Miracle-dz/UniFAR-FTUs huggingface dataset:
Strains of Klebsiella Pneumoniae from Intensive Care Unit Producing CTX-M-15 Extended Spectrum Beta Lactamases

Problem statement: Resistance to third generation cephalosporins due to acquisition and expression of Extended Spectrum β-Lactamase (ESBL) among Gram-negative bacteria is on the increase. Infections involving extended spectrum beta lactamase bacteria are associated with significant morbidity and mortality. Therefore, infections due to ESBL isolates continue to pose a serious challenge to infection management worldwide. Since screening for ESBL is not a common practice in hospitals in Enugu state, this study was undertaken to characterize ESBL genes in K. pneumoniae strains from intensive care unit of the University of Nigeria Teaching Hospital (UNTH) Enugu. Approach: Over a period of 29 months, 57 patients out of 140 receiving treatment in the intensive care unit of the University of Nigeria Teaching Hospitals Enugu were found to be infected with extended-spectrum β-lactamase-producing strains of K. pneumoniae. Species identification of K. pneumoniae strains was performed by Standard Microbiology methods and re-confirmed by MALDI-TOF technology. Phenotypic characterization of Extended Spectrum Beta Lactamase (ESBL) was determined by double disc synergy test and presence of ESBL genes was determined by specific PCR. Results: All ESBL producers were positive in a PCR for blaCTX-M-1 cluster and on sequencing, blaCTXM-15 were found to be present. Genotypic characterization of extended spectrum beta-lactamase producing K. pneumoniae showed that all isolates carried CTX-M-15and SHV genes, 41(71.9%) carried aac (6’)-Ib-cr and blaOXA-1, 19(33%) carried blaTEM. ISEcp1 was found upstream and ORF 477 downstream of blaCTX-M. in all strains. Random amplified polymorphic DNA analysis grouped the strains into two clonal groups- A and B and majority of the strains belong to clonal group A (n = 42). Conclusion: This study shows for the first time the presence of ESBL genes in K. pneumoniae from the ICU of UNTH Enugu and therefore strongly butresses the need for regular screening for ESBL-producing bacteria in clinical specimen in ICU and other wards in Nigerian hospitals.
Evaluation of Amplicor PCR for direct detection of Mycobacterium tuberculosis from sputum specimens

We evaluated the Amplicor PCR assay (Roche Molecular Systems, Branchburg, N.J.) for direct detection of Mycobacterium tuberculosis in sputum. A total of 532 specimens from 270 patients were decontaminated and stored at 4 or -75 degrees C until assayed by PCR. This assay used three-step sample preparation, biotinylated primer pairs, AmpErase, and a microtiter format for amplicon capture and detection. Amplicor PCR results were compared with clinical history, culture from a Lowenstein-Jensen slant, and results from the BACTEC TB-460 system. Eighty-seven cultures from 15 patients grew M. tuberculosis; of these, 83 (95%) were positive with the Amplicor PCR test. The false negatives were most likely due to sample variation and inhibitors. Of the 445 specimens from which M. tuberculosis was not isolated, 428 (96%) were negative with the Amplicor PCR test. Of the 17 M. tuberculosis culture-negative, Amplicor-positive specimens, 15 were reclassified as true positives because previous cultures grew M. tuberculosis. Of the 445 specimens which did not grow M. tuberculosis, Mycobacterium spp. other than M. tuberculosis were isolated from 150 specimens. Three of these 150 specimens were Amplicor positive; two were from a patient with a history of tuberculosis, and one specimen gave a false-positive result. We do not feel that this represents cross-reactivity, because repeated Amplicor testing of the isolate gave negative results. The microtiter plate has 96 wells. Allowing for six controls, 90 decontaminated specimens can be tested by one technologist in 7.5 h. This PCR assay took 7.5 h to complete and is a sensitive and specific, rapid method for the direct detection of M. tuberculosis from sputum.
Stationary-Phase Regulation of RpoS Translation in Escherichia coli

ABSTRACT In enteric bacteria, adaptation to a number of different stresses is mediated by the RpoS protein, one of several sigma factors that collectively allow a tailored transcriptional response to environmental cues. Stress stimuli including low temperature, osmotic shock, nutrient limitation, and growth to stationary phase (SP) all result in a substantial increase in RpoS abundance and activity. The mechanism of regulation depends on the specific signal but may occur at the level of transcription, translation, protein activity, or targeted proteolysis. In both Escherichia coli and Salmonella enterica, SP induction of RpoS in rich medium is >30 fold and includes effects on both transcription and translation. Recently, we found that SP control of rpoS transcription in S. enterica involves repression of the major rpoS promoter during exponential phase by the global transcription factor Fis. Working primarily with E. coli, we now show that 24 nucleotides of the rpoS ribosome-binding site (RBS) are necessary and sufficient for a large part of the increase in rpoS translation as cells grow to SP. Genetic evidence points to an essential role for the leader nucleotides just upstream of the Shine-Dalgarno sequence but is conflicted on the question of whether sequence or structure is important. SP regulation of rpoS is conserved between E. coli and S. enterica. When combined with an fis mutation to block transcriptional effects, replacement of the rpoS RBS sequence by the lacZ RBS eliminates nearly all SP induction of RpoS.
A succinct rating scale for radiology report quality

Context: Poorly written radiology reports are common among residents and are a significant challenge for radiology education. While training may improve report quality, a professionally developed reliable and valid scale to measure report quality does not exist. Objectives: To develop a measurement tool for report quality, the quality of report scale, with rigorous validation through empirical data. Methods: A research team of an experienced psychometrician and six senior radiologists conducted qualitative and quantitative studies. Five items were identified for the quality of report scale, each measuring a distinct aspect of report quality. Two dedicated training sessions were designed and implemented to help residents generate high-quality reports. In a blinded fashion, the quality of report scale was applied to 804 randomly selected reports issued before (n = 403) and after (n = 401) training. Full-scale psychometrical assessments were implemented onto the quality of report scale’s item- and scale-scores from the reports. The quality of report scale scores were correlated with report professionalism and attendings’ preference and were compared pre-/post-training. Results: The quality of report scale showed sound psychometrical properties, with high validity and reliability. Reports with higher quality of report scale score were more professional and preferable by attendings. Training improved the quality of report scale score, empirically validating the quality of report scale further. Conclusion: While succinct and practitioner friendly, the quality of report scale is a reliable and valid measure of radiology report quality and has the potential to be easily adapted to other fields such as pathology, where similar training would be beneficial.
Quantitative Measures of Modic Changes in Lumbar Spine Magnetic Resonance Imaging: Intra- and Inter-rater Reliability

Study Design. A measurement reliability study. Objective. To develop quantitative measures for Modic changes (MCs) on magnetic resonance (MR) images and evaluate measurement reliability. Summary of Background Data. MCs have been studied for more than 20 years but the clinical significance remains controversial. Little effort has been made to improve the measurement of MCs. Methods. The study was approved by the responsible institutional review board. On the basis of Modic classification, a series of quantitative dimension and signal intensity measures were developed for assessing MCs. Midsagittal T1- and T2-weighted MR images from 83 lumbar spines were then qualitatively and quantitatively assessed by two observers independently. Kappa and intraclass correlation coefficient (ICC) were used to examine intra- and inter-rater reliability. Pearson correlation coefficient was used to assess the relationships between the quantitative measurements of MCs. Mean absolute deviation (MAD) and Bland-Altman plots also were used to evaluate measurement errors and limits of agreement for selected measures. Results. For Modic classification, intrarater agreement was excellent (&kgr; = 0.88) and inter-rater agreement was substantial (&kgr; = 0.79). Intrarater agreement also was excellent when obtaining dimension measurements (ICC = 0.82–0.96) from T1- or T2-weighted images and inter-rater agreement was slightly greater using T1-weighted images (ICC = 0.73–0.88) than T2-weighted images (ICC = 0.66–0.82). Signal intensity measurements on T2-weighted images were found to have almost perfect intra- and inter-rater reliability (ICC = 0.92–0.99). The correlation analysis demonstrated that the quantitative measures represent different constructs. The MAD and Bland-Altman Plots further confirmed the high reliability of the area ratio, MCs mean signal intensity and MCs total signal intensity measurements. Conclusion. Three quantitative measures are suggested to assess the severity of MCs, which provide reliable, precise measurements for research on the etiology, pathogenesis, and clinical relevance of MCs.
Oxygen gradients in tissue‐engineered Pegt/Pbt cartilaginous constructs: Measurement and modeling

The supply of oxygen within three‐dimensional tissue‐engineered (TE) cartilage polymer constructs is mainly by diffusion. Oxygen consumption by cells results in gradients in the oxygen concentration. The aims of this study were, firstly, to identify the gradients within TE cartilage polymer constructs and, secondly, to predict the profiles during in vitro culture. A glass microelectrode system was adapted and used to penetrate cartilage and TE cartilaginous constructs, yielding reproducible measurements with high spatial resolution. Cartilage polymer constructs were cultured for up to 41 days in vitro. Oxygen concentrations, as low as 2–5%, were measured within the center of these constructs. At the beginning of in vitro culture, the oxygen gradients were steeper in TE constructs in comparison to native tissue. Nevertheless, during the course of culture, oxygen concentrations approached the values measured in native tissue. A mathematical model was developed which yields oxygen profiles within cartilage explants and TE constructs. Model input parameters were assessed, including the diffusion coefficient of cartilage (2.2 × 10−9) + (0.4 × 10−9 m2 s−1), 70% of the diffusion coefficient of water and the diffusion coefficient of constructs (3.8 × 10−10 m2 s−1). The model confirmed that chondrocytes in polymer constructs cultured for 27 days have low oxygen requirements (0.8 × 10−19 mol m−3 s−1), even lower than chondrocytes in native cartilage. The ability to measure and predict local oxygen tensions offers new opportunities to obtain more insight in the relation between oxygen tension and chondrogenesis. © 2004 Wiley Periodicals, Inc.
Mitigate erroneous operations of 2T-2MTJ STT-MRAM based on dynamic voltage threshold

2T-2MTJ STT-MRAM suffers from the intrinsic stochastic switching behaviors of MTJ, “source degeneration” and leakage current problem of its access transistors, which could cause erroneous operations including write error and hold error. To mitigate those erroneous operations, Dynamic Voltage Threshold based High Voltage Threshold NMOS (HVTnDTMOS) is used as access transistors of 2T-2MTJ to increase writing current and reducing leakage current. Simulation results show that the optimized design reduces write error rate by about 13.3% and 0.062‰ reduction in hold error rate for each memory cell on the same condition of cell area and operating scheduling, compared with traditional 2T-2MTJ structure.
FINITE ELEMENT ANALYSIS OF STRESSSTIFFENING EFFECTS INCMUTS

We use finite element analysis (FEA) to model capacitive micromachined ultrasonic transducer (CMUT) cells where stress stiffening affects static deflection, pull-in voltage, resonance frequency, and small-signal sensitivity. Determining the small-signal sensitivity is challenging because it requires a prestressed harmonic response analysis in which the geometric nonlinearities are activated during the static analysis to prestress the structure. The goal is a correct static operation point calculation for CMUT plates that exceed a static deflection-to-thickness ratio of 20%. Assuming only a small AC excitation, we use a linear but updated stiffness matrix to calculate the harmonic response. We achieve this by using a prestressed mode superposition harmonic response analysis, which uses the sum of factored mode shapes obtained from a nonlinear prestressed modal analysis. We test our FEA for two CMUTs, of which one operates in a more membranedominated regime. Comparisons to measurements demonstrate that only the FEA that accounts for stress stiffening features good agreement for both designs. Our FEA allows us to model CMUTs that operate in a more membranedominated regime.
New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.)

Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy–Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles.
Vagal Fibers Form Associations With Interstitial Cells of Cajal During Fetal Development

Vagal intramuscular arrays (IMAs) have been shown to form complexes with intramuscular interstitial cells of Cajal (ICC). We tested the hypothesis that associations between vagal nerve endings and ICC arise in fetal development. Intraganglionic laminar endings (IGLEs) and IMAs were identified by applying 1,1’‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanineperchlorate (DiI) to vagal nerve trunks and myenteric plexus (MP) and intramuscular (IM) ICC were immunolabeled with antibodies to c‐Kit in fetal and early postnatal mice (E16‐P7). At E16, c‐Kit immunoreactive cells were abundant in the primordial smooth muscle, with early ICC networks discernable by E18 and ongoing organization at P1 and P7. The distribution of vagal endings was found to change during the course of development, with significantly more putative IGLEs in the prenatal compared to the postnatal period and less IMAs in the prenatal compared to postnatal period. Associations of ICC with both IGLEs and IMAs were detected as early as E16 and were maintained into postnatal life. These findings suggest that vagal fibers begin to associate with ICC during prenatal development. Future studies will be needed to determine the mechanisms through which vagal endings and ICC interact. Anat Rec, 298:1780–1785, 2015. © 2015 Wiley Periodicals, Inc.
Antidepressant-like deliverables from the sea: evidence on the efficacy of three different brown seaweeds via involvement of monoaminergic system

Brown seaweeds exhibit several health benefits in treating and managing wide array of ailments. In this study, the antidepressant-like effect of methaolic extracts from Sargassum swartzii (SS), Stoechospermum marginatum (SM), and Nizamuddinia zanardinii (NZ) was examined in forced swimming test (FST), in rats. Oral administration of SS, SM, and NZ extract (30–60 mg/kg) exhibited antidepressant-like activity in FST by reducing immobility time as compared to control group, without inducing significant change in ambulatory behavior in open field test. In order to evaluate the involvement of monoaminergic system, rats were pretreated with the inhibitor of brain serotonin stores p-chlorophenylalanin (PCPA), dopamine (SCH23390 and sulpiride), and adrenoceptor (prazosin and propranolol) antagonists. Rats receiving treatment for 28 days were decapitated and brains were analyzed for monoamine levels. It may be concluded that the extracts of SS, SM, and NZ produces antidepressant-like activity via modulation of brain monoaminergic system in a rat model. Antidepressant-like activities of selected brown seaweeds via modulation of monoaminergic system.
Prevention of NSAID-induced gastroduodenal ulcers.

BACKGROUND Non-steroidal anti-inflammatory drugs (NSAIDs) are important agents in the management of arthritic and inflammatory conditions, and are among the most frequently prescribed medications in North America and Europe. However, there is overwhelming evidence linking these agents to a variety of gastrointestinal (GI) toxicities. OBJECTIVES To review the effectiveness of common interventions for the prevention of NSAID induced upper GI toxicity. SEARCH STRATEGY A literature search was conducted, according to the Cochrane methodology for identification of randomized controlled trials in electronic databases, including MEDLINE from 1966 to January 2000, Current Contents for 6 months prior to January 2000, Embase to Febuary 1999, and a search of the Cochrane Controlled Trials Register from 1973 to 1999. Recent conference proceedings were reviewed and content experts and companies were contacted. SELECTION CRITERIA Randomized controlled clinical trials (RCTs) of prostaglandin analogues (PA), H2-receptor antagonists (H2RA) or proton pump inhibitors (PPI) for the prevention of chronic NSAID induced upper GI toxicity were included. DATA COLLECTION AND ANALYSIS Two independent reviewers extracted data regarding population characteristics, study design, methodological quality and number of patients with endoscopic ulcers, ulcer complications, symptoms, overall drop-outs, drop outs due to symptoms. Dichotomous data was pooled using Revman V3.1. Heterogeneity was evaluated using a chi square test. MAIN RESULTS Thirty-three RCTs met the inclusion criteria. All doses of misoprostol significantly reduced the risk of endoscopic ulcers. Misoprostol 800 ug/day was superior to 400 ug/day for the prevention of endoscopic gastric ulcers (RR=0.18, and RR=0.38 respectively, p=0.0055). A dose response relationship was not seen with duodenal ulcers. Misoprostol caused diarrhea at all doses, although significantly more at 800ug/day than 400ug/day (p=0.0012). Misoprostol was the only prophylactic agent documented to reduce ulcer complications. Standard doses of H2RAs were effective at reducing the risk of endoscopic duodenal (RR=0.24; 95% CI: 0.10-0.57) but not gastric ulcers(RR=0.73; 95% CI:0.50-1.09). Both double dose H2RAs and PPIs were effective at reducing the risk of endoscopic duodenal and gastric ulcers (RR=0.44; 95% CI:0.26-0.74 and RR=0.37;95% CI;0.27-0.51 respectively for gastric ulcer), and were better tolerated than misoprostol. REVIEWER'S CONCLUSIONS Misoprostol, PPIs, and double dose H2RAs are effective at preventing chronic NSAID related endoscopic gastric and duodenal ulcers. Lower doses of misoprostol are less effective and are still associated with diarrhea. Only Misoprostol 800ug/day has been directly shown to reduce the risk of ulcer complications.
Self-Organized Aggregation Triggers Collective Decision Making in a Group of Cockroach-Like Robots

Self-amplification processes are at the origin of several collective decision phenomena in insect societies. Understanding these processes requires linking individual behavioral rules of insects to a choice dynamics at the colony level. In a homogeneous environment, the German cockroach Blattella germanica displays self-amplified aggregation behavior. In a heterogeneous environment where several shelters are present, groups of cockroaches collectively select one of them. In this article, we demonstrate that the restriction of the self-amplified aggregation behavior to distinct zones in the environment can explain the emergence of a collective decision at the level of the group. This hypothesis is tested with robotics experiments and dedicated computer simulations. We show that the collective decision is influenced by the available spaces to explore and to aggregate in, by the size of the population involved in the aggregation process and by the probability of encounter zones while the robots explore the environment. We finally discuss these results from both a biological and a robotics point of view.
Entropy analysis of estimating systems

A study of the use of entropy as a criterion function for analyzing the performance of sampled-data estimating systems is presented, and performance bounds are obtained for a broad class of such systems. The general result is that the difference between the entropy of the signal to be estimated and the entropy of its estimate based on the output of a noisy sensor can never be larger than the mutual information between the sensor input and output. An interesting, but not totally satisfactory, sufficient condition for attainment of the bound is developed.
Dynamics of Circumstellar Disks

We present a series of two-dimensional hydrodynamic simulations of massive disks around protostars. We simulate the same physical problem using both a Piecewise Parabolic Method (PPM) code and a Smoothed Particle Hydrodynamic (SPH) code and analyze their differences. The disks studied here range in mass from 0.05M* to 1.0M* and in initial minimum Toomre Q value from 1.1 to 3.0. We adopt simple power laws for the initial density and temperature in the disk with an isothermal (γ = 1) equation of state. The disks are locally isothermal. We allow the central star to move freely in response to growing perturbations. The simulations using each code are compared to discover differences due to error in the methods used. For this problem, the strengths of the codes overlap only in a limited fashion, but similarities exist in their predictions, including spiral arm pattern speeds and morphological features. Our results represent limiting cases (i.e., systems evolved isothermally) rather than true physical systems. Disks become active from the inner regions outward. From the earliest times, their evolution is a strongly dynamic process rather than a smooth progression toward eventual nonlinear behavior. Processes that occur in both the extreme inner and outer radial regions affect the growth of instabilities over the entire disk. Effects important for the global morphology of the system can originate at quite small distances from the star. We calculate approximate growth rates for the spiral patterns; the one-armed (m = 1) spiral arm is not the fastest growing pattern of most disks. Nonetheless, it plays a significant role because of factors that can excite it more quickly than other patterns. A marked change in the character of spiral structure occurs with varying disk mass. Low-mass disks form filamentary spiral structures with many arms while high-mass disks form grand design spiral structures with few arms. In our SPH simulations, disks with initial minimum Q = 1.5 or lower break up into protobinary or protoplanetary clumps. However, these simulations cannot follow the physics important for the flow and must be terminated before the system has completely evolved. At their termination, PPM simulations with similar initial conditions show uneven mass distributions within spiral arms, suggesting that clumping behavior might result if they were carried further. Simulations of tori, for which SPH and PPM are directly comparable, do show clumping in both codes. Concerns that the pointlike nature of SPH exaggerates clumping, that our representation of the gravitational potential in PPM is too coarse, and that our physics assumptions are too simple suggest caution in interpretation of the clumping in both the disk and torus simulations.