hyperglycemia in streptozotocin-induced diabetic rats (STZ-diabetic rats). The extract of Hibiscus taiwanensis showed a significant plasma glucose-lowering action in STZ-diabetic rats. Stems of Hibiscus taiwanensis are more effective than other parts to decrease the plasma glucose in a dose-dependent manner. Oral administration of Hibiscus taiwanensis three times daily for 3 days into STZ-diabetic rats increased the sensitivity to exogenous insulin showing an increase in insulin sensitivity. Moreover, similar repeated administration of Hibiscus taiwanensis for 3 days in STZ-diabetic rats produced a marked reduction of phosphoenolpyruvate carboxykinase (PEPCK) expression in liver and an increased expression of glucose transporter subtype 4 (GLUT 4) in skeletal muscle. Taken together, our results suggest that Hibiscus taiwanensis has the ability to lower plasma glucose through an increase in glucose utilization via elevation of skeletal GLUT 4 and decrease of hepatic PEPCK in STZ-diabetic rats.
Dissociating Response Conflict and Error Likelihood in Anterior Cingulate Cortex

Neuroimaging studies consistently report activity in anterior cingulate cortex (ACC) in conditions of high cognitive demand, leading to the view that ACC plays a crucial role in the control of cognitive processes. According to one prominent theory, the sensitivity of ACC to task difficulty reflects its role in monitoring for the occurrence of competition, or “conflict,” between responses to signal the need for increased cognitive control. However, a contrasting theory proposes that ACC is the recipient rather than source of monitoring signals, and that ACC activity observed in relation to task demand reflects the role of this region in learning about the likelihood of errors. Response conflict and error likelihood are typically confounded, making the theories difficult to distinguish empirically. The present research therefore used detailed computational simulations to derive contrasting predictions regarding ACC activity and error rate as a function of response speed. The simulations demonstrated a clear dissociation between conflict and error likelihood: fast response trials are associated with low conflict but high error likelihood, whereas slow response trials show the opposite pattern. Using the N2 component as an index of ACC activity, an EEG study demonstrated that when conflict and error likelihood are dissociated in this way, ACC activity tracks conflict and is negatively correlated with error likelihood. These findings support the conflict-monitoring theory and suggest that, in speeded decision tasks, ACC activity reflects current task demands rather than the retrospective coding of past performance.
Linking Ventilation Heterogeneity Quantified via Hyperpolarized He-3 MRI to Dynamic Lung Mechanics and Airway Hyperresponsiveness Lutchen

Advancements in hyperpolarized helium-3 MRI (HP He-MRI) have introduced the ability to render and quantify ventilation patterns throughout the anatomic regions of the lung. The goal of this study was to establish how ventilation heterogeneity relates to the dynamic changes in mechanical lung function and airway hyperresponsiveness in asthmatic subjects. In four healthy and nine mild-to-moderate asthmatic subjects, we measured dynamic lung resistance and lung elastance from 0.1 to 8 Hz via a broadband ventilation waveform technique. We quantified ventilation heterogeneity using a recently developed coefficient of variation method from HP He-MRI imaging. Dynamic lung mechanics and imaging were performed at baseline, post-challenge, and after a series of five deep inspirations. AHR was measured via the concentration of agonist that elicits a 20% decrease in the subject’s forced expiratory volume in one second compared to baseline (PC20) dose. The ventilation coefficient of variation was correlated to low-frequency lung resistance (R = 0.647, P < 0.0001), the difference between high and low frequency lung resistance (R = 0.668, P < 0.0001), and low-frequency lung elastance (R = 0.547, P = 0.0003). In asthmatic subjects with PC20 values <25 mg/mL, the coefficient of variation at baseline exhibited a strong negative trend (R = -0.798, P = 0.02) to PC20 dose. Our findings were consistent with the notion of peripheral rather than central involvement of ventilation heterogeneity. Also, the degree of AHR appears to be dependent on the degree to which baseline airway constriction creates baseline ventilation heterogeneity. HP He-MRI imaging may be a powerful predictor of the degree of AHR and in tracking the efficacy of therapy. PLOS ONE | DOI:10.1371/journal.pone.0142738 November 16, 2015 1 / 14 OPEN ACCESS Citation: Lui JK, Parameswaran H, Albert MS, Lutchen KR (2015) Linking Ventilation Heterogeneity Quantified via Hyperpolarized He MRI to Dynamic Lung Mechanics and Airway Hyperresponsiveness. PLoS ONE 10(11): e0142738. doi:10.1371/journal. pone.0142738 Editor: Josué Sznitman, Technion Israel Institute of Technology, ISRAEL Received: April 23, 2015 Accepted: October 25, 2015 Published: November 16, 2015 Copyright: © 2015 Lui et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This work was funded by the National Heart, Lung, and Blood Institute Grants R01 HL62269-04 and R01 HL-096797. Competing Interests: The authors have declared that no competing interests exist.
Cognitive inflexibility and the development and use of strategies for solving complex dynamic problems: effects of different types of training

Performance in dynamic complex problem tasks is affected by cognitive inflexibility, whereby people are sometimes unable to adapt their strategies to unexpected changes in their surroundings. This cognitive inflexibility only affects a person's performance when the environmental changes are relevant to the particular problem-solving strategy that they are using. This paper describes a new methodology to detect cognitive flexibility in the use of strategies and presents an experiment designed to test the hypothesis, proving that the type of training affects cognitive flexibility.
Thermal Conductivities of Some Common Soils in Trinidad

Thermal conductivity (k) of twelve soils from Trinidad was measured in the field and the laboratory using a portable sensor and probe. The effect on k of compacting three of the soils (a sandy loam, clay loam and clay) using 5, 15 and 25 Proctor hammer blows at water contents which ranged from 5% to 40% was further investigated in the laboratory. Bulk density (ρb) achieved during soil compaction was measured to assist in the interpretation of the results. The k measured in the field ranged from 0.90 to 1.55 W m C and was within 0.1 W m C of the corresponding laboratory-measured values for the individual soils. The k of the laboratory-compacted soils, which ranged from 0.5 to 2.00 W m C, increased with increasing water contents with maximum ρb being reached before the maximum k. The clay soil had lower values of k and ρb than the clay loam and the sandy loam soil. Good agreement was found between the field and laboratory measured k as well as the k values predicted using the Campbell model. The results obtained are discussed in relation to pipe laying in Trinidad. Apart from soils with appreciable sand contents, most soils because of their large clay contents would require standard backfills during cable laying.
Germany SOIL MANAGEMENT PRACTICES AND LANDSCAPE ATTRIBUTE IMPACTS ON FIELD-SCALE CORN PRODUCTIVITY

The influence of terrain attributes on response of corn (Zea mays L.) to soil management practices has rarely evaluated, especially on degraded soils. Five management zones (MZ) were delineated in a 9-ha Alabama field (Typic and Aquic Paleudults) using a soil survey, topography and surfaces of soil electrical conductivity (EC), soil organic carbon (SOC) and soil texture. From 2001-2004, a conventional system (chisel plowing/disking with no cover crops) with or without manure (CTmanure or CT), and a conservation system (no-till and cover crops) with and without manure (NTmanure or NT), were established in strips traversing the landscape in a corn-cotton (Gossypium hirsutum L.) rotation, following long-term conventional tillage. Conservation systems had greater yield than conventional systems in all MZ in 2002 (dry season; 8.88 vs. 6.71 Mg ha), and in four of five MZ in 2003 (wet season; 13.04 vs. 12.33 Mg ha); no differences existed in the initial year, 2001, (9.85 Mg ha). In 2004, CT (8.43 Mg ha) had the lowest yield in all MZ; NTmanure (11.12 Mg ha) had greater yield than NT and CTmanure (10.46 and 10.19 Mg ha respectively) in some MZ. Yield differences between high and low productivity MZ within years were lower in conservation than in conventional systems. Soil degradation and field-scale water dynamics had significant impacts on yield variability. Soil texture, SOC and EC were typically related with yield in all treatments, and explained 15-71 % of yield variation. The aggregate of data indicates for degraded soils in warm humid climates, conservation systems increase corn productivity and spatial and temporal stability of yields even during initial adoption years.
Efficacy of Ramosetron in Male Patients With Irritable Bowel Syndrome With Diarrhea (Neurogastroenterol Motil 2011;23:1098-1104)

Serotonin (5-Hydroxytryptamine [5-HT]) plays an important role in gastrointestinal (GI) motility and sensation, and abnormal levels have been shown in patients with irritable bowel syndrome (IBS). 1,2 Drugs acting on 5-HT receptors have the potential to reduce the smooth muscle spasm, abdominal pain, and changes in bowel habit in IBS. Recently, Lee et al3 assessed the efficacy and safety of ramosetron, a 5-HT3 receptor antagonist, compared with mebeverine in male patients with diarrhea-predominant IBS (IBS-D). This study was performed in a multicenter, randomized, open-label, parallel-group, non-inferiority comparative design. A total of 343 male patients with IBS-D were randomized to either ramosetron 5 µg once daily or mebeverine 135 mg 3 times daily for 4 weeks. The weekly responder rates for global IBS symptoms, abdominal pain/discomfort and abnormal bowel habits in the ramosteron and mebeverine groups significantly increased during the treatment period (P < 0.001). The severity scores of abdominal pain/discomfort and urgency, the stool form scores and the stool frequency recorded daily were reduced significantly in both treatment arms, compared with the baselines (P < 0.001). There were no significant differences in the weekly responder rates (37% vs 38% at 4-week) and in the adverse event profiles between the ramosetron and mebeverine groups. Neither severe constipation nor ischemic colitis was reported. The authors concluded that the ramosetron 5 µg once daily was as effective as mebeverine 3 times daily in male patients with IBS-D.
CHAPITRE IV : Mesure de la réactivité atmosphérique totale avec les radicaux hydroxyles à Paris pendant la campagne

Hydroxyl radicals play a central role in the troposphere as they control the lifetime of many trace gases. Measurement of OH reactivity (OH loss rate) is important to better constrain the OH budget and also to evaluate the completeness of measured VOC budget. Total atmospheric OH reactivity was measured for the first time in an European Megacity: Paris and its surrounding areas with 12 million inhabitants, during the MEGAPOLI winter campaign 2010. The method deployed was the Comparative Reactivity Method (CRM). The measured dataset contains both measured and calculated OH reactivity from CO, NOx and VOCs measured via PTR-MS, GC-FID and GC-MS instruments. The reactivities observed in Paris covered a range from 10s to 130s, indicating a large loading of chemical reactants. The present study showed that, when clean marine air masses influenced Paris, the purely local OH reactivity (20s) is well explained by the measured species. Nevertheless, when there is a continental import of air masses, high levels of OH reactivity were obtained (120 – 130 s) and the missing OH reactivity measured in this case jumped to 75%. Using covariations of the missing OH reactivity to secondary inorganic species in fine aerosols, we suggest that the missing OH reactants were most likely highly oxidized compounds issued from photochemically processed air masses of anthropogenic origin. Chapitre 4 : Mesure de la réactivité OH à Paris pendant MEGAPOLI hiver 2010 146 Mesure de la réactivité atmosphérique totale avec les radicaux OH : Développement et applications en Ile-de-France
ELEFAN in R : A new tool for length-frequency analysis 2013

A review is presented of methods for the analysis of length frequency (L/F) data for estimation of growth and related life-history parameters of fish populations (including aquatic invertebrates), with emphasis on the ELEFAN software system. Details are provided on methods for the estimation of asymptotic length and K (of the von Bertalanffy growth function), including the frequent cases where growth oscillates seasonally, and on the ELEFAN software system, with which such curve can be fitted to L/F data. Length-converted catch curves are also discussed, again with emphasis on the effect of seasonal growth, and of their use for estimating probabilities of capture, and hence, for the (partial) correction of L/F samples for the effect of gear selection and incomplete recruitment. The method for construction of annual recruitment patterns are provided, as are equations for yield-and biomass-per-recruit analyses. Application examples are provided which highlight various aspects of the ELEFAN system.
µ-Opioid Receptor Gene (OPRM1) Polymorphism A118G: Lack of Association in Finnish Populations with Alcohol Dependence or Alcohol Consumption

Aims: The molecular epidemiological studies on the association of the opioid receptor µ-1 (OPRM1) polymorphism A118G (Asn40Asp, rs1799971) and alcohol use disorders have given conflicting results. The aim of this study was to test the possible association of A118G polymorphism and alcohol use disorders and alcohol consumption in three large cohort-based study samples. Methods: The association between the OPRM1 A118G (Asn40Asp, rs1799971) polymorphism and alcohol use disorders and alcohol consumption was analyzed using three different population-based samples: (a) a Finnish cohort study, Health 2000, with 503 participants having a DSM-IV diagnosis for alcohol dependence and/or alcohol abuse and 506 age- and sex-matched controls; (b) a Finnish cohort study, FINRISK (n = 2360) and (c) the Helsinki Birth Cohort Study (n = 1384). The latter two populations lacked diagnosis-based phenotypes, but included detailed information on alcohol consumption. Results: We found no statistically significant differences in genotypic or allelic distribution between controls and subjects with alcohol dependence or abuse diagnoses. Likewise no significant effects were observed between the A118G genotype and alcohol consumption. Conclusion: These results suggest that A118G (Asn40Asp) polymorphism may not have a major effect on the development of alcohol use disorders at least in the Finnish population.
ADM‐Aeolus Doppler wind lidar Observing System Simulation Experiment

Within the Atmospheric Dynamics Mission Aeolus (ADM‐Aeolus), the European Space Agency (ESA) has approved a Doppler wind lidar (DWL) to fly on a dedicated platform orbiting dawn to dusk at 400 km altitude, planned for launch in 2008. Rigorous design trade‐offs have resulted in a lidar concept capable of delivering high‐quality wind component profiles, but with a limited coverage. A companion paper describes the realistic simulation of this DWL, whereas this paper sets out to assess the impact of such a lidar in meteorological analyses and forecasts. To this end, an Observing System Simulation Experiment (OSSE) is run. The superior conventional observation coverage of 1993 is used to simulate all conventional observations, although a limited set of satellite observations is simulated. As a consequence, only the northern hemisphere DWL impact in the OSSE is assumed realistic. Here, over a 15‐day period with variable weather, out of 15 daily forecasts, 14 show beneficial impact of the DWL. Although the experiment is limited, it corroborates other practical and theoretical evidence that the ADM DWL will demonstrate a beneficial impact in meteorological analyses and forecasts. Copyright © 2006 Royal Meteorological Society
Variability of the reverse transcription step: practical implications.

BACKGROUND The reverse transcription (RT) of RNA to cDNA is a necessary first step for numerous research and molecular diagnostic applications. Although RT efficiency is known to be variable, little attention has been paid to the practical implications of that variability. METHODS We investigated the reproducibility of the RT step with commercial reverse transcriptases and RNA samples of variable quality and concentration. We quantified several mRNA targets with either singleplex SYBR Green I or dualplex probe-based reverse transcription real-time quantitative PCR (RT-qPCR), with the latter used to calculate the correlation between quantification cycles (Cqs) of mRNA targets amplified in the same real-time quantitative PCR (qPCR) assay. RESULTS RT efficiency is enzyme, sample, RNA concentration, and assay dependent and can lead to variable correlation between mRNAs from the same sample. This translates into relative mRNA expression levels that generally vary between 2- and 3-fold, although higher levels are also observed. CONCLUSIONS Our study demonstrates that the variability of the RT step is sufficiently large to call into question the validity of many published data that rely on quantification of cDNA. Variability can be minimized by choosing an appropriate RTase and high concentrations of RNA and characterizing the variability of individual assays by use of multiple RT replicates.
Interannual Variability of the Rainy Season and Rainfall in the Brazilian Amazon Basin

Interannual variability of seasonal rainfall in the Brazilian Amazon basin is examined in context of its relationship to sea surface temperatures in the tropical Pacific and Atlantic Oceans. Linear correlations reveal strong relationships, but rainfall patterns are of regional scale. Areas of rainfall exhibiting strong relationships with SST are confined to the equatorial region of the Brazilian Amazon. The best relationships are found either during the season of transition between wet and dry regimes, or entirely within the dry season. It is hypothesized, and results are shown in support, that during the transition seasons, an important contributor to the SST control on seasonal totals is its influence on the timing on the rainy season onset or end. That influence appears to be stronger than the SST influence on the rainy season rain rate.