LLukas22/scidocs huggingface dataset:
Relationship of biofilm formation and different virulence genes in uropathogenic Escherichia coli isolates from Northwest Iran

BACKGROUND AND OBJECTIVES
The Escherichia coli (E. coli) bacterium is one of the main causative agents of urinary tract infections (UTI) worldwide. The ability of this bacterium to form biofilms on medical devices such as catheters plays an important role in the development of UTI. The aim of the present study was to investigate the possible relationship between virulence factors and biofilm formation of E. coli isolates responsible for urinary tract infection.


MATERIALS AND METHODS
A total of 100 E. coli isolates isolated from patients with UTI were collected and characterized by routine bacteriological methods. In vitro biofilm formation by these isolates was determined using the 96-well microtiter-plate test, and the presence of fimA, papC, and hly virulence genes was examined by PCR assay. Data analysis was performed using SPSS 16.0 software.


RESULTS
From 100 E. coli isolates isolated from UTIs, 92% were shown to be biofilm positive. The genes papC, fimA, and hly were detected in 43%, 94% and 26% of isolates, respectively. Biofilm formation in isolates that expressed papC, fimA, and hly genes was 100%, 93%, and 100%, respectively. A significant relationship was found between presence of the papC gene and biofilm formation in E. coli isolates isolated from UTI (P<0.01), but there was no statistically significant correlation between presence of fimA and hly genes with biofilm formation (P<0.072, P<0.104).


CONCLUSION
RESULTS showed that fimA and hly genes do not seem to be necessary or sufficient for the production of biofilm in E. coli, but the presence of papC correlates with increased biofilm formation of urinary tract isolates. Overall, the presence of fimA, papC, and hly virulence genes coincides with in vitro biofilm formation in uropathogenic E. coli isolates.
Green Genes—Comparative Genomics of the Green Branch of Life

As more plant genome sequences become available, researchers are increasingly using comparative genomics to address some of the major questions in plant biology. Such questions include the evolution of photosynthesis and multicellularity, the developmental genetic changes responsible for alterations in body plan, and the origin of important plant innovations such as roots, leaves, and vascular tissue.
When and how to update systematic reviews.

BACKGROUND
Systematic reviews are most helpful if they are up-to-date. We did a systematic review of strategies and methods describing when and how to update systematic reviews.


OBJECTIVES
To identify, describe and assess strategies and methods addressing: 1) when to update systematic reviews and 2) how to update systematic reviews.


SEARCH STRATEGY
We searched MEDLINE (1966 to December 2005), PsycINFO, the Cochrane Methodology Register (Issue 1, 2006), and hand searched the 2005 Cochrane Colloquium proceedings.


SELECTION CRITERIA
We included methodology reports, updated systematic reviews, commentaries, editorials, or other short reports describing the development, use, or comparison of strategies and methods for determining the need for updating or updating systematic reviews in healthcare.


DATA COLLECTION AND ANALYSIS
We abstracted information from each included report using a 15-item questionnaire. The strategies and methods for updating systematic reviews were assessed and compared descriptively with respect to their usefulness, comprehensiveness, advantages, and disadvantages.


MAIN RESULTS
Four updating strategies, one technique, and two statistical methods were identified. Three strategies addressed steps for updating and one strategy presented a model for assessing the need to update. One technique discussed the use of the "entry date" field in bibliographic searching. Statistical methods were cumulative meta-analysis and predicting when meta-analyses are outdated.


AUTHORS' CONCLUSIONS
Little research has been conducted on when and how to update systematic reviews and the feasibility and efficiency of the identified approaches is uncertain. These shortcomings should be addressed in future research.
Spatial and temporal imaging of long-range charge transport in perovskite thin films by ultrafast microscopy.

Charge carrier diffusion coefficient and length are important physical parameters for semiconducting materials. Long-range carrier diffusion in perovskite thin films has led to remarkable solar cell efficiencies; however, spatial and temporal mechanisms of charge transport remain unclear. Here we present a direct measurement of carrier transport in space and in time by mapping carrier density with simultaneous ultrafast time resolution and ∼50-nm spatial precision in perovskite thin films using transient absorption microscopy. These results directly visualize long-range carrier transport of ∼220 nm in 2 ns for solution-processed polycrystalline CH3NH3PbI3 thin films. Variations of the carrier diffusion coefficient at the μm length scale have been observed with values ranging between 0.05 and 0.08 cm(2) s(-1). The spatially and temporally resolved measurements reported here underscore the importance of the local morphology and establish an important first step towards discerning the underlying transport properties of perovskite materials.
Clinical outcomes of cervical spinal cord injuries without radiographic evidence of trauma

We investigated 33 cervical spinal cord injury patients (25 males and eight females) without bony injury. Patients whose neurologic recovery had reached a plateau and who had evidence on imaging of persistent spinal cord compression were considered candidates for surgical decompression. When imaging did not show spinal cord compression or patients were maintaining a good neurologic recovery from the early days after injury, we pursued conservative treatment. Age at injury varied from 20 to 76 years (mean, 55.6). Average follow-up was 31 months. Twelve patients were treated conservatively (Group 1). Groups 2 and 3 had surgery. Group 2 (14 cases) had multi-level compression of spinal cord due to pre-existing cervical spine conditions such as ossification of posterior longitudinal ligament, cervical canal stenosis, and cervical spondylosis. Group 3 (7 cases) patients existed single-level compression of spinal cord by cervical disc herniations or spondylosis. We evaluated clinical results according to the Frankel classification, the American Spinal Injury Association (ASIA) scales and Japanese Orthopaedic Association (JOA) scores. Overall improvement of JOA and ASIA scores after treatment was 56.3±35.5% and 67.1±38.0%, respectively. Patients in Group 1 showed very good recovery after conservative treatment, with improvement of JOA and ASIA scores being 70.4±40.2% and 77.4±34.2%, respectively. The average interval between injury and operation was 4.3±4.4 months. The improvement of the surgically treated patients (Groups 2 and 3) in JOA and ASIA score was 48.2±30.7% and 61.2±39.6% respectively. We obtained good neurological recovery after operation, with significantly more improvement in Group 3 than in Group 2. No significant neurologic recovery had occurred preoperatively in these groups. In such patients operative intervention is essential for neurologic recovery.
Effects of Positive Psychology Interventions in Depressive Patients—A Randomized Control Study

Effects of Positive Psychology (PP) have been shown in several studies to alleviate depressive symptoms in patients suffering from major depression or dysthymia when administered within psychotherapy. The present study served to test for the effects of two interventions from PP (best possible self, three good things) when practised by depressive patients for three weeks without any other concomitant psychotherapy. Seventeen depressive patients were randomly assigned to either the PP group or the control group. Patients in the PP group wrote down the best possible self for one week and then three good things for another two weeks. Patients in the control group wrote down images of the future of mankind for one week and early memories for two weeks. Prior to the intervention and again after it had finished, depressive symptoms, satisfaction with life, positive and negative affect, optimism, and resilience were assessed. While in both groups of patients well-being and resilience increased and depressive symptoms declined, the decline of depressive symptoms and the increase of positive affect and resilience were more pronounced in the PP group. The results support the notion that even a short intervention using PP alone alleviates depressive symptoms and increases well-being. Although the effects were of marginal significance, this may be attributed to the relatively small sample size. Likewise, the use of an Intent-to-Treat analysis may have affected the PP group more than the control group, indicating an underestimation of the potency of PP in the present study.
Room-temperature Tamm-plasmon exciton-polaritons with a WSe2 monolayer

Solid-state cavity quantum electrodynamics is a rapidly advancing field, which explores the frontiers of light-matter coupling. Metal-based approaches are of particular interest in this field, as they carry the potential to squeeze optical modes to spaces significantly below the diffraction limit. Transition metal dichalcogenides are ideally suited as the active material in cavity quantum electrodynamics, as they interact strongly with light at the ultimate monolayer limit. Here, we implement a Tamm-plasmon-polariton structure and study the coupling to a monolayer of WSe2, hosting highly stable excitons. Exciton-polariton formation at room temperature is manifested in the characteristic energy-momentum dispersion relation studied in photoluminescence, featuring an anti-crossing between the exciton and photon modes with a Rabi-splitting of 23.5 meV. Creating polaritonic quasiparticles in monolithic, compact architectures with atomic monolayers under ambient conditions is a crucial step towards the exploration of nonlinearities, macroscopic coherence and advanced spinor physics with novel, low-mass bosons.
Effects of yoga practice on stress-related symptoms in the aftermath of an earthquake: A community-based controlled trial.

OBJECTIVES
To evaluate the effect of an integrated hatha yoga practice on perceived stress and stress-related symptoms in the aftermath of an earthquake.


DESIGN AND SETTING
Inhabitants, aged 20-67 years, from highly exposed earthquake areas of two villages in South Iceland were offered to participate in a yoga program subsequent to an earthquake. Sixty-six individuals were self-selected into the study and divided by residential convenience into an experimental group (n=31) and a waiting list control group (n=35).


INTERVENTION
The yoga program was conducted twice a week for six weeks, in normal situations among the inhabitants in the community.


MAIN OUTCOME MEASURES
Several validated questionnaires assessing stress and stress-related symptoms, posttraumatic symptoms, depression, anxiety and health related quality of life were administered at pre- and post-intervention.


RESULTS
Multivariate analysis of variance (MANOVA) revealed differences between the experimental group and waiting list control group on sleep quality (p=.03) and social relations (p=.04). These differences did not prevail at Bonferroni correction for multiple testing (at alpha level of .005). Participants in both groups showed significant improvements in stress and some stress-related symptoms such as sleep, concentration, well-being, quality of life, depression and anxiety from pre- to post-intervention.


CONCLUSIONS
The data from this small study show no statistically significant improvement of an integrated hatha yoga program above and beyond waiting list control, following exposure to an earthquake. However, the observed trend toward improved sleep quality and social relations deserve further exploration in larger effectiveness studies on the impact of Hatha yoga on recovery after natural disaster.
Accuracy of Billing Codes Used in the Therapeutic Care of Diabetic Retinopathy.

Importance
Insurance billing claim databases represent a growing field of scientific inquiry within ophthalmology. Validating the accuracy of billing claim codes used during the care of diabetic retinopathy is a necessary precursor to fully understanding the underlying data and subsequent results of these types of studies.


Objective
To determine the accuracy of diagnostic, procedural, and therapeutic billing codes used in the treatment of diabetic retinopathy.


Design, Setting, and Participants
This retrospective medical record review was conducted at 3 clinical practices (1 academic and 2 private). Insured patients with diabetic retinopathy were seen by the practices between 2011 and 2013. Each patient then had every visit for 2 years reviewed twice, once for billing data and the second for data from the medical record. Data were collected and analyzed from October 2015 to July 2016.


Main Outcomes and Measures
The positive predictive value (PPV) and negative predictive value (NPV) for each code of interest. Sensitivity and specificity were secondary outcomes.


Results
A total of 146 patients (mean [SD] age, 60.3 [12.5] years) from 11 physicians had 1072 encounters reviewed over 2 calendar years. Among the included patients, 49.3% were female (n = 72), 48.6% were white (n = 71), 37.0% were black (n = 54), and 18.5% had type 1 diabetes and a mean (SD) hemoglobin A1C level of 7.7% (1.8) (n = 27). Nearly all codes of interest that were used frequently also had a high PPV (range, 89.5%-100%) and NPV (88.6%-100%) including billing codes for intravitreal injection, focal laser, panretinal photocoagulation, laterality of procedure, ranibizumab, bevacizumab, fundus photographs, fluorescein angiography, and optical coherence tomography. Codes that were used infrequently (<20 instances) but still had a high PPV (all 100%) and NPV (99.7%-100%) were codes for aflibercept, triamcinolone, and the dexamethasone implant. Only the codes for infrequently used B-scan ultrasonography (PPV, 69.6%) and subtenon injection (PPV, 100%; NPV, 99.7%, but sensitivity of only 40%) were found to be of questionable accuracy. Other than subtenon injection (40%), all codes were also found to have a high sensitivity (range, 87.6%-100%) and a high specificity (range, 97.2%-100%).


Conclusions and Relevance
These data suggest diagnostic, procedure, and therapeutic codes derived from insurance billing claims accurately reflect the medical record for patients with diabetic retinopathy.
[General practitioner and mental diseases among children and adolescents].

BACKGROUND
Child and adolescent psychiatry in primary health care is scarcely investigated. The purpose of this article is to describe some aspects of the role of the general practitioner in the care of young patients with psychiatric problems.


MATERIAL AND METHODS
Data were collected from four focus group interviews with 19 general practitioners. The material was analysed in a phenomenological perspective. The aim was to develop new and documented descriptions seen from the participants' point of view, interpreted within the framework of available knowledge about care for children and adolescents with psychiatric problems.


RESULTS AND INTERPRETATION
The general practitioner is in a good position to provide psychiatric care for these patients because of his or her unique knowledge about the families and the local communities. They have their patients' confidence and acquired skills from their unselected practice to recognise serious and abnormal conditions. The majority of the informants did not feel sufficiently skilled in order to treat more specific child and adolescent psychiatric disorders. Some informants were actively involved in multidisciplinary networks concerning their young patients, while others were neither involved nor informed about it. In addition, local health and welfare services to a lesser extent involved these doctors. Because of this, children and adolescents who might have been assessed and treated in primary health care could be referred directly to specialists. A need for guidance and updating on relevant knowledge from the specialist health care was expressed. From the results we might assume that specialists might give some general practitioners the professional security needed in order to take on the role of medical co-coordinator of the multidisciplinary services to young patients with mental health problems.
Inhibition of CYP3A by erythromycin: in vitro-in vivo correlation in rats.

The prediction of in vivo drug-drug interactions from in vitro enzyme inhibition parameters remains challenging, particularly when time-dependent inhibition occurs. This study was designed to examine the accuracy of in vitro-derived parameters for the prediction of inhibition of CYP3A by erythromycin (ERY). Chronically cannulated rats were used to estimate the reduction in in vivo and in vitro intrinsic clearance (CL(int)) of midazolam (MDZ) after single and multiple doses of ERY; in vitro recovery of CL(int) was determined at 1, 2, 3, and 4 days after discontinuation of ERY. Enzyme inhibition parameters (k(inact), K(I), and K(i)) of ERY were estimated in vitro by using untreated rat liver microsomes. In vivo enzyme kinetic analysis indicated that single and multiple doses of ERY (150 mg/kg i.v. infusion over 4 h) reduced MDZ CL(int) by reversible and irreversible mechanisms, respectively. CYP3A inactivation after multiple doses of ERY treatment reflected metabolic intermediate complex formation without a significant change in hepatic CYP3A2 mRNA. A physiologically based pharmacokinetic model of the interaction between ERY and MDZ predicted a 2.6-fold decrease in CYP3A activity after repeated ERY treatment using in vitro-estimated enzyme inhibition parameters and in vivo degradation half-life of the enzyme (20 + or - 6 h). The observed -fold decreases were 2.3-fold and 2.1-fold for the in vitro-estimated CYP3A activity and the in vivo CL(int), respectively. This study demonstrates that in vivo DDIs are predictable from in vitro data when the appropriate model and parameter estimates are available.
Early and midterm outcome after off-pump and on-pump surgery in Beating Heart Against Cardioplegic Arrest Studies (BHACAS 1 and 2): a pooled analysis of two randomised controlled trials

BACKGROUND
Although no randomised controlled trial has assessed the midterm effects of coronary-artery bypass surgery on the beating heart, this technique is being used in more and more patients. We did two randomised trials to compare the short-term morbidity associated with off-pump and on-pump myocardial revascularisation. Our aim was to pool the results to assess midterm outcomes.


METHODS
From March, 1997, to November, 1999, we randomly allocated 200 patients to off-pump and 201 to on-pump coronary surgery. In Beating Heart Against Cardioplegic Arrest Study (BHACAS) 1, we excluded patients who had had myocardial infarction in the past month or who required grafting of the circumflex artery distal to the first obtuse marginal branch. In BHACAS 2, we included such patients. Primary outcomes were all-cause mortality and cardiac-related events at midterm follow-up (1-3 years). Analysis was by intention to treat.


FINDINGS
Analyses of combined data from both trials showed the following risk differences with off-pump compared with on-pump surgery: atrial fibrillation -25% (95% CI -33% to -16%); chest infection -12% (-19% to -5%); inotropic requirement -18% (-25% to -10%); transfusion of red blood cells -31% (-41 to -21); and hospital stay longer than 7 days -13% (-21 to -5). Mean follow-up was 25 0 months (SD 9.1) for BHACAS 1 and 13.7 months (5 5) for BHACAS 2. Four (2%) of 200 patients in the off-pump groups died from any cause, compared with seven (3%) of 201 in the on-pump group (hazard ratio 0.57, 95% CI 0.17-1.96). 33 (17%) of 200 patients in the off-pump group died or had a cardiac-related event, compared with 42 (21%) of 201 in the on-pump group (0.78, 0 49-1.22).


INTERPRETATION
Off-pump coronary surgery significantly lowers in-hospital morbidity without compromising outcome in the first 1-3 years after surgery compared with conventional on-pump coronary surgery.
Validation of a B-type natriuretic peptide as a prognostic marker in pneumonia patients: a prospective cohort study.

OBJECTIVES
To validate a B-type natriuretic peptide (BNP) as a prognostic marker in pneumonia patients.


DESIGN
A prospective cohort study.


SETTING
Kanazawa Medical University Himi Municipal (a 250-bed community hospital in Himi-shi, Toyama-ken, Japan).


PARTICIPANTS
All patients diagnosed with pneumonia by the physician and admitted to our hospital between 1 January 2012 and 31 March 2015 whose BNP levels had been determined in the first 24 h of admission. A total of 673 patients were enrolled. Of these, BNP levels were measured for a total of 369 patients on admission.


INTERVENTION
After enrolment, baseline, demographic, clinical and laboratory characteristics including levels of suspected prognostic markers for pneumonia proposed in previous papers, were collected. All patients were followed up until discharge. During analysis, they were divided into categories as follows: community-acquired pneumonia (CAP), aspiration pneumonia (AP), healthcare-associated pneumonia (HCAP) and pneumonia with acute heart failure (PAHF). A univariate and multivariable Cox-regression analysis were applied to each parameter to identify predictors of death. Three cut-off points, namely 40, 100 and 200 pg/mL, as well as the mean, were applied when comparing BNP levels.


MAIN OUTCOME MEASURES
30-day mortality.


RESULTS
Of the 369 patients finally included, 137 were diagnosed with CAP, 122 with AP, 74 with HCAP, and 36 with PAHF. In the univariate analysis, BNP levels (mean, cut-off points 100 pg/mL and 200 pg/mL, p<0.01, respectively) were associated with death in CAP, and similar situation was found for BNP (cut-off points 200 pg/mL, p<0.05) in AP, but not for HCAP, or PAHF. In multivariable Cox-regression analysis, BNP remained an independent mortality predictor (HR 10.01, 95% CI 1.32 to 75.7, p=0.03) in CAP.


CONCLUSIONS
BNP levels may be a useful single prognostic marker for CAP. Further research for validation is warranted.
Asymptotically optimal quantum circuits for d-level systems.

Scalability of a quantum computation requires that the information be processed on multiple subsystems. However, it is unclear how the complexity of a quantum algorithm, quantified by the number of entangling gates, depends on the subsystem size. We examine the quantum circuit complexity for exactly universal computation on many d-level systems (qudits). Both a lower bound and a constructive upper bound on the number of two-qudit gates result, proving a sharp asymptotic of theta(d(2n)) gates. This closes the complexity question for all d-level systems (d finite). The optimal asymptotic applies to systems with locality constraints, e.g., nearest neighbor interactions.
The role of the engineering library

The timely article on “The role of the engineering library,” by Harrison W. Craver, published in the July issue of Electrical Engineering (pages 291–4) is interesting and challenging to both educators and engineers in industry.
Classifying heart sounds using peak location for segmentation and feature construction

In this paper we describe our methodology and results for the Classifying Heart Sounds PASCAL Challenge. We present our algoritm and results for segmentation and classification of S1 and S2 heart sounds.