Miracle-dz/UniFAR-FTUs huggingface dataset:
Attributes of carbapenemase encoding conjugative plasmid pNDM-SAL from an extensively drug-resistant Salmonella enterica Serovar Senftenberg

A carbapenem resistant Salmonella enterica serovar Senftenberg isolate BCH 2406 was isolated from a diarrheal child attending an outpatient unit of B.C. Roy Hospital in Kolkata, India. This isolate was positive for the blaNDM-1 in the PCR assay, which was confirmed by amplicon sequencing. Except for tetracycline, this isolate was resistant to all the tested antimicrobials. The blaNDM-1 was found to be located on a 146.13-kb mega plasmid pNDM-SAL, which could be conjugally transferred into Escherichia coli and other enteric pathogens such as Vibrio cholerae O1 Ogawa and Shigella flexneri 2a. However, the expression of β-lactam resistance is not the same in different bacteria. The whole genome sequence of pNDM-SAL was determined and compared with other pNDM plasmids available in public domain. This plasmid is an IncA/C incompatibility type composed of 155 predicted coding sequences and shares homology with plasmids of E. coli pNDM-1_Dok01, Klebsiella pNDM-KN, and Citrobacter pNDM-CIT. In pNDM-SAL, gene cluster containing blaNDM-1 was located between IS26 and IS4321 elements. Between the IS26 element and the blaNDM-1, a truncated ISAba125 insertion sequence was identified. Downstream of the blaNDM-1, other genes, such as bleMBL, trpF, tat, and an ISCR1 element with class 1 integron containing aac(6′)-Ib were detected. Another β-lactacamase gene, blaCMY -4 was found to be inserted in IS1 element within the type IV conjugative transfer loci of the plasmid. This gene cluster had blc and sugE downstream of the blaCMY -4. From our findings, it appears that the strain S. Senftenberg could have acquired the NDM plasmid from the other members of Enterobacteriaceae. Transfer of NDM plasmids poses a danger in the management of infectious diseases.
JMTP: an architecture for exploiting concurrency in embedded Java applications with real-time considerations

Using Java in embedded systems is plagued by problems of limited runtime performance and unpredictable runtime behavior. The Java Multi-Threaded Processor (JMTP) provides solutions to these problems. The JMTP architecture is a single chip containing an off-the-shelf general purpose processor core coupled with an array of Java Thread Processors (JTPs). Performance can be improved using this architecture by exploiting coarse-grained parallelism in the application. These performance improvements are achieved with relatively small hardware costs. Runtime predictability is improved by implementing a subset of the Java Virtual Machine (JVM) specification in the JTP and trimming away complexity without excessively restricting the Java code a JTP can handle. Moreover the JMTP architecture incorporates hardware to adaptively manage shared JMTP resources in order to satisfy JTP thread timing constraints or provide an early warning for a timing violation. This is an important feature for applications with quality-of-service demands. In addition to the hardware architecture, we describe a software framework that analyzes a Java application for expressed and implicit coarse-grained concurrent threads to execute on JTPs. This framework identifies the optimal mapping of an application to a JMTP with an arbitrary number of JTPs. We have tested this framework on a variety of applications including IDEA encryption with different JTP configurations and confirmed that the algorithm was able to obtain desired results in each case.
Cosmology with modified Newtonian dynamics (MOND)

It is well known that the application of Newtonian dynamics to an expanding spherical region leads to the correct relativistic expression (the Friedmann equation) for the evolution of the cosmic scalefactor. Here, the cosmological implications of Milgrom's modified Newtonian dynamics (MOND) are considered by means of a similar procedure. Earlier work by Felten demonstrated that in a region dominated by modified dynamics the expansion cannot be uniform (separations cannot be expressed in terms of a scalefactor) and that any such region will eventually recollapse regardless of the initial expansion velocity and mean density. Here I show that, because of the acceleration threshold for the MOND phenomenology, a region dominated by MOND will have a finite size which, in the earlier Universe (z>3), is smaller than the horizon scale. Therefore, uniform expansion and homogeneity on the horizon scale are consistent with MOND-dominated non-uniform expansion and the development of inhomogeneities on smaller scales. In the radiation-dominated era, the amplitude of MOND-induced inhomogeneities is much smaller than that implied by observations of the cosmic background radiation, and the thermal and dynamical history of the Universe is identical to that of the standard big bang model. In particular, the standard results for primordial nucleosynthesis are retained. When matter first dominates the energy density of the Universe, the cosmology diverges from that of the standard model. Objects of galaxy mass are the first virialized objects to form (by z = 10), and larger structure develops rapidly. At present, the Universe would be inhomogeneous out to a substantial fraction of the Hubble radius.
Identification and characterization of a symbiotic alga from soil bryophyte for lipid profiles

ABSTRACT A symbiotic alga was successfully isolated from the soil moss Entodon obtusatus found in the Guandi Mountains, Shanxi Province, China, and cultivated under axenic conditions. Morphological observations showed that the symbiotic alga was similar to Chlorococcum. Based on phylogenetic analysis of 18S rRNA and rbcL genes and internal transcribed spacer (ITS) regions, Chlorococcum sp. GD was identified as Chlorococcum sphacosum. The three data sets were congruent for those aspects of the topologies that were relatively robust, and differed for those parts of the topologies that were not. This strain was cultured in BG11 medium to test its growth and biodiesel properties. It produced a lipid content of nearly 40%, and achieved biomass concentration of 410 mg l−1 and lipid productivity of 6.76 mg l−1 day−1, with favorable C16:0 (23.10%) and C18:1 (21.62%) fatty acid content. This alga appears to have potential for use in biodiesel production. Summary: A symbiotic alga Chlorococcum sp. GD was successfully isolated from the soil moss and successfully cultivated under axenic conditions. It has nearly 40% lipid content, and thus appears to have potential for use in biodiesel production.
Deamination-Independent Inhibition of Hepatitis B Virus Reverse Transcription by APOBEC3G

ABSTRACT The APOBEC3 family of mammalian cytidine deaminases, including APOBEC3G (A3G), has been shown to function as innate antiviral factors against retroviruses and can also suppress the replication of the hepatitis B virus (HBV). The mechanism by which A3G inhibits HBV replication remains to be elucidated. In this study, we show that the inhibitory effect of APOBEC3 proteins on HBV replication was mainly at the DNA level, with only a minor effect on viral RNA packaging. The anti-HBV effect of A3G was independent of the DNA-editing function, and the mode of inhibition was not due to HBV DNA degradation. The editing-independent antiviral activity of A3G could target DNA-RNA hybrids as well as single-stranded DNA. Finally, we show that there was a preferential decrease in the accumulation of longer minus-strand DNA by A3G, compared to the shorter minus-strand DNA, and suggest that A3G exerts its inhibitory effect at very early stages during viral reverse transcription.
Spectral and spatial selectivity of luminance vision in reef fish

Luminance vision has high spatial resolution and is used for form vision and texture discrimination. In humans, birds and bees luminance channel is spectrally selective—it depends on the signals of the long-wavelength sensitive photoreceptors (bees) or on the sum of long- and middle-wavelength sensitive cones (humans), but not on the signal of the short-wavelength sensitive (blue) photoreceptors. The reasons of such selectivity are not fully understood. The aim of this study is to reveal the inputs of cone signals to high resolution luminance vision in reef fish. Sixteen freshly caught damselfish, Pomacentrus amboinensis, were trained to discriminate stimuli differing either in their color or in their fine patterns (stripes vs. cheques). Three colors (“bright green”, “dark green” and “blue”) were used to create two sets of color and two sets of pattern stimuli. The “bright green” and “dark green” were similar in their chromatic properties for fish, but differed in their lightness; the “dark green” differed from “blue” in the signal for the blue cone, but yielded similar signals in the long-wavelength and middle-wavelength cones. Fish easily learned to discriminate “bright green” from “dark green” and “dark green” from “blue” stimuli. Fish also could discriminate the fine patterns created from “dark green” and “bright green”. However, fish failed to discriminate fine patterns created from “blue” and “dark green” colors, i.e., the colors that provided contrast for the blue-sensitive photoreceptor, but not for the long-wavelength sensitive one. High resolution luminance vision in damselfish, Pomacentrus amboinensis, does not have input from the blue-sensitive cone, which may indicate that the spectral selectivity of luminance channel is a general feature of visual processing in both aquatic and terrestrial animals.
Efficient Probabilistic Diagnostics for Electrical Power Systems

We consider in this work the probabilistic approach to model-based diagnosis when applied to electrical power systems (EPSs). Our probabilistic approach is formally well-founded, as it based on Bayesian networks and arithmetic circuits. We investigate the diagnostic task known as fault isolation, and pay special attention to meeting two of the main challenges . model development and real-time reasoning . often associated with real-world application of model-based diagnosis technologies. To address the challenge of model development, we develop a systematic approach to representing electrical power systems as Bayesian networks, supported by an easy-to-use speci.cation language. To address the real-time reasoning challenge, we compile Bayesian networks into arithmetic circuits. Arithmetic circuit evaluation supports real-time diagnosis by being predictable and fast. In essence, we introduce a high-level EPS speci.cation language from which Bayesian networks that can diagnose multiple simultaneous failures are auto-generated, and we illustrate the feasibility of using arithmetic circuits, compiled from Bayesian networks, for real-time diagnosis on real-world EPSs of interest to NASA. The experimental system is a real-world EPS, namely the Advanced Diagnostic and Prognostic Testbed (ADAPT) located at the NASA Ames Research Center. In experiments with the ADAPT Bayesian network, which currently contains 503 discrete nodes and 579 edges, we . nd high diagnostic accuracy in scenarios where one to three faults, both in components and sensors, were inserted. The time taken to compute the most probable explanation using arithmetic circuits has a small mean of 0.2625 milliseconds and standard deviation of 0.2028 milliseconds. In experiments with data from ADAPT we also show that arithmetic circuit evaluation substantially outperforms joint tree propagation and variable elimination, two alternative algorithms for diagnosis using Bayesian network inference.
Assessment of essential fatty acids status in different blood components in Austrian adults

Epidemiologische und tierexperimentelle Studien belegen die schutzende und vorbeugende Wirkung von langkettigen n-3 PUFA in Hinblick auf die Senkung des Blutdrucks, sowie die Verringerung koronarer Herzkrankheit und Herzrhythmusstorungen. Des Weiteren gibt es Hinweise darauf, dass die erhohte Aufnahme mehrfach ungesattigter Fettsauren bei reduziertem n-6-Fettsaure- aber gelichzeitig gesteigertem n-3-Fettsaure-Anteil der Entwicklung einer Hypertonie vorbeugt (de Wilde et al.; 2003). Studien mit teils jedoch geringer Fallzahl, unterstreichen die Beziehung zwischen einer ungunstigen Fettsaure-Zusammensetzung von Membranen und neurologischen sowie psychischen Erkrankungen (Wiest et al.; 2009). Einige Studien zeigen einen deutlichen Zusammenhang zwischen der nutritiven Aufnahme von n-3 PUFAs und einigen psychischen Storungen wie Depressionen, Aufmerksamkeitsstorungen und Hyperaktivitat, Impulskontrollestorungen , darunter aggressives Verhalten, und Schizophrenie. Tierversuche verdeutlichen, dass ein Mangel an n-3 PUFA chemische Ablaufe, sowie die Entwicklung und Neurotransmission im Gehirn verandert. Populationen mit hohem Fischkonsum weisen zudem eine vergleichsweise niedrigere Rate von postpartalen Depression und Selbstmord auf. Bei erhohter Aufnahme an n-3-Fettsauren zeigt sich eine schnelle Verbesserung der Stimmung und eine Verringerung des impulsiven und aggressiven Verhaltens da die aufgenommenen Fettsauren rasch uber das Blut ins Gehirn transportiert werden (Conklin et al.; 2007). Basierend auf Dr. Harris, sollte daher der Erfassung des Omega-3-Index mit einer standardisierten Methode bzw. der Entwicklung eines solchen Tests sowie einer entsprechenden Qualitatskontrolle eine hohe Prioritat eingeraumt werden (Harriset al.; 2004).
Survival and DNA degradation in anhydrobiotic tardigrades

SUMMARY Anhydrobiosis is a highly stable state of suspended animation in an organism due to its desiccation, which is followed by recovery after rehydration. Changes occurring during drying could damage molecules, including DNA. Using the anhydrobiotic tardigrade Paramacrobiotus richtersi as a model organism, we have evaluated the effects of environmental factors, such as temperature and air humidity level (RH), on the survival of desiccated animals and on the degradation of their DNA. Tardigrades naturally desiccated in leaf litter and tardigrades experimentally desiccated on blotting paper were considered. Replicates were kept at 37°C and at different levels of RH for 21 days. RH values and temperature, as well as time of exposure to these environmental factors, have a negative effect on tardigrade survival and on the time required by animals to recover active life after desiccation. DNA damages (revealed as single strand breaks) occurred only in desiccated tardigrades kept for a long time at high RH values. These results indicate that during the anhydrobiotic state, damages take place and accumulate with time. Two hypotheses can be formulated to explain the results: (i) oxidative damages occur in desiccated specimens of P. richtersi, and (ii) high temperatures and high RH values change the state of the disaccharide trehalose, reducing its protective role.
Coinvasion of Dentinal Tubules byPorphyromonas gingivalis and Streptococcus gordonii Depends upon Binding Specificity of Streptococcal Antigen I/II Adhesin

ABSTRACT Cell wall-anchored polypeptides of the antigen I/II family are produced by many species of oral streptococci. These proteins mediate adhesion of streptococci to salivary glycoproteins and to other oral microorganisms and promote binding of cells to collagen type I and invasion of dentinal tubules. Since infections of the root canal system have a mixed anaerobic bacterial etiology, we investigated the hypothesis that coadhesion of anaerobic bacteria with streptococci may facilitate invasive endodontic disease. Porphyromonas gingivalis ATCC 33277 cells were able to invade dentinal tubules when cocultured with Streptococcus gordonii DL1 (Challis) but not when cocultured with Streptococcus mutans NG8. An isogenic noninvasive mutant of S. gordonii, with production of SspA and SspB (antigen I/II family) polypeptides abrogated, was deficient in binding to collagen and had a 40% reduced ability to support adhesion of P. gingivalis. Heterologous expression of the S. mutans SpaP (antigen I/II) protein in this mutant restored collagen binding and tubule invasion but not adhesion toP. gingivalis or the ability to promote P. gingivalis coinvasion of dentin. An isogenic afimbrial mutant ofP. gingivalis had 50% reduced binding to S. gordonii cells but was unaffected in the ability to coinvade dentinal tubules with S. gordonii wild-type cells. Expression of the S. gordonii SspA or SspB polypeptide on the surface of Lactococcus lactis cells endowed these bacteria with the abilities to bind P. gingivalis, penetrate dentinal tubules, and promote P. gingivaliscoinvasion of dentin. The results demonstrate that collagen-binding andP. gingivalis-binding properties of antigen I/II polypeptides are discrete functions. Specificity of antigen I/II polypeptide recognition accounts for the ability of P. gingivalis to coinvade dentinal tubules with S. gordonii but not with S. mutans. This provides evidence that the specificity of interbacterial coadhesion may influence directly the etiology of pulpal and periapical diseases.
Large-Scale Assessment of the Zebrafish Embryo as a Possible Predictive Model in Toxicity Testing

Background In the drug discovery pipeline, safety pharmacology is a major issue. The zebrafish has been proposed as a model that can bridge the gap in this field between cell assays (which are cost-effective, but low in data content) and rodent assays (which are high in data content, but less cost-efficient). However, zebrafish assays are only likely to be useful if they can be shown to have high predictive power. We examined this issue by assaying 60 water-soluble compounds representing a range of chemical classes and toxicological mechanisms. Methodology/Principal Findings Over 20,000 wild-type zebrafish embryos (including controls) were cultured individually in defined buffer in 96-well plates. Embryos were exposed for a 96 hour period starting at 24 hours post fertilization. A logarithmic concentration series was used for range-finding, followed by a narrower geometric series for LC50 determination. Zebrafish embryo LC50 (log mmol/L), and published data on rodent LD50 (log mmol/kg), were found to be strongly correlated (using Kendall's rank correlation tau and Pearson's product-moment correlation). The slope of the regression line for the full set of compounds was 0.73403. However, we found that the slope was strongly influenced by compound class. Thus, while most compounds had a similar toxicity level in both species, some compounds were markedly more toxic in zebrafish than in rodents, or vice versa. Conclusions For the substances examined here, in aggregate, the zebrafish embryo model has good predictivity for toxicity in rodents. However, the correlation between zebrafish and rodent toxicity varies considerably between individual compounds and compound class. We discuss the strengths and limitations of the zebrafish model in light of these findings.
Women and Spirit

The rules that guide the process of knowing in Western cultures are linked with the exclusion of certain realities. These rules of knowing shape what is known and are also linked with patriarchy, hierarchy, and oppression. Euro-American political, economic, and intellectual history forms a hegemony of interacting forces affecting the fabric of our lives and the nature and direction of our thoughts. This article, through the discussion of spirituality within psychology, explores the domination of certain ways of knowing and the necessity of including multiple epistemoloies and multiple experiences within feminist psychology.
Treatment satisfaction in cystic fibrosis: early patient experience with tobramycin inhalation powder

Background This study assessed treatment satisfaction of cystic fibrosis (CF) patients in a routine clinical setting for tobramycin inhalation powder (TIP), the first dry powder–inhaled antibiotic for Pseudomonas aeruginosa infection. Methods CF patients aged 6 years or older treated with at least one cycle of TIP completed a web survey on experience with TIP, including the Treatment Satisfaction Questionnaire for Medication (TSQM). Regression analysis determined the factors associated with TSQM global satisfaction. Results Eighty patients (mean age ± standard deviation: 24.4±9.4 years; 57.5% female; mean forced expiratory volume in 1 second ± standard deviation: 67.1%±27.3% predicted) completed the survey. The majority expressed satisfaction with TIP’s administration time (100%), time to clean (97.1%), portability (97.1%), and ease of use (94.3%). Effectiveness was significantly associated with TSQM global satisfaction (regression R-squared: 0.54). Conclusion Patient preferences for TIP were based on administration time and ease of use. Global satisfaction was related to greater patient-perceived effectiveness.
Hepatitis C (chronic).

INTRODUCTION 60-85% of people infected with hepatitis C virus will go on to develop chronic hepatitis C, which is now believed to affect 3% of the world's population. METHODS AND OUTCOMES We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of interventions in treatment-naïve people with chronic infection, but without liver decompensation? What are the effects of interventions in people with chronic infection, but without liver decompensation, who have not responded to interferon treatment? What are the effects of interventions in people with chronic infection, but without liver decompensation, who relapse after interferon treatment? What are the effects of interventions in people with chronic hepatitis C infection, who also have HIV? We searched: Medline, Embase, The Cochrane Library and other important databases up to May 2006 (Clinical Evidence reviews are updated periodically, please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). RESULTS We found 24 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. CONCLUSIONS In this systematic review we present information relating to the effectiveness and safety of the following interventions: interferon monotherapy, interferon alfa plus ribavirin, and peginterferon monotherapy or with ribavirin.
Are investigations anxiolytic or anxiogenic? A randomised controlled trial of neuroimaging to provide reassurance in chronic daily headache

Objectives: Aims were to investigate (a) whether neuroimaging in patients with chronic daily headache reassures patients or fails to reassure them and/or worsens outcome, impacting on service use, costs, health anxieties, and symptoms, and (b) whether this reassurance process occurs differentially in patients with different levels of psychological morbidity. Methods: Design: randomised controlled trial; setting: headache clinic in secondary care, South London; participants: 150 patients fulfilling criteria for chronic daily headache, stratified using the Hospital Anxiety and Depression Scale (HADS); intervention: treatment as usual or the offer of an MRI brain scan; main outcome measures: use of services, costs, and health anxiety. Results: Seventy six patients were randomised to the offer of a brain scan and 74 patients to treatment as usual. One hundred and thirty seven (91%) primary care case notes were examined at 1 year, 103 (69%) patients completed questionnaires at 3 months and 96 (64%) at 1 year. Sixty six (44%) patients were HADS positive (scored >11 on either subscale). Patients offered a scan were less worried about a serious cause of the headaches at 3 months (p = 0.004), but this was not maintained at 1 year; other health anxiety measures did not differ by scan status. However, at 1 year HADS positive patients offered a scan cost significantly less, by £465 (95% confidence interval (CI): −£1028 to −£104), than such patients not offered a scan, due to lower utilisation of medical resources. Conclusions: Neuroimaging significantly reduces costs for patients with high levels of psychiatric morbidity, possibly by changing subsequent referral patterns of the general practitioner.