Miracle-dz/UniFAR-FTUs huggingface dataset:
Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

Tandem duplications are among the most common mutation events. The high loss rate of duplication suggested that the frequency of duplications in a bacterial population (1/1000) might reflect a steady state dictated by relative rates of formation (kF) and loss (kL). This possibility was tested for three genetic loci. Without homologous recombination (RecA), duplication loss rate dropped essentially to zero, but formation rate decreased only slightly and a steady state was still reached rapidly. Under all conditions, steady state was reached faster than predicted by formation and loss rates alone. A major factor in determining steady state proved to be the fitness cost, which can exceed 40% for some genomic regions. Depending on the region tested, duplications reached 40–98% of the steady-state frequency within 30 generations—approximately the growth required for a single cell to produce a saturated overnight culture or form a large colony on solid medium (109 cells). Long-term bacterial populations are stably polymorphic for duplications of every region of their genome. These polymorphisms contribute to rapid genetic adaptation by providing frequent preexisting mutations that are beneficial whenever imposed selection favors increases in some gene activity. While the reported results were obtained with the bacterium Salmonella enterica, the genetic implications seem likely to be of broader biological relevance.
Soluble epoxide hydrolase inhibitor, TUPS, protects against isoprenaline‐induced cardiac hypertrophy

We have previously shown that isoprenaline‐induced cardiac hypertrophy causes significant changes in the expression of cytochromes P450 (CYP) and soluble epoxide hydrolase (sEH) genes. Therefore, it is important to examine whether the inhibition of sEH by 1‐(1‐methanesulfonyl‐piperidin‐4‐yl)‐3‐(4‐trifluoromethoxy‐phenyl)‐urea (TUPS) will protect against isoprenaline‐induced cardiac hypertrophy.
Helicobacter pylori clarithromycin resistance detected by Etest and TaqMan real‐time polymerase chain reaction: a comparative study

The aim of the work was to compare H. pylori clarithromycin‐resistance according two methods. Etest was performed on H. pylori isolated from gastric biopsy samples. TaqMan Real‐Time‐PCR (RT‐PCR) was performed on paraffin‐embedded gastric biopsy samples of the same patients. Forty‐seven out of 88 strains were resistant to clarithromycin by Etest, whereas RT‐PCR detected this resistance on paraffin‐embedded specimens of 50 patients. RT‐PCR performed on paraffin‐embedded biopsy specimens of 47 patients infected with H. pylori resistant to clarithromycin as detected by Etest, revealed the presence of a resistant strain only in 40 samples. RT‐PCR performed on samples of 41 patients harbouring clarithromycin‐susceptible H. pylori strains showed the presence of 31 susceptible and 10 resistant strains. RT‐PCR detected 18 cases with heteroresistant status. The difference between the two tests in detecting clarithromycin‐resistance was not statistically significant even if RT‐PCR detected more resistant cases. The genotyping resistance on paraffin‐embedded gastric biopsy specimens may be used to establish resistance to clarithromycin before the treatment when culture and susceptibility testing are not available. In case of failure of an empirical clarithromycin‐based triple antimicrobial treatment, RT‐PCR performed on paraffin‐embedded biopsy sample will establish the primary resistance to clarithromycin. In addition, this test can be useful for epidemiological investigation as well as for monitoring the evolution of clarithromycin resistance along the time.
Profiling the Location and Extent of Musicians’ Pain Using Digital Pain Drawings

According to existing literature, musicians are at risk of experiencing a range of painful musculoskeletal conditions. Recently, a novel digital technology was developed to investigate pain location and pain extent. The aim of this study was to describe pain location and pain extent in musicians using a digital method for pain drawing (PD) analysis. Additionally, the association between PD variables and clinical features were explored in musicians with pain.
A new adaptive Soft-in Soft-out decoding method of error resilient arithmetic codes

Iterative Joint Source Channel Decoding(IJSCD) is an effective technique to improve the overall performance of communication systems. However, it is based on Soft-in Soft-out (SISO) decoding of error correcting codes. In this paper, a new SISO decoding method of error resilient arithmetic codes (ERAC) is proposed, which is based on the conventional BCJR algorithm but sequentially prune nodes according to the channel conditions. The performance of this decoding method across AWGN channel is evaluated. Simulation results show that there are about 1.2dB gains with respect to the performance of traditional decoding of arithmetic codes, and its performance is even better than the existing SISO decoding method of ERAC implemented by the M-BCJR algorithm.
Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies

ABSTRACT The restricted neutralization breadth of vaccine-elicited antibodies is a major limitation of current human immunodeficiency virus-1 (HIV-1) candidate vaccines. In order to permit the efficient identification of vaccines with enhanced capacity for eliciting cross-reactive neutralizing antibodies (NAbs) and to assess the overall breadth and potency of vaccine-elicited NAb reactivity, we assembled a panel of 109 molecularly cloned HIV-1 Env pseudoviruses representing a broad range of genetic and geographic diversity. Viral isolates from all major circulating genetic subtypes were included, as were viruses derived shortly after transmission and during the early and chronic stages of infection. We assembled a panel of genetically diverse HIV-1-positive (HIV-1+) plasma pools to assess the neutralization sensitivities of the entire virus panel. When the viruses were rank ordered according to the average sensitivity to neutralization by the HIV-1+ plasmas, a continuum of average sensitivity was observed. Clustering analysis of the patterns of sensitivity defined four subgroups of viruses: those having very high (tier 1A), above-average (tier 1B), moderate (tier 2), or low (tier 3) sensitivity to antibody-mediated neutralization. We also investigated potential associations between characteristics of the viral isolates (clade, stage of infection, and source of virus) and sensitivity to NAb. In particular, higher levels of NAb activity were observed when the virus and plasma pool were matched in clade. These data provide the first systematic assessment of the overall neutralization sensitivities of a genetically and geographically diverse panel of circulating HIV-1 strains. These reference viruses can facilitate the systematic characterization of NAb responses elicited by candidate vaccine immunogens.
Accuracy of blood pressure measurement by the Dinamap monitor in infants and children.

Indirect BPs measured by the Dinamap monitor, an oscillometric device, and the conventional auscultatory method were compared with the direct radial artery pressure in infants and children. There were 29 patients in the Dinamap group with a median age of 18 months (ranges 1 month to 16 years) and 20 patients in the auscultatory group with a median age of 3.5 years (ranges 3 months to 16 years). The direct radial artery pressures were recorded on a strip chart and the ranges of pressures were obtained for systolic, diastolic, and mean pressures. The range of the direct readings was converted to a weighted single reading, and comparisons were made between the direct and indirect readings. The linear regression equation between the direct (x) and the Dinamap (y) readings (with correlation coefficient) was y = 1.05x - 5.36 (r = .97) for systolic, y = 1.10x - 4.65 (r = .903) for diastolic, and y = 1.06x - 4.21 (r = .917) for mean pressures. The linear regression equation (with correlation coefficient) for the auscultatory pressure was y = 1.60x - 68.23 (r = .872) and y = 1.38x - 16.47 (r = .874) for diastolic pressures. The error was defined as the indirect reading minus the direct reading. The mean error +/- SD was -0.24 +/- 3.26 for systolic, 1.28 +/- 4.74 for diastolic, and 0.10 +/- 4.56 mm Hg for mean pressures by the Dinamap method. It was -1.65 +/- 6.68 for systolic, and 8.70 +/- 5.97 for diastolic pressures by the auscultatory method. (ABSTRACT TRUNCATED AT 250 WORDS)
Toward a Model for E-learning Recommender System Adoption: a Pilot Study

Over the past decade universities all over the world have realized the value of providing educational information and services electronically. With this growing interest in e-learning, the question of how to increase learner's adoption and usage of e-learning services including recommender systems has been raised. In order to facilitate students' adoption and use the e-learning service channel, educational institutions and e-learning researchers need to understand factors that influence students' adoption and usage of e-learning recommender systems. Grounded in the Technology Acceptance Model (TAM) framework, this paper develops a unique conceptual model by integrating the TAM with a set of new factors identified in the literature: user experience and service quality. The revised TAM model developed in this paper is to study, at a later stage, the impact of these factors on students' adoption of e-learning recommender systems in developing countries. As part of a larger research project, this paper reports the survey instrument development and validation in the field. We administered a survey instrument to a sample of 75 students randomly chosen from university students in Saudi Arabia. Although the sample was small, it indicates that the reliability of the scales is within an acceptable range and it can be used to test the main study hypotheses.
Anatomical Segregation of Component Processes in an Inductive Inference Task

Inductive inference underlies much of human cognition. The essential component of induction is hypothesis selection based on some criterion of relevance. The purpose of this study was to determine the neural substrate of inductive inference, particularly hypothesis selection, using fMRI. Ten volunteers were shown stimuli consisting of novel animals under two task conditions, and asked to judge whether all the animals in the set were the same type of animal. In one condition, subjects were given a rule that specified the criteria for same type of animal. In the other condition, subjects had to infer the rule without instruction. The two conditions were further factored into easy and difficult components. Rule inference was specifically associated with bilateral hippocampal activation while the task by difficulty interaction was associated with activation in right lateral orbital prefrontal cortex. We interpret the former in terms of semantic encoding of novel stimuli, and the latter in terms of hypothesis selection. Thus, we show an anatomical dissociation between task implementation and task difficulty that may correspond to a critical psychological distinction in the processes necessary for inductive inference.
Role of N-Linked Glycosylation for Sindbis Virus Infection and Replication in Vertebrate and Invertebrate Systems

ABSTRACT Each Sindbis virus (SINV) surface glycoprotein has two sites for N-linked glycosylation (E1 positions 139 and 245 [E1-139 and E1-245] and E2 positions 196 and 318 [E2-196 and E2-318]). Studies of SINV strain TE12 mutants with each site eliminated identified the locations of carbohydrates by cryo-electron microscopy (S. V. Pletnev et al., Cell 105:127-136, 2001). In the current study, the effects of altered glycosylation on virion infectivity, growth in cells of vertebrates and invertebrates, heparin binding, virulence in mice, and replication in mosquitoes were assessed. Particle-to-PFU ratios for E1-139 and E2-196 mutant strains were similar to that for TE12, but this ratio for the E1-245 mutant was 100-fold lower than that for TE12. Elimination of either E2 glycosylation site increased virus binding to heparin and increased replication in BHK cells. Elimination of either E1 glycosylation site had no effect on heparin binding but resulted in an approximately 10-fold decrease in virus yield from BHK cells compared to the TE12 amount. No differences in pE2 processing were detected. E2-196 and E2-318 mutants were more virulent in mice after intracerebral inoculation, while E1-139 and E1-245 mutants were less virulent. The E1-245 mutant showed impaired replication in C7/10 mosquito cells and in Culex quinquefasciatus after intrathoracic inoculation. We conclude that the increased replication and virulence of E2-196 and E2-318 mutants are primarily due to increased efficiency of binding to heparan sulfate on mammalian cells. Lack of glycosylation at E1-139 or E1-245 impairs replication in vertebrate cells, while E1-245 also severely affects replication in invertebrate cells.
Smoking cessation counseling beliefs and behaviors of outpatient oncology providers.

PURPOSE Many cancer patients continue to smoke after diagnosis, increasing their risk for treatment complications, reduced treatment efficacy, secondary cancers, and reduced survival. Outpatient oncology providers may not be using the "teachable moment" of cancer diagnosis to provide smoking cessation assistance. PROVIDERS AND METHODS: Physicians and midlevel providers (n = 74) who provide outpatient oncology services completed an online survey regarding smoking cessation counseling behaviors, beliefs, and perceived barriers. Outpatient medical records for 120 breast, lung, head and neck, colon, prostate, and acute leukemia cancer patients were reviewed to assess current smoking cessation assessment and intervention documentation practices. RESULTS Providers reported commonly assessing smoking in new patients (82.4% frequently or always), but rates declined at subsequent visits for both current smokers and recent quitters. Rates of advising patients to quit smoking were also high (86.5% frequently or always), but <30% of providers reported frequently or always providing intervention to smoking patients (e.g., nicotine replacement therapy or other medications, self-help materials, and/or referrals). Only 30% of providers reported that they frequently or always followed up with patients to assess progress with quitting. Few providers (18.1%) reported high levels of confidence in their ability to counsel smoking patients. Patients' lack of motivation was identified as the most important barrier to smoking cessation. CONCLUSIONS Although beliefs about providing cessation services to smoking patients were generally positive, few providers reported commonly providing interventions beyond advice to quit. Additional training and clinic-based interventions may improve adherence to tobacco cessation practice guidelines in the outpatient oncology setting.
Expression of CaT-like, a Novel Calcium-selective Channel, Correlates with the Malignancy of Prostate Cancer*

The regulation of intracellular Ca2+ plays a key role in the development and growth of cells. Here we report the cloning and functional expression of a highly calcium-selective channel localized on the human chromosome 7. The sequence of the new channel is structurally related to the gene product of the CaT1 protein cloned from rat duodenum and is therefore called CaT-like (CaT-L). CaT-L is expressed in locally advanced prostate cancer, metastatic and androgen-insensitive prostatic lesions but is undetectable in healthy prostate tissue and benign prostatic hyperplasia. Additionally, CaT-L is expressed in normal placenta, exocrine pancreas, and salivary glands. New markers with well defined biological function that correlate with aberrant cell growth are needed for the molecular staging of cancer and to predict the clinical outcome. The human CaT-L channel represents a marker for prostate cancer progression and may serve as a target for therapeutic strategies.
Etude des différents mécanismes de dépôt conduisant à l'encrassement particulaire en phase gazeuse des tubes d'échangeurs de chaleur

Ce travail porte sur l'etude experimentale et numerique des differents mecanismes de depot conduisant a l'encrassement particulaire des tubes d'echangeurs de chaleur. Par l'intermediaire d'un nouveau dispositif experimental concu et realise dans le cadre de cette etude, la cinetique de depot dans les premiers instants du processus d'encrassement a ete analysee dans des conditions encrassantes controlees. Les travaux experimentaux ont permis de mettre en evidence l'existence de differents regimes de transport suivant les parametres hydrauliques et particulaires : pour les particules de taille submicronique, la diffusion convective, augmentee par la thermophorese en presence d'un gradient de temperature, regit le depot de particules ; l'impaction inertielle est le principal mecanisme responsable du depot de particules supermicroniques ; dans la gamme granulometrique intermediaire, l'action combinee des mecanismes inertiels et thermophoretiques est mise en evidence. En complement, des campagnes de mesures sur une boucle d'essais existante mettant en uvre un aerosol beaucoup plus concentre ont permis d'etablir des cinetiques plus completes de depot et de mettre en evidence la modification des mecanismes de depot au cours du temps et l'influence de la forme du depot sur le depot de particules. Un modele numerique de prediction du depot, utilisant le logiciel trio developpe au cea et une approche lagrangienne, est propose et valide avec des resultats experimentaux issus de la litterature et obtenus lors de cette etude. L'approche numerique a egalement permis une comprehension plus fine des phenomenes mis en jeu par l'acces aux grandeurs locales (vitesses et positions d'impact des particules). Au terme de cette etude, les differents mecanismes regissant le depot de particules sur des tubes d'echangeurs ont ete identifies et modelises et specialement juste avant le debut du mecanisme d'impaction inertielle.
Using Predictive Techniques within CNC Machine Tools Feed Drives

The paper presents a hierarchical predictive control architecture dedicated to axis feed drives of machining centres. The primary level is built with Generalized Predictive Control (GPC) strategy, without considering any constraints action. The controller is formulated under the polynomial RST form, as a convenient framework for CNC systems. Robustification of this controller towards measurement noises that often drastically affect machine-tool environment is also examined. This basic level is further enhanced with a predictive-based mechanism allowing constraints avoidance by an adequate local change of the tool path. Finally, if this is action is not sufficient, as the full path during machining is known, an advanced constraints avoidance option is added, that may recompute the whole remaining trajectory with a lower speed profile. This strategy is validated in a virtual machining centre.
Cultivation of Fastidious Bacteria by Viability Staining and Micromanipulation in a Soil Substrate Membrane System

ABSTRACT Soil substrate membrane systems allow for microcultivation of fastidious soil bacteria as mixed microbial communities. We isolated established microcolonies from these membranes by using fluorescence viability staining and micromanipulation. This approach facilitated the recovery of diverse, novel isolates, including the recalcitrant bacterium Leifsonia xyli, a plant pathogen that has never been isolated outside the host.
News and the Public Sphere: The Boston Marathon Bombing in The New York Times and Le Figaro

The current dissertation explores the online mediatization of the Boston Marathon bombing crisis by an American newspaper (The New York Times) and a French one (Le Figaro) and their publics’ reactions to it. The research was conducted along two main analysis axes: (1) the main frames and themes through which the journalists and the publics gave meaning to the event, and (2) the characteristics of the online public spheres therefore created. The comparative perspective on the journalistic frames showed a strong tendency of homogenization, as the same main frames appeared in both analyzed newspapers. However, the online comments analysis revealed that in both cases, while the publics debated the event within those journalistic frames, they also negotiated or assigned new meanings, therefore creating new themes. The comparative perspective on the online public spheres showed that the major normative conditions of a public sphere were achieved. Nevertheless, certain differences were found that could be explained as pertaining to different cultures: the French debates were characterized by more moments of subjective personal involvement and flaming. From a journalistic practice standpoint the findings indicated that both the American and French publics critically scrutinized every piece of news information, addressed precise requests, and expected journalists to reply and fulfill their informational needs.
Morphological and quantitative studies in the otic region of the neural tube in chick embryos suggest a neuroectodermal origin for the otic placode

Careful histological observation of the development of the anlage of the inner ear in chicken embryos led us to question the traditional view of otic placode (OP) formation. First, morphological studies in the cephalic region carried out on stages preceding the appearance of the placodal epithelium revealed that the medial placodal cells are continuous temporally and spatially with cells belonging to the neural fold (NF). Second, both the formation of the basal lamina between the dorsal region of the neural tube (NT) and ectoderm and the pattern of formation of the neural crest present distinctive characteristics between otic levels and regions located anteriorly and posteriorly. Third, numerical comparisons of parameters for the NT and the OP between different levels of the rhombencephalon allowed us to assign a differential behaviour in the growth pattern of the otic region. These results indicated that the medial part of the OP is not derived from already independent ectoderm that increases in thickness under the influence of the NT (as previously accepted) but that it develops directly from the NFs. Although we do not exclude other possibilities, we propose that at least a proportion of the OP cells originate directly from cells committed to be neural crest. After this incorporation, basal laminal formation would delimit the NT from the OP without transition of the otic cells to ectoderm. This hypothesis would imply that part of the otic cells originate directly from neuroepithelial cells having a neuroectodermal (rather than the previously established ectodermal) origin.
Prognostic value of nuclear grading in patients with intracapsular (pT1‐pT2) renal cell carcinoma

The TNM classification system considers tumor size and, in particular tumor, greatest dimension as the only prognostic indicator for intracapsular renal cell carcinoma (RCC). The objective of the current study was to evaluate the role of nuclear grading and its importance as a prognostic indicator in patients with intracapsular (T1‐T2) RCC.