Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Transition from Pathogenicity to Commensalism: Global Regulator Mutations Mediate Fitness Gains through Virulence Attenuation

Symbiotic interactions are indispensable for metazoan function, but their origin and evolution remain elusive. We use a controlled evolution experiment to demonstrate the emergence of novel commensal interactions between Pseudomonas aeruginosa, an initially pathogenic bacterium, and a metazoan host, Caenorhabditis elegans. We show that commensalism evolves through loss of virulence, because it provides bacteria with a double fitness advantage: Increased within-host fitness and a larger host population to infect. Commensalism arises irrespective of host immune status, as the adaptive path in immunocompromised C. elegans knockouts does not differ from that in wild type. Dissection of temporal dynamics of genomic adaptation for 125 bacterial populations reveals highly parallel evolution of incipient commensalism across independent biological replicates. Adaptation is mainly achieved through frame shift mutations in the global regulator lasR and nonsynonymous point mutations in the polymerase gene rpoB that arise early in evolution. Genetic knockouts of lasR not only corroborate its role in virulence attenuation but also show that further mutations are necessary for the fully commensal phenotype. The evolutionary transition from pathogenicity to commensalism as we observe here is facilitated by mutations in global regulators such as lasR, because few genetic changes cause pleiotropic effects across the genome with large phenotypic effects. Finally, we found that nucleotide diversity increased more quickly in bacteria adapting to immunocompromised hosts than in those adapting to immunocompetent hosts. Nevertheless, the outcome of evolution was comparable across host types. Commensalism can thus evolve independently of host immune state solely as a side-effect of bacterial adaptation to novel hosts.
Modelling liking networks in an online healthcare community: An exponential random graph model analysis approach

The value and role of the Like button in social media have gained increased attention/focus, yet we know little about how liking relations form between Likers and Likeds. We study this problem in an online healthcare context from a social network perspective. Taking into account the effects of both the network structures and the attributes of Likers and Likeds, we utilize a theory-grounded statistical modelling approach, Exponential Random Graph Models (ERGMs), to model the liking network in an online healthcare community. The results of ERGM analysis reveal that, while network degree exhibits a big effect in the liking process, individual attributes like the level of past involvement and degree of activity also positively influence members’ future liking behaviour and performance. The evaluation indicates that our model is an effective method to identify the formation of liking networks. The findings extend the understanding of online liking behaviour and provide insights into harnessing the power of liking.
Targeting dexamethasone to Kupffer cells: Effects on liver inflammation and fibrosis in rats

Kupffer cells (KC) play an important role in the pathogenesis of inflammatory liver diseases leading to fibrosis. Anti‐inflammatory drugs are only effective when administered at high doses that may cause side effects. Therefore, dexamethasone coupled to mannosylated albumin (Dexa5‐Man10‐HSA) was designed by us to selectively deliver this anti‐inflammatory drug to the KC. The effectiveness of Dexa5‐Man10‐HSA was studied both in organ cultures and fibrosis induced by bile duct ligation (BDL) in rats. Dexa5‐Man10‐HSA accumulated in livers of both healthy and fibrotic rats (67% ± 5% and 70% ± 9% of the dose, respectively) and uptake was found almost exclusively in KC. Active dexamethasone was liberated from its carrier, because Dexa5‐Man10‐HSA could effectively inhibit nitric oxide (NO) and tumor necrosis factor α (TNF‐α) release in endotoxin‐activated liver slices. In vivo, however, this was associated with increased collagen I and III depositions and enhanced tissue inhibitor of metalloproteinase‐1 (TIMP‐1) mRNA expression. This was accompanied by a decreased influx of reactive oxygen species (ROS) producing cells in the livers of BDL animals treated with Dexa5‐Man10‐HSA as compared with untreated BDL rats. Dexa5‐Man10‐HSA treatment also replenished the depleted glycogen stores in hepatocytes of BDL livers. In conclusion, our studies showed selective delivery of dexamethasone to KC with Dexa5‐Man10‐HSA. This conjugate reduced intrahepatic ROS in vivo and TNF‐α production in vitro and prevented glycogen depletion in vivo, indicating effective pharmacologic targeting. Dexa5‐Man10‐HSA, however, also accelerated fibrogenesis, which was paralleled by TIMP‐1 mRNA induction. Targeting of dexamethasone to KC provides evidence for a dual role of this cell type in fibrogenesis of BDL rats.
Antecedents and the Performance Outcome of Transactive Memory in Daycare Work Groups

Laboratory experiments provide evidence that ongoing social interactions support the formation, functioning, and maintenance of transactive memory (TM), which in turn has positive performance implications in dyads and groups. Because most studies have been conducted with students, relatively little is known about TM in work settings. This study examined the mediating role of TM between interpersonal communication, group potency, supportive supervision, and self-reported group performance in 33 daycare work groups. Hierarchical regression analysis showed that TM fully mediated the interpersonal communication and group performance linkage, and partially mediated the group potency and group performance linkage. Implications and suggestions for future research are offered.
The effect of surfactant on long bubbles rising in vertical capillary tubes

In this letter we investigate the effect of interfacial surfactant on the motion of an air bubble rising in a vertical capillary tube filled with a viscous fluid and sealed at one end. A thin layer of liquid, with almost constant thickness b, exists between the bubble interface and the tube wall. The fluid displaced by the front meniscus flows down through this layer because the tube is sealed far up at the top. The steady rising velocity U of the bubble is related to the thickness b. An upper bound for U is obtained in terms of b and other physical data of the problem, which is in good agreement with previous experimental results. It is proved here analytically that the presence of surfactant on the bubble interface causes a thinning and a delay effect: the thickness of the liquid layer behind the bubble and the rise velocity of the bubble are smaller than those for the ‘clean’ case. Exactly the opposite effect of surfactant in the horizontal case has been derived analytically by Daripa and Pasa (2010 J. Stat. Mech. L02002) and numerically by Ratulowski and Chang (1990 J. Fluid Mech. 210 303). These effects of interfacial surfactant are consistent with previous experimental and numerical results.
Harnessing Collaborative Annotations on Online Formative Assessments

This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate formative assessments, manage collaborative annotations, and spot blockades to student learning in an efficient way. The experiment spanned one semester and underwent midterm and final exams. The results showed that adopting collaborative annotations on formative assessments significantly enhanced the learning achievements of students and extended retention time in the proposed system. Through a questionnaire and interviews, most students expressed positive attitudes toward using the proposed system.
Does income matter for subjective well-being in developing countries?: Empirical evidence from Thailand microdata

ABSTRACT Given that subjective well-being is a valid measure of mental well-being and that subjective well-being is cardinally measurable and interpersonally comparable, does income matter for subjective well-being in developing countries? We estimated life satisfaction and happiness level using various sociodemographic and socioeconomic determinants for a case of a developing country by using Thailand as an empirical study. We find that income has no effect on life satisfaction while having a statistically significant effect on happiness. Similarly, gender has no effect on being satisfied with life but has a statistically significant effect on happiness. The results for marital status suggest that people who are single are as happy as but are less satisfied with life than those who are married. Being divorced or widowed, however, reduces happiness. The effects of some life satisfaction/happiness determinants may significantly change after controlling for endogeneity of income.
Power infrastructure monitoring and damage detection using drone captured images

Infrastructure detection and monitoring is a difficult task. Due to the advances in unmanned vehicles and image analytics, it is possible to decrease the human effort and achieve consistent results in infrastructure assessments using aerial image processing. Reliable detection and integrity checking of power infrastructure including conductor lines, pylons and insulators in a diverse background is the most challenging task in drone based automatic infrastructure monitoring. Most techniques in literature use first principle approach that tries to represent the image as features of interest. This paper proposes a deep learning approach for power infrastructure detection. Graph based post processing is applied for improving the outcomes of the generated deep model. A f-score of 75% is achieved using the deep model which is further improved using spectral clustering for the conductor lines, pylons and insulators that form the core parts of power infrastructure.
Effectiveness of milk whey protein‐based ready‐to‐use therapeutic food in treatment of severe acute malnutrition in Malawian under‐5 children: a randomised, double‐blind, controlled non‐inferiority clinical trial

Abstract The cost of ready‐to‐use therapeutic food (RUTF) used in community‐based management of acute malnutrition has been a major obstacle to the scale up of this important child survival strategy. The current standard recipe for RUTF [peanut‐based RUTF (P‐RUTF )] is made from peanut paste, milk powder, oil, sugar, and minerals and vitamins. Milk powder forms about 30% of the ingredients and may represent over half the cost of the final product. The quality of whey protein concentrates 34% (WPC34) is similar to that of dried skimmed milk (DSM) used in the standard recipe and can be 25–33% cheaper. This blinded, parallel group, randomised, controlled non‐inferiority clinical trial tested the effectiveness in treating severe acute malnutrition (SAM) of a new RUTF formulation WPC‐RUTF in which WPC34 was used to replace DSM. Average weight gain (non‐inferiority margin Δ = −1.2 g kg−1 day−1) and recovery rate (Δ = −10%) were the primary outcomes, and length of stay (LOS) was the secondary outcome (Δ = +14 days). Both per‐protocol (PP) and intention‐to‐treat (ITT) analyses showed that WPC‐RUTF was not inferior to P‐RUTF for recovery rate [difference and its 95% confidence interval (CI) of 0.5% (95% CI –2.7, 3.7) in PP analysis and 0.6% (95% CI –5.2, 6.3) in ITT analysis] for average weight gain [0.2 (−0.5; 0.9) for both analyses] and LOS [−1.6 days (95% CI, −4.6, 1.4 days) in PP analysis and −1.9 days (95% CI, −4.6, 0.8 days) for ITT analysis]. In conclusion, whey protein‐based RUTF is an effective cheaper alternative to the standard milk‐based RUTF for the treatment of SAM.
Peripheral small cell undifferentiated carcinoma of the lung. Clinicopathologic features of 17 cases

Seventeen cases of resectable peripheral small cell undifferentiated carcinoma of the lung were studied (average size, 2.1 cm; range, 0.9–3.5 cm). The carcinomas exhibited predominantly mixed intermediate and fusiform/spindle subtypes; in seven carcinomas there were at least some foci of oat cell subtype. There was no histologic evidence of typical carcinoid tumor. Seven cases were fixed in solutions appropriate for immunohistologic study; these exhibited prominent neuron‐specific enolase activity but less prominent and more variable staining for the carcinoembryonic antigen and cytokeratins. All 17 cases were deemed resectable and had no clinical or radiologic evidence of metastasis. Seven (41%) patients died with recurrent and/or metastatic carcinoma (average survival, 1.7 years); five of these patients had carcinomas with at least some foci of oat cell foci subtype.
Differing responses to radiation of murine bone marrow stem cells in relation to the cell cycle.

The response to radiation of murine bone marrow stem cells in different portions of the cell cycle has been obtained. Murine bone marrow stem cells were injected into suitable recipients and synchronized in vivo with hydroxyurea. At varying times thereafter, radiation was given, and surviving stem cells were assayed by the spleen colony technique. There was a 10-fold difference between the maximum survival at 9 hr and minimum survival at 10 hr. For determination of the position of the S (synthetic) phase of the cell cycle, another experiment was performed consisting of a second injection of hydroxyurea instead of radiation. A nearly inverse curve was obtained with a minimum survival at 8 hr. This allowed determination of the S phase of the cell cycle. It thus appears that murine bone marrow stem cells are most resistant in late S and are quite sensitive in the G2-M phase.
Economic evaluation of the increase in production capacity of a high technology products manufacturing cell using discrete event simulation

This paper presents an application of the modeling and simulation methodology along with the Design of Experiments (DOE) to aid the decision makers to know the economic risk they are taking when there are many scenarios. Firstly, the production process was studied and documented by a SIPOC, an IDEF0 and a Flowchart. These techniques were combined to elaborate the simulation conceptual model. After that, the probability distributions were chosen and fed the computer model, built to emulate the real system. The simulation model was verified and statistically validated. Sixty four possible scenarios were tested, and in this case, the DOE may contribute to select the scenarios which are relevant to the economic analysis. The simulator used was Promodel® which provided the output to fed the cash flow of each scenario. Finally, the Net Present Value (NPV) and the economic risk of each scenario were calculated.
On the Convergence of the Lagged Diffusivity Fixed Point Method in Total Variation Image Restoration

In this paper we show that the lagged diffusivity fixed point algorithm introduced by Vogel and Oman in [ SIAM J. Sci. Comput. , 17 (1996), pp. 227--238] to solve the problem of total variation denoising, proposed by Rudin, Osher, and Fatemi in [ Phys. D, 60 (1992), pp. 259--268], is a particular instance of a class of algorithms introduced by Voss and Eckhardt in [ Computing, 25 (1980), pp. 243--251], whose origins can be traced back to Weiszfeld's original work for minimizing a sum of Euclidean lengths [ Tohoku Math. J., 43 (1937), pp. 355--386]. There have recently appeared several proofs for the convergence of this algorithm [G. Aubert et al., Technical report 94-01, Informatique, Signaux et Systemes de Sophia Antipolis, 1994], [A. Chambolle and P.-L. Lions, Technical report 9509, CEREMADE, 1995], and [D. C. Dobson and C. R. Vogel, SIAM J. Numer. Anal. , 34 (1997), pp. 1779--1791]. Here we present a proof of the global and linear convergence using the framework introduced in [H. Voss and U. Eckhart, Computing, 25 (1980), pp. 243--251] and give a bound for the convergence rate of the fixed point iteration that agrees with our experimental results. These results are also valid for suitable generalizations of the fixed point algorithm.
Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases

Purpose of review The authors present evidence published during the past 2 years of the roles of commensal and pathogenic bacteria in the pathogenesis of the inflammatory bowel diseases. Recent findings Rodent models conclusively implicate commensal enteric bacteria in chronic, immune-mediated, experimental colitis, and genetically determined defects in bacterial killing by innate immune cells are found in a subset of patients with Crohn's disease. There is no evidence that a single pathogen, including Mycobacterium avium subspecies paratuberculosis, causes Crohn's disease or ulcerative colitis. However, adherent/invasive Escherichia coli are associated with ileal Crohn's disease, with the mechanisms and genetics of adherent/invasive E. coli virulence being elucidated. Molecular characterization of the microbiota in patients with inflammatory bowel diseases reveals decreased biodiversity of commensal bacteria, most notably the phyla Bacteroidetes and Firmicutes, including the clinically relevant Faecalibacterium prausnitzii, and increased E. coli concentrations. VSL#3 is one probiotic preparation shown to be efficacious in certain clinical situations in small clinical trials. Summary Further characterization of altered microbiota in patients with inflammatory bowel diseases and linking dysbiosis with host genetic alterations in immunoregulation, innate microbial killing and barrier function are critical, so that individualized treatments to increase beneficial commensals and their metabolic products (probiotic and prebiotic administration) and diminish deleterious species such as adherent/invasive E. coli can be tailored for defined patient subsets.
Understanding Knowledge Management Performance: A Test of an Integrated Model

Although management studies have identified a wide variety of factors that influence knowledge management, little analysis has been completed showing the relative influence of these factors on performance. This paper develops an integrated model to illustrate and better understand how these factors affect knowledge management performance. The research offers insights into the determinants of knowledge management performance, and specific factors that influence performance. The goal of this research is to provide decision makers with specific advice to improve knowledge management performance.
Efficient Nonlinear Markov Models for Human Motion

Dynamic Bayesian networks such as Hidden Markov Models (HMMs) are successfully used as probabilistic models for human motion. The use of hidden variables makes them expressive models, but inference is only approximate and requires procedures such as particle filters or Markov chain Monte Carlo methods. In this work we propose to instead use simple Markov models that only model observed quantities. We retain a highly expressive dynamic model by using interactions that are nonlinear and non-parametric. A presentation of our approach in terms of latent variables shows logarithmic growth for the computation of exact log-likelihoods in the number of latent states. We validate our model on human motion capture data and demonstrate state-of-the-art performance on action recognition and motion completion tasks.
Correlation between cytology and histopathology of the salivary glam.

BACKGROUND Salivary gland swellings can result from tumours, an inflammatory process, or cysts. It can sometimes be difficult to establish whether pathology arises from the salivary gland itself or adjacent structures. Fine needle aspiration cytology (FNAC) is a simple, rapid and safe method to diagnose salivary gland swelling. FNAC has high sensitivity, specificity and accuracy. The aims of this study are to correlate FNAC diagnoses with histopathology and to establish the sensitivity and specificity of FNAC in diagnosis of salivary gland swellings in our institution. METHOD The study was conducted in the department of pathology, Sri Venkateshwara Medical college Hospital and research Centre, Pondicherry, India. Data was collected retrospectively for the time period 2007-2008 and prospectively for that obtained between January 2009 and June 2010. Results of cytologicial assessment were compared with histopathological data where possible to establish sensitivity and specificity of FNAC. RESULTS During the study period, 1309 FNAC were undertaken of which 96 FNAC were of salivary gland swellings. Correlation of cytology from FNAC with histopathology tissue was possible in 56 cases. Of the 96 cases for which FNAC data was available, 38.56% were from male and 61.45% were from female patients. The age of the patients ranged from 8 to 69 years. 48.95% cases were benign swellings, 13.54% were malignant, 6.25% were cysts and 31.25% had an inflammatory aetiology. Comparison of FNAC findings with histopathology specimens was available for 56 (58.33%) cases, following which the sensitivity and specificity of cytology were found to be 76.9% and 97.1% respectively. CONCLUSION FNAC is highly sensitive and specific technique for diagnosis of most of the salivary gland swelling. FNAC can be used preoperatively to avoid unnecessary surgery and discomfort associated with open biopsy.
Antimicrobial activity of clove oil dispersed in a concentrated sugar solution.

Essential oil of clove, dispersed (0.4% v/v) in a concentrated sugar solution, had a marked germicidal effect against various bacteria and Candida albicans. Staphylococcus aureus (five strains), Klebsiella pneumoniae, Pseudomonas aeruginosa, Clostridium perfringens, and Escherichia coli inoculated at a level of 10(7) cfu/ml, and C. albicans (inoculum 4.0 x 10(5) cfu/ml) were killed (greater than 99.999%) after 2-7 min in a laboratory broth supplemented with 63% (v/w) of sugar, and containing 0.4% (v/w) of essential oil of clove. Added organic matter (i.e. human or bovine serum) did not impair its antimicrobial activity. Sugar was not necessary for the antimicrobial activity of clove oil, but the concentrated sugar solution provided a good vehicle for obtaining an oil dispersion that is relatively stable for certain practical applications.