Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiome Diversity in the Bronchial Tracts of Patients with Chronic Obstructive Pulmonary Disease

ABSTRACT Culture of bacteria from bronchial secretions in respiratory patients has low sensitivity and does not allow for complete assessment of microbial diversity across different bronchial compartments. In addition, a significant number of clinical studies are based on sputum samples, and it is not known to what extent they describe the real diversity of the mucosa. In order to identify previously unrecognized lower airway bacteria and to investigate the complexity and distribution of microbiota in patients with chronic obstructive pulmonary disease (COPD), we performed PCR amplification and pyrosequencing of the 16S rRNA gene in patients not showing signs or symptoms of infection. Four types of respiratory samples (sputum, bronchial aspirate, bronchoalveolar lavage, and bronchial mucosa) were taken from each individual, obtaining on average >1,000 16S rRNA sequences per sample. The total number of genera per patient was >100, showing a high diversity, with Streptococcus, Prevotella, Moraxella, Haemophilus, Acinetobacter, Fusobacterium, and Neisseria being the most commonly identified. Sputum samples showed significantly lower diversity than the other three sample types. Lower-bronchial-tree samples, i.e., bronchoalveolar lavage and bronchial mucosa, showed a very similar bacterial compositions in contrast to sputum and bronchial aspirate samples. Thus, sputum and bronchial aspirate samples are upper bronchial tree samples that are not representative of the lower bronchial mucosa flora, and bronchoalveolar lavage samples showed the results closest to those for the bronchial mucosa. Our data confirm that the bronchial tree is not sterile in COPD patients and support the existence a different microbiota in the upper and lower compartments.
Carbapenemase Detection among Carbapenem-Resistant Glucose-Nonfermenting Gram-Negative Bacilli

ABSTRACT Accurate detection of carbapenemase-producing glucose-nonfermenting Gram-negative bacilli (CPNFs), including Pseudomonas aeruginosa and Acinetobacter baumannii, is necessary to prevent their dissemination within health care settings. We performed a method comparison study of 11 phenotypic carbapenemase detection assays to evaluate their accuracy for the detection of CPNFs. A total of 96 carbapenem-resistant glucose-nonfermenting isolates were included, of which 29% produced carbapenemases. All CPNFs were molecularly characterized to identify β-lactamase genes. A total of 86% of the carbapenemase-producing P. aeruginosa isolates produced class B carbapenemases. Several assays performed with a sensitivity of >90% for the detection of carbapenemase-producing P. aeruginosa, including all rapid chromogenic assays and the modified carbapenem inactivation method. Most included assays, with the exception of the Manual Blue Carba assay, the Modified Carba NP assay, the boronic acid synergy test, and the metallo-β-lactamase Etest, had specificities of >90% for detecting carbapenemase-producing P. aeruginosa. Class D carbapenemases were the most prevalent carbapenemases among the carbapenemase-producing A. baumannii strains, with 60% of the carbapenemase-producing A. baumannii isolates producing acquired OXA-type carbapenemases. Although several assays achieved >90% specificity in identifying carbapenemase-producing A. baumannii, no assays achieved a sensitivity of greater than 90%. Our findings suggest that the available phenotypic tests generally appear to have excellent sensitivity and specificity for detecting carbapenemase-producing P. aeruginosa isolates. However, further modifications to existing assays or novel assays may be necessary to accurately detect carbapenemase-producing A. baumannii.
Genotyping of Human Papillomaviruses by a Novel One-Step Typing Method with Multiplex PCR and Clinical Applications

ABSTRACT We describe here a rapid, high-throughput genotyping procedure that allows the simultaneous detection of 16 high- and low-risk genital human papillomavirus (HPV) types by multiplex PCR in a single reaction tube. Multiplex PCR is based on the amplification of HPV DNA by sets of HPV genotype-specific primers, and the genotypes of HPV are visually identified by the sizes of amplicons after they are separated by capillary electrophoresis. The procedure does not include a hybridization step with HPV-specific probes and is rapid and labor-saving. We detected all 16 HPV genotypes (types 16, 58, 52, 51, 56, 31, 18, 39, 66, 59, 6, 33, 30, 35, 45, and 11) with a high sensitivity and a high degree of reproducibility. By using this newly developed method, we conducted a pilot study to examine the correlation between the prevalence and genotype distributions of HPV and the cytological group classifications for 547 cervical samples. Compared with the group of samples considered normal (14.7%), there was a significant increase in the prevalence of HPV in women with atypical squamous cells of unknown significance (61.3%), low-grade intraepithelial lesions (75.8%), and high-grade intraepithelial lesions (HSILs) (82.2%). The prevalence and distribution of type 58 were correlated with cytological malignancies, with the highest prevalence in women with HSILs. In conclusion, the novel multiplex PCR method described appears to be highly suitable not only for the screening of cervical cancer precursor lesions but also for the characterization of genotype distributions in large-scale epidemiological studies and HPV vaccination trials.
Audit of fidelity of clinicians to the Mental Capacity Act in the process of capacity assessment and arriving at best interests decisions

Purpose – The purpose of this paper is to evaluate health professionals' fidelity to the Mental Capacity Act (MCA) principles on determining mental capacity and arriving at best interests decisions in the care of individuals found to lack the relevant decision‐making capacity.Design/methodology/approach – A retrospective review of the case records of 68 patients previously determined by clinicians as lacking mental capacity in at least one of three identified areas: treatment consenting capacity, capacity to decide on place of abode and capacity to manage financial affairs, was conducted. Notes were examined to determine how mental capacity was assessed and the process of arriving at best interests decisions in the care of the non‐capacitous individuals.Findings – It was difficult to locate relevant entries as there were no designated folders for MCA related issues. There were (mostly) minimal entries made about the assessment process, only patchy documentation of the legal criteria used in capacity asses.
Secondary Control for Voltage Quality Enhancement in Microgrids

In this paper, a hierarchical control scheme is proposed for enhancement of sensitive load bus (SLB) voltage quality in microgrids. The control structure consists of primary and secondary levels. The primary control level comprises distributed generators (DGs) local controllers. Each of these controllers includes a selective virtual impedance loop which is considered to improve sharing of fundamental and harmonic components of load current among the DG units. The sharing improvement is provided at the expense of increasing voltage unbalance and harmonic distortion. Thus, the secondary control level is applied to manage the compensation of SLB voltage unbalance and harmonics by sending proper control signals to the primary level. DGs compensation efforts are controlled locally at the primary level. The system design procedure for selecting proper control parameters is discussed. Simulation results are provided in order to demonstrate the effectiveness of the proposed control scheme.
Stool Culture for Diagnosis of Pulmonary Tuberculosis in Children

ABSTRACT Bacteriological confirmation of Mycobacterium tuberculosis is achieved in the minority of young children with tuberculosis (TB), since specimen collection is resource intensive and respiratory secretions are mostly paucibacillary, leading to limited sensitivity of available diagnostic tests. Although molecular tests are increasingly available globally, mycobacterial culture remains the gold standard for diagnosis and determination of drug susceptibility and is more sensitive than molecular methods for paucibacillary TB. We evaluated stool culture as an alternative to respiratory specimens for the diagnosis of suspected intrathoracic TB in a subgroup of 188 children (median age, 14.4 months; 15.4% HIV infected) enrolled in a TB diagnostic study at two local hospitals in Cape Town, South Africa. One stool culture was compared to overall bacteriological confirmation by stool Xpert and by Xpert and culture of multiple respiratory specimens. After decontamination/digestion with NALC (N-acetyl-l-cysteine)-NaOH (1.25%), concentrated fluorescent smear microscopy, Xpert MTB/RIF, and liquid culture were completed for all specimens. Culture contamination of stool specimens was high at 41.5%. Seven of 90 (7.8%) children initiating TB treatment were stool culture positive for M. tuberculosis. Excluding contaminated cultures, the sensitivity of stool culture versus confirmed TB was 6/25 (24.0%; 95% confidence interval [CI] = 9.4 to 45.1%). In addition, stool culture detected TB in 1/93 (1.1%) children with “unconfirmed TB. ” Testing the same stool by Xpert increased sensitivity to 33.3% (95% CI = 18.0 to 51.8%). In conclusion, stool culture had low sensitivity for M. tuberculosis detection in children with intrathoracic TB. Reducing culture contamination through improved laboratory protocols may enable more reliable estimates of its diagnostic utility.
INNOVATIVE SERVICE DELIVERY MODELS: LESSONS LEARNED IN PROVIDING CARE FOR OLDER PEOPLE AND PEOPLE WITH DISABILITIES

An evaluation is reported of six projects funded under the HACC (Home and Community Care) Program from Commonwealth Unmatched Monies. Each project provided an innovative service delivery model and two of the key purposes of the evaluation were to determine whether or not these models had been effective in meeting individual needs and to determine the factors most critical to supporting people at home. The evaluation found that the projects had been effective from both a service and a cost perspective and identified as the key factors a sense of security based on a belief in one's ability to manage care in the home setting, access to available services, flexibility in the provision of services and supports, effective case management and the presence of a caregiver. An analysis of costs was also undertaken and the projects were found to be cost-effective and considerably less expensive than equivalent care in a residential setting.
Quality adjusted life year gains associated with administration of recombinant tissue-type plasminogen activator for treatment of acute ischemic stroke: 1998–2011

Background Intravenous recombinant tissue-type plasminogen activator (r-tPA) is an approved treatment for select patients with acute ischemic stroke (AIS). Data indicate r-tPA improves functional outcome three months after AIS compared with placebo. This study models the increase in quality adjusted life years (QALYs) associated with r-tPA compared with similar patients not treated with r-tPA. Methods Hospital discharge data for AIS and r-tPA were obtained from the Nationwide Inpatient Sample from 1998 to 2011. Discharge location (home, rehabilitation, long-term care, death) was mapped to modified Rankin Scale (mRS) scores based on National Institute of Neurological Disorders and Stroke (NINDS) Study Group Part 1 and 2 clinical studies. The mRS scores were mapped to relative risk of death and QALYs obtained from the literature. The model estimated expected survival and QALYs by age, gender and mRS for patients receiving r-tPA. Life expectancy and QALYs for patients not receiving r-tPA were estimated based on discharge location and mRS for placebo patients in the NINDS study. Results AIS discharges declined from over 635,000 in 1998 to over 593,000 in 2011. A total of 183,235 patients received r-tPA. Utilization of r-tPA increased from 1% of AIS patients in 1998 to over 4% in 2011. Estimated projections for QALYs gained from utilization of r-tPA to QALYS without r-tPA were just under 240,000 for the 13 years and with no discounting, and just over 165,000 assuming 3% annual discounting. In the most conservative scenario, assuming no difference in proportional discharge status (i.e. patients not treated with r-tPA are discharged in the same manner as r-tPA patients), the estimated life years gained are approximately 35,000 and QALYS gained are approximately 90,000. Conclusions r-tPA for AIS has resulted in estimated gains in quality-adjusted life years due to reduction in disability and improvement in functioning since its introduction in 1998.
Spurious Amplification of a Plasmodium vivax Small-Subunit RNA Gene by Use of Primers Currently Used To Detect P. knowlesi

ABSTRACT The PCR primers commonly used to detect Plasmodium knowlesi infections in humans were found to cross-react stochastically with P. vivax genomic DNA. A nested primer set that targets one of the P. knowlesi small-subunit rRNA genes was validated for specificity and for sensitivity of detection of <10 parasite genomes.
Performance Analysis and Comparison on Energy Storage Devices for Smart Building Energy Management

A smart building energy system usually contains multiple energy sources such as power grids, autonomous generators, renewable resources, storage devices, and schedulable loads. Storage devices such as batteries, ice/heat storage units, and water tanks play an important role in reducing energy cost in building energy systems since they can help sufficiently utilize renewable energy resources and time-of-use electricity prices. It is important to plan, schedule, and coordinate all the storage devices together with schedulable loads in a building facilitated by microgrid technology. To consider the above problem with uncertainties in solar radiation and demand profiles, a stochastic optimization problem is formulated and solved by the scenario tree method. The best combination and the optimal capacities of storage devices for specific building energy systems are then determined. Furthermore, the optimal operating strategy of building energy systems can be obtained. The performance analysis on the storage devices is conducted and the numerical results show that thermal storage devices (e.g., ice storage units, water tanks) are good for saving energy costs but batteries may not be economical due to their high investment cost and short lifetime. It is also observed that the aforementioned uncertainties have an impact on selecting which type and capacity of storage device should be used.
Factors associated with abuse in residential child care institutions

Confidence in the public care system in the United Kingdom (UK) has been shaken by numerous and widespread scandals surrounding the abuse of children and young people, particularly those in residential child care institutions. This paper examines factors associated with such abuse, including: failings in relation to staff recruitment, training, and supervision; ineffective management and systems of accountability; the development of inappropriate institutional cultures; public ambivalence towards children in care; the slow footed response to the threat posed to children and young people by dangerous men and other youngsters in care; and the long-term policy failure to develop coherent and integrated systems of child welfare in the UK.
Yellow Fever Virus: Diagnostics for a Persistent Arboviral Threat

Yellow fever (YF) is the prototypical hemorrhagic fever and results from infection with yellow fever virus (YFV), which is endemic to regions of Africa and South America. Despite the availability of an effective vaccine, YFV continues to cause disease throughout regions where it is endemic, including intermittent large outbreaks among undervaccinated populations. ABSTRACT Yellow fever (YF) is the prototypical hemorrhagic fever and results from infection with yellow fever virus (YFV), which is endemic to regions of Africa and South America. Despite the availability of an effective vaccine, YFV continues to cause disease throughout regions where it is endemic, including intermittent large outbreaks among undervaccinated populations. A number of diagnostic methods and assays have been described for the detection of YFV infection, including viral culture, molecular testing, serology, and antigen detection. Commercial diagnostics are not widely available, and testing is generally performed at a small number of reference laboratories. The goal of this article, therefore, is to review available clinical diagnostics for YFV, which may not be familiar to many practitioners outside areas where it is endemic. Additionally, we identify gaps in our current knowledge about YF that pertain to diagnosis and describe interventions that may improve YFV detection.
Evaluation of the Verigene Gram-Positive Blood Culture Nucleic Acid Test for Rapid Detection of Bacteria and Resistance Determinants

ABSTRACT Rapid identification of pathogens from blood cultures can decrease lengths of stay and improve patient outcomes. We evaluated the accuracy of the Verigene Gram-positive blood culture (BC-GP) nucleic acid test for investigational use only (Nanosphere, Inc., Northbrook, IL) for the identification of Gram-positive bacteria from blood cultures. The detection of resistance genes (mecA in Staphylococcus aureus and Staphylococcus epidermidis and vanA or vanB in Enterococcus faecium and Enterococcus faecalis) by the BC-GP assay also was assessed. A total of 186 positive blood cultures (in BacT/Alert FA bottles) with Gram-positive cocci observed with Gram staining were analyzed using the BC-GP assay. The BC-GP results were compared with the identification and susceptibility profiles obtained with routine methods in the clinical laboratory. Discordant results were arbitrated with additional biochemical, cefoxitin disk, and repeat BC-GP testing. The initial BC-GP organism identification was concordant with routine method results for 94.6% of the blood cultures. Only 40% of the Streptococcus pneumoniae identifications were correct. The detection of the mecA gene for 69 blood cultures with only S. aureus or S. epidermidis was concordant with susceptibility testing results. For 3 of 6 cultures with multiple Staphylococcus spp. , mecA detection was reported but was correlated with oxacillin resistance in a species other than S. aureus or S. epidermidis. The detection of vanA agreed with susceptibility testing results for 45 of 46 cultures with E. faecalis or E. faecium. Comparison of the mean times to results for each organism group showed that BC-GP results were available 31 to 42 h earlier than phenotypic identifications and 41 to 50 h earlier than susceptibility results.
Analysis of Consumer Preferences for Electric Vehicles

Due to the recent global trend toward stricter restrictions on both greenhouse gases emission and energy consumption, there is an emerging attention on electric vehicles (EVs). It is anticipated that proliferation of EV will be expanded rapidly in the near future. Accordingly, there is a need to analyze the consumer preferences for the EVs as the basic data for developing the relevant industries' strategies in the newly emerging market of EVs or establishing the government policies to popularize EVs. This paper analyzes the consumer preferences for the EV on the basis of the stated preference data from consumers in Korea. A conjoint method and a mixed logit model using the Bayesian approach were used to estimate the preferences of consumers. The stated preference data of the conjoint method is collected through a face-to-face survey conducted in June 2009. The consumer preferences on the key attributes that affect the choices of EV are estimated by a mixed logit model. Marginal willingness to pay is calculated to quantitatively analyze the consumer preferences on the key attributes. The results of this paper show that the consumers have greater preference for EV with swappable battery rather than unswappable battery, and for lump-sum payment rather than installment of the subsidies.
Learning from Failure Across Multiple Clusters: A Trace-Driven Approach to Understanding, Predicting, and Mitigating Job Terminations

In large-scale computing platforms, jobs are prone to interruptions and premature terminations, limiting their usability and leading to significant waste in cluster resources. In this paper, we tackle this problem in three steps. First, we provide a comprehensive study based on log data from multiple large-scale production systems to identify patterns in the behaviour of unsuccessful jobs across different clusters and investigate possible root causes behind job termination. Our results reveal several interesting properties that distinguish unsuccessful jobs from others, particularly w.r. t. resource consumption patterns and job configuration settings. Secondly, we design a machine learning-based framework for predicting job and task terminations. We show that job failures can be predicted relatively early with high precision and recall, and also identify attributes that have strong predictive power of job failure. Finally, we demonstrate in a concrete use case how our prediction framework can be used to mitigate the effect of unsuccessful execution using an effective task-cloning policy that we propose.
Identification of Coagulase-Negative Staphylococci by Using the BD Phoenix System in the Low-Inoculum Mode

ABSTRACT The new “low-inoculum” mode of the Phoenix system was evaluated to identify clinical coagulase-negative staphylococci. API ID32 Staph panels were used as comparators, and discrepancies were resolved by 16S rRNA and tuf gene analysis. The system correctly identified 90.5% of isolates, with a mean time of 10.2 h. Accuracy was satisfactory for Staphylococcus epidermidis, S. saprophyticus, and S. haemolyticus.
Bodyweight Training: A Return To Basics

FOR CENTURIES, MAN HAS SOUGHT OUT THE MOST EFFECTIVE METHODS TO BUILD STRENGTH, VIGOR, AND VITALITY. OVER THE YEARS, METHODS HAVE EVOLVED, SOME HAVE VANISHED, AND SOME NEVER WENT AWAY, ALTHOUGH SOMETIMES NEGLECTED AND FORGOTTEN. THIS COLUMN HIGHLIGHTS THE ADVANTAGES, DISADVANTAGES, AND TRAINING PROGRESSIONS TO ONE OF THE SIMPLEST METHODS OF TRAINING AND CONDITIONING KNOWN TO MAN, BODYWEIGHT TRAINING.
Etiology and pathogenesis of Moyamoya Disease: An update on disease prevalence

Moyamoya disease is a chronic cerebrovascular occlusive disease that is characterized by progressive stenosis of the terminal portion of the internal carotid artery and its main branches. The occurrence of Moyamoya disease is related to immune, genetic, and other factors. Though the research of Moyamoya disease has made great strides in the past 60 years, the etiology and pathogenesis are largely unknown. This review will focus on the genetic pathogenic and inflammation factors of Moyamoya disease.