Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotypic and Phenotypic Diversity among Induced, stx2-Carrying Bacteriophages from Environmental Escherichia coli Strains

ABSTRACT Shiga toxin 2 (stx2) gene-carrying bacteriophages have been shown to convert Escherichia coli strains to Shiga toxin-producing Escherichia coli (STEC). In this study, 79 E. coli strains belonging to 35 serotypes isolated from wastewaters of both human and animal origin were examined for the presence of stx2-carrying bacteriophages in their genomes. The lytic cycle of the bacteriophages was induced by mitomycin, and the bacteriophage fraction was isolated and used for morphological and genetic characterization. The induced bacteriophages showed morphological diversity, as well as restriction fragment length polymorphism variation, in the different strains belonging to different serotypes. The ability to infect new hosts was highly variable, although most of the induced phages infected Shigella sonnei host strain 866. In summary, in spite of carrying either the same or different stx2 variants and in spite of the fact that they were isolated from strains belonging to the same or different serotypes, the induced bacteriophages were highly variable. The high level of diversity and the great infectious capacity of these phages could enhance the spread of the stx2 gene and variants of this gene among different bacterial populations in environments to which humans may be exposed.
Multidrug and Mupirocin Resistance in Environmental Methicillin-Resistant Staphylococcus aureus (MRSA) Isolates from Homes of People Diagnosed with Community-Onset MRSA Infection

ABSTRACT Patients with community-onset (CO) methicillin-resistant Staphylococcus aureus (MRSA) infections contribute to MRSA contamination of the home environment and may be reexposed to MRSA strains from this reservoir. This study evaluates One Health risk factors, which focus on the relationship between humans, animals, and the environment, for the increased prevalence of multiple antimicrobial-resistant MRSA isolates in the home environment. During a trial of patients with CO-MRSA infection, MRSA was isolated from the household environment at the baseline and 3 months later, following randomization of patients and household members to mupirocin-based decolonization therapy or an education control group. Up to two environmental MRSA isolates collected at each visit were tested. MRSA isolates were identified in 68% (65/95) of homes at the baseline (n = 104 isolates) and 51% (33/65) of homes 3 months later (n = 56 isolates). The rates of multidrug resistance (MDR) were 61% among isolates collected at the baseline and 55% among isolates collected at the visit 3 months later. At the baseline, 100% (14/14) of MRSA isolates from rural homes were MDR. While antimicrobial use by humans or pets was associated with an increased risk for the isolation of MDR MRSA from the environment, clindamycin use was not associated with an increased risk for the isolation of MDR MRSA. Incident low-level mupirocin-resistant MRSA strains were isolated at 3 months from 2 (5%) of 39 homes that were randomized to mupirocin treatment but none of the control homes. Among patients recently treated for a CO-MRSA infection, MRSA and MDR MRSA were common contaminants in the home environment. This study contributes to evidence that occupant use of antimicrobial drugs, except for clindamycin, is associated with MDR MRSA in the home environmental reservoir. (This study has been registered at ClinicalTrials.gov under registration no. NCT00966446.) IMPORTANCE MRSA is a common bacterial agent implicated in skin and soft tissue infections (SSTIs) in both community and health care settings. Patients with CO-MRSA infections contribute to environmental MRSA contamination in these settings and may be reexposed to MRSA strains from these reservoirs. People interact with natural and built environments; therefore, understanding the relationships between humans and animals as well as the characteristics of environmental reservoirs is important to advance strategies to combat antimicrobial resistance. Household interactions may influence the frequency and duration of exposure, which in turn may impact the duration of MRSA colonization or the probability for recurrent colonization and infection. Therefore, MRSA contamination of the home environment may contribute to human and animal recolonization and decolonization treatment failure. The aim of this study was to evaluate One Health risk factors that may be amenable to intervention and may influence the recovery of MDR and mupirocin resistance in CO-MRSA isolates.
Mental health effects following the eruption in Eyjafjallajökull volcano in Iceland: A population-based study

Aim: Volcanic eruptions and other natural disasters may affect survivor’s physical and mental health. The aim of this study was to examine the mental health effects of the 2010 Eyjafjallajökull volcanic eruption in Iceland on nearby residents, by exposure level and experience. Methods: This population-based study included 1615 residents living in an area close to the Eyjafjallajökull volcano at the time of the eruption and a sample of 697 residents from a non-exposed area. All participants received a questionnaire 6–9 months after the eruption assessing mental health (GHQ-12, PSS-4 and PC-PTSD). The exposed group also received questions related to the experience of the eruption. Results: Replies were received from 1146 participants in the exposed group (71%) and 510 participants in the non-exposed group (73%). Compared to the non-exposed group, participants living in the high-exposed area were at increased risk of experiencing mental distress (GHQ) 6–9 months following the eruption (odds ratio (OR) 1.45%; 95% confidence interval (CI) 1.11–1.90). High-exposed participants were furthermore at increased risk of experiencing symptoms of post-traumatic stress disorder (PTSD) compared to those living in the low-exposed area (OR 3.71; 95% CI 1.34–15.41). We further found that those who had direct experience of the eruption were more likely to suffer from symptoms of mental distress, PTSD symptoms and perceived stress, compared to those less exposed. Conclusions: The findings indicate that screening for these factors (e.g. experience of the event) could potentially aid in identifying those most vulnerable to developing psychological morbidity after this unique type of disaster.
Adhesion of Human and Animal Escherichia coli Strains in Association with Their Virulence-Associated Genes and Phylogenetic Origins

ABSTRACT Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors. Escherichia coli carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize E. coli isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (Capreolus capreolus) and the European hedgehog ( Erinaceus europaeus). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic E. coli isolates carried exVAGs with the highest prevalence, followed by badger (Meles meles) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines: afa-dra, daaD, tsh, vat, ibeA, fyuA, mat, sfa-foc, malX, pic, irp2, and papC. In summary, we established new screening methods which enabled us to characterize large numbers of E. coli isolates. We defined reservoirs for potential pathogenic E. coli. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.
Does D2 plus Para-Aortic Nodal Dissection surgery offer a better survival outcome compared to D2 surgery only for gastric cancer consistently? A definite result based on a hospital population of nearly two decades

Background and Aims: Curative resection is the treatment of choice for gastric cancer. Although it has been concluded that D2 lymphadenectomy plus para-aortic nodal dissection does not improve survival rate in curable gastric cancer, it is unclear whether D2 plus para-aortic nodal dissection has a benefit in some groups of patients. We conducted a retrospective study in our hospital, in which we compared D2 with D2 plus para-aortic nodal dissection lymphadenectomy for gastric cancer in subgroups of each clinical characteristic in terms of long-term survival after surgery. Material and Methods: We selected 1792 patients who had undergone the treatment with curative intent between 1990 and 2007, 1344 in the D2 group and 448 in the D2 plus para-aortic nodal dissection group. Each procedure was verified by pathological analyses. The primary end points were 5-year overall survival. Results and Conclusions: Median follow-up periods were 50 months for patients assigned to D2 group and 54 months for patients assigned to D2 plus para-aortic nodal dissection group. Overall 5-year survival was not significantly higher in patients assigned to D2 plus para-aortic nodal dissection surgery compared to those assigned to D2 surgery (31.2% (95% confidence interval: 19.8%–42.6%) vs 26.6% (95% confidence interval: 20.3%–32.9%); log-rank p = 0.433). D2 plus para-aortic nodal dissection surgery should only be used for curable gastric cancer of T3-4 and N2 stage and should not be used for T1 disease and total gastrectomy.
Broadening and Enhancing Functions of Antibodies by Self-Assembling Multimerization at Cell Surface

Monoclonal antibody therapy has offered treatment benefits. Nonetheless, a lack of efficacy still exists, partially because monovalent binding of antibodies to specific receptors fails to translate into an active response. Here, we report a pretargeting–postassembly approach that exploits the selective Watson–Crick base pairing properties of oligonucleotides and multivalently tethers receptor-prebound antibodies to albumin at the cell surface. We demonstrate that this two-step self-assembling strategy allows sequential actions of receptor binding and clustering that broadens and strengthens the functions of antibodies. We show that anti-CD20 obinutuzumab (OBN) modified with one morpholino oligonucleotide (OBN-MORF1) maintains the feature of naked OBN antibody upon CD20 binding, and results in actin redistribution, homotypic adhesion, and lysosome-mediated cell death. Consecutive treatment with albumin grafted with multiple copies of a complementary morpholino oligonucleotide (HSA-(MORF2)x) hybridizes with surface-attached OBN-MORF1, manipulates CD20 clustering, and engages additional signals to induce calcium influx and caspase-related apoptosis. With the two types of different mechanisms collaborating in one system, the simple design exerted a notable survival extension of mice bearing disseminated B-cell lymphomas.
Face Recognition Under Varying Illumination Using Gradientfaces

In this correspondence, we propose a novel method to extract illumination insensitive features for face recognition under varying lighting called the gradient faces. Theoretical analysis shows gradient faces is an illumination insensitive measure, and robust to different illumination, including uncontrolled, natural lighting. In addition, gradient faces is derived from the image gradient domain such that it can discover underlying inherent structure of face images since the gradient domain explicitly considers the relationships between neighboring pixel points. Therefore, gradient faces has more discriminating power than the illumination insensitive measure extracted from the pixel domain. Recognition rates of 99.83% achieved on PIE database of 68 subjects, 98.96% achieved on Yale B of ten subjects, and 95.61% achieved on Outdoor database of 132 subjects under uncontrolled natural lighting conditions show that gradient faces is an effective method for face recognition under varying illumination. Furthermore, the experimental results on Yale database validate that gradient faces is also insensitive to image noise and object artifacts (such as facial expressions).
Steerable Wavelet Frames Based on the Riesz Transform

We consider an extension of the 1-D concept of analytical wavelet to n-D which is by construction compatible with rotations. This extension, called a monogenic wavelet, yields a decomposition of the wavelet coefficients into amplitude, phase, and phase direction. The monogenic wavelet is based on the hypercomplex monogenic signal which is defined using Riesz transforms and perfectly isotropic wavelets frames. Employing the new concept of Clifford frames, we can show that the monogenic wavelet generates a wavelet frame. Furthermore, this approach yields wavelet frames that are steerable with respect to direction. Applications to descreening and contrast enhancement illustrate the versatility of this approach to image analysis and reconstruction.
Assessment of Pharmacists’ Patient Care Competencies: Validity Evidence from Ontario (Canada)’s Quality Assurance and Peer Review Process

Maintenance of competence is integral to health care practitioners’ continuing professional development. The adequacy and value of indirect assessment of competence (through, for example, learning portfolios or attendance at educational events) has been questioned. Direct assessment (such as written tests of clinical knowledge or objective structured clinical examinations, OSCEs) has been advocated as a more meaningful indicator of a practitioner’s competence. This paper describes the Ontario (Canada) College of Pharmacists’ experience with direct assessment through the Peer Review/Quality Assurance process. This process consists of a self- assessment questionnaire, ongoing maintenance of a learning portfolio, a written test of clinical knowledge, and an OSCE. Each year, a randomly selected group of pharmacists in Ontario undertake the Peer Review process. After five years of operation, 992 pharmacists had participated in this program; 86% of participants met or exceeded standards and were encouraged to continue with their own professional development while 14% of participants did not meet standards in identified assessment areas, and were directed to a peer-assisted process to facilitate professional development. Findings suggest individuals who were educated outside Canada or the United States, those in community pharmacy practice, and those who had been in practice 25 years or more demonstrated greatest difficulty in meeting standards. The implications of these results for pharmacy practice and professional development are discussed as are issues related to direct and indirect assessment of clinical skills.
Integron Prevalence and Diversity in Manured Soil

ABSTRACT The levels of integron abundance and diversity in soil amended with pig slurry were studied. Real-time PCR illustrated a significant increase in class 1 integron prevalence after slurry application, with increased prevalence still evident at 10 months after application. Culture-dependent data revealed 10 genera, including putative human pathogens, carrying class 1 and 2 integrons.
Synergistic Inactivation of Spores of Proteolytic Clostridium botulinum Strains by High Pressure and Heat Is Strain and Product Dependent

ABSTRACT The combined high pressure and heat resistances of spores of five proteolytic Clostridium botulinum strains and of the nonpathogenic surrogate strain Clostridium sporogenes PA3679 were compared with their heat-only resistances on the basis of equivalent accumulated thermal lethality, expressed as equivalent minutes at a reference temperature of 105°C (F105°C). Comparisons were made with three model (i.e., diluted) products, namely, 30% (wt/wt) Bolognese sauce, 50% (wt/wt) cream sauce, and rice water agar. Pressure was determined to act synergistically with heat during high-pressure thermal (HPT) processing for C. botulinum FRRB 2802 (NCTC 7273) and C. botulinum FRRB 2804 (NCTC 3805 and 62A) in the Bolognese and cream sauces and for C. botulinum FRRB 2807 (213B) in the Bolognese sauce only. No synergy was observed for C. botulinum FRRB 2803 (NCTC 2916) or FRRB 2806 (62A) or C. sporogenes FRRB 2790 (NCTC 8594 and PA3679) in any of the model products. No significant protective effect of pressure against spore inactivation was determined for any Clostridium strain in any product. Because synergy was not consistently observed among strains of C. botulinum or among products, the prediction of inactivation of C. botulinum spores by HPT sterilization (HPTS) for the present must assume a complete lack of synergy. Therefore, any HPTS process for low-acid shelf-stable foods must be at least thermally equivalent to an F0 process of 2.8 min, in line with current good manufacturing practices. The results of this study suggest that the use of C. sporogenes PA3679 as a surrogate organism may risk overestimating inactivation of C. botulinum by HPT processing.
The Host as the Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster

ABSTRACT Most associations between animals and their gut microbiota are dynamic, involving sustained transfer of food-associated microbial cells into the gut and shedding of microorganisms into the external environment with feces, but the interacting effects of host and microbial factors on the composition of the internal and external microbial communities are poorly understood. This study on laboratory cultures of the fruit fly Drosophila melanogaster reared in continuous contact with their food revealed time-dependent changes of the microbial communities in the food that were strongly influenced by the presence and abundance of Drosophila. When germfree Drosophila eggs were aseptically added to nonsterile food, the microbiota in the food and flies converged to a composition dramatically different from that in fly-free food, showing that Drosophila has microbiota-independent effects on the food microbiota. The microbiota in both the flies that developed from unmanipulated eggs (bearing microorganisms) and the associated food was dominated by the bacteria most abundant on the eggs, demonstrating effective vertical transmission via surface contamination of eggs. Food coinoculated with a four-species defined bacterial community of Acetobacter and Lactobacillus species revealed the progressive elimination of Lactobacillus from the food bearing few or no Drosophila, indicating the presence of antagonistic interactions between Acetobacter and Lactobacillus. Drosophila at high densities ameliorated the Acetobacter/Lactobacillus antagonism, enabling Lactobacillus to persist. This study with Drosophila demonstrates how animals can have major, coordinated effects on the composition of microbial communities in the gut and immediate environment.
Surgical complications following 1670 consecutive adult renal transplantations: a single center study

Background and Aims: The aim of the study was to clarify the frequency and the sequel of surgical complications occurring within 1 year after renal transplantation. Patients and Methods: Surgical complications after 1670 consecutive adult kidney transplantations performed between 2000 and 2009 were retrospectively analyzed. In 2%, a living-related allograft was used, and 10% were retransplantations. An intravesical technique without stenting was used for the ureteric implantation. Results: There were 282 surgical complications occurring in 259 (15.5%) transplantations. Ureteral obstruction occurred in 53 (3.1%), lymphoceles in 39 (1.5%), postoperative hemorrhage in 36 (2.1%), and renal vein thrombosis in 22 (1.3%) patients, respectively. Out of the 17 lung emboli, 4 were fatal. Male recipients had twice as much ureteral stenosis as female (2.4 vs 1.2%, p < 0.05), and the opposite was true of urinary leakage (1.8% vs 4.0%, p < 0.025). Five-year patient and graft survival was impaired in patients with complications compared with patients without complications. Five-year patient survival was 92% versus 88% and graft survival 87% versus 74%. Conclusion: Surgical complications impair patient and graft survival after kidney transplantation.
Production of Verotoxin and Distribution of O Islands 122 and 43/48 among Verotoxin-Producing Escherichia coli O103:H2 Isolates from Cattle and Humans

ABSTRACT This study investigated variations in the occurrence of markers of O islands 122 and 43/48 and in verotoxin 1 production in 91 verotoxin-producing Escherichia coli (VTEC) O103:H2 strains of bovine and human origins. None of the genes that were investigated appear to be virulence indicators for human O103:H2 VTEC.
Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

ABSTRACT Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.
Optimal Inversion of the Generalized Anscombe Transformation for Poisson-Gaussian Noise

Many digital imaging devices operate by successive photon-to-electron, electron-to-voltage, and voltage-to-digit conversions. These processes are subject to various signal-dependent errors, which are typically modeled as Poisson-Gaussian noise. The removal of such noise can be effected indirectly by applying a variance-stabilizing transformation (VST) to the noisy data, denoising the stabilized data with a Gaussian denoising algorithm, and finally applying an inverse VST to the denoised data. The generalized Anscombe transformation (GAT) is often used for variance stabilization, but its unbiased inverse transformation has not been rigorously studied in the past. We introduce the exact unbiased inverse of the GAT and show that it plays an integral part in ensuring accurate denoising results. We demonstrate that this exact inverse leads to state-of-the-art results without any notable increase in the computational complexity compared to the other inverses. We also show that this inverse is optimal in the sense that it can be interpreted as a maximum likelihood inverse. Moreover, we thoroughly analyze the behavior of the proposed inverse, which also enables us to derive a closed-form approximation for it. This paper generalizes our work on the exact unbiased inverse of the Anscombe transformation, which we have presented earlier for the removal of pure Poisson noise.