Miracle-dz/UniFAR-FTUs huggingface dataset:
Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus

ABSTRACT Aliphatic hydrocarbons are highly appealing targets for advanced cellulosic biofuels, as they are already predominant components of petroleum-based gasoline and diesel fuels. We have studied alkene biosynthesis in Micrococcus luteus ATCC 4698, a close relative of Sarcina lutea (now Kocuria rhizophila), which 4 decades ago was reported to biosynthesize iso- and anteiso-branched, long-chain alkenes. The underlying biochemistry and genetics of alkene biosynthesis were not elucidated in those studies. We show here that heterologous expression of a three-gene cluster from M. luteus (Mlut_13230-13250) in a fatty acid-overproducing Escherichia coli strain resulted in production of long-chain alkenes, predominantly 27:3 and 29:3 (no. carbon atoms: no. C＝C bonds). Heterologous expression of Mlut_13230 (oleA) alone produced no long-chain alkenes but unsaturated aliphatic monoketones, predominantly 27:2, and in vitro studies with the purified Mlut_13230 protein and tetradecanoyl-coenzyme A (CoA) produced the same C27 monoketone. Gas chromatography-time of flight mass spectrometry confirmed the elemental composition of all detected long-chain alkenes and monoketones (putative intermediates of alkene biosynthesis). Negative controls demonstrated that the M. luteus genes were responsible for production of these metabolites. Studies with wild-type M. luteus showed that the transcript copy number of Mlut_13230-13250 and the concentrations of 29:1 alkene isomers (the dominant alkenes produced by this strain) generally corresponded with bacterial population over time. We propose a metabolic pathway for alkene biosynthesis starting with acyl-CoA (or-ACP [acyl carrier protein]) thioesters and involving decarboxylative Claisen condensation as a key step, which we believe is catalyzed by OleA. Such activity is consistent with our data and with the homology (including the conserved Cys-His-Asn catalytic triad) of Mlut_13230 (OleA) to FabH (β-ketoacyl-ACP synthase III), which catalyzes decarboxylative Claisen condensation during fatty acid biosynthesis.
Hacking in the public interest: Authority, legitimacy, means, and ends

The cultural appropriation of ideas about hacking and opening knowledge have had significant impact on ways of developing participation in creating public interest knowledge and knowledge commons. In particular, the ideal of hacking as developed through studies of free and open source (F/OS) has highlighted the value of processes of participation, including participatory governance, in relation to the value of expanded accessibility of knowledge, including knowledge commons. Yet, these means and ends are often conflated. This article employs three examples of projects where hacker-inspired perspectives on scientific knowledge conflict with institutional perspectives. Each example develops differently the relationships between means and ends in relation to authority and legitimacy. The article’s analysis suggests that while hacker culture’s focus on authority through participation has had great traction in business and in public interest science, this may come limit the contribution to knowledge in the public interest - especially knowledge commons.
Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions

ABSTRACT Understanding the mechanisms behind the typicity of regional wines inevitably brings attention to microorganisms associated with their production. Oenococcus oeni is the main bacterial species involved in wine and cider making. It develops after the yeast-driven alcoholic fermentation and performs the malolactic fermentation, which improves the taste and aromatic complexity of most wines. Here, we have evaluated the diversity and specificity of O. oeni strains in six regions. A total of 235 wines and ciders were collected during spontaneous malolactic fermentations and used to isolate 3,212 bacterial colonies. They were typed by multilocus variable analysis, which disclosed a total of 514 O. oeni strains. Their phylogenetic relationships were evaluated by a second typing method based on single nucleotide polymorphism (SNP) analysis. Taken together, the results indicate that each region holds a high diversity of strains that constitute a unique population. However, strains present in each region belong to diverse phylogenetic groups, and the same groups can be detected in different regions, indicating that strains are not genetically adapted to regions. In contrast, greater strain identity was seen for cider, white wine, or red wine of Burgundy, suggesting that genetic adaptation to these products occurred. IMPORTANCE This study reports the isolation, genotyping, and geographic distribution analysis of the largest collection of O. oeni strains performed to date. It reveals that there is very high diversity of strains in each region, the majority of them being detected in a single region. The study also reports the development of an SNP genotyping method that is useful for analyzing the distribution of O. oeni phylogroups. The results show that strains are not genetically adapted to regions but to specific types of wines. They reveal new phylogroups of strains, particularly two phylogroups associated with white wines and red wines of Burgundy. Taken together, the results shed light on the diversity and specificity of wild strains of O. oeni, which is crucial for understanding their real contribution to the unique properties of wines.
Clinical Competence and Self-confidence of New Graduate Nurses with an Integrated Nursing Curriculum of Simulation with Problem-Based Learning

The purpose of this study was to verify the effectiveness of an integrated nursing curriculum based on simulation with problem-based learning (PBL) by comparing the clinical competence and the self-confidence of newly graduated nurses. A non-equivalent control group post-test design was employed to compare the clinical competence and the self-confidence in the clinical performance examination using standardized patients between 39 newly graduated nurses with the traditional nursing curriculum and 35 with the integrated nursing curriculum. Data analysis involved Fisher's exact test, t-test, Pearson's correlation coefficient, and ANCOVA with the SPSS 19.0 program. The total clinical competence mean score graded by the standardized patients was not different between the two groups. However, the total clinical competence mean score graded by faculty was significantly higher in the integrated curriculum group than the traditional curriculum group. The mean self-confidence score was significantly higher in the integrated curriculum group than the traditional curriculum group. Active teaching-learning strategies including simulation or PBL in the nursing curriculum could benefit for nursing students by inducing favorable clinical competence and self-confidence. Longitudinal follow-up studies based on observation are needed to explore the patient outcomes in addition to the learner outcomes in clinical settings.
Renal Function and Blood Volume in Newborn Infant Related to Placental Transfusion

Inulin and PAH clearances, urine flow, filtration fraction, electrolyte excretion and blood volume studies were performed on 43 term vaginally delivered female normal infants during the first 12 hours of life and 26 during the 2nd to the 5th day of age. The umbilical cords of 22 infants were clamped within 5 seconds after birth and in 47 infants, the cords were clamped after their arterial pulsation had stopped.
Role of Ceftiofur in Selection and Dissemination of blaCMY-2-Mediated Cephalosporin Resistance in Salmonella enterica and Commensal Escherichia coli Isolates from Cattle

ABSTRACT Third-generation cephalosporin resistance of Salmonella and commensal Escherichia coli isolates from cattle in the United States is predominantly conferred by the cephamycinase CMY-2, which inactivates β-lactam antimicrobial drugs used to treat a wide variety of infections, including pediatric salmonellosis. The emergence and dissemination of blaCMY-2--bearing plasmids followed and may in part be the result of selection pressure imposed by the widespread utilization of ceftiofur, a third-generation veterinary cephalosporin. This study assessed the potential effects of ceftiofur on blaCMY-2 transfer and dissemination by (i) an in vivo experimental study in which calves were inoculated with competent blaCMY-2-bearing plasmid donors and susceptible recipients and then subjected to ceftiofur selection and (ii) an observational study to determine whether ceftiofur use in dairy herds is associated with the occurrence and frequency of cephalosporin resistance in Salmonella and commensal E. coli. The first study revealed blaCMY-2 plasmid transfer in both ceftiofur-treated and untreated calves but detected no enhancement of plasmid transfer associated with ceftiofur treatment. The second study detected no association (P = 0.22) between ceftiofur use and either the occurrence of ceftiofur-resistant salmonellosis or the frequency of cephalosporin resistance in commensal E. coli. However, herds with a history of salmonellosis (including both ceftiofur-resistant and ceftiofur-susceptible Salmonella isolates) used more ceftiofur than herds with no history of salmonellosis (P = 0.03) These findings fail to support a major role for ceftiofur use in the maintenance and dissemination of blaCMY-2-bearing plasmid mediated cephalosporin resistance in commensal E. coli and in pathogenic Salmonella in these dairy cattle populations.
Some Like It Hot: Evolution and Ecology of Novel Endosymbionts in Bat Flies of Cave-Roosting Bats (Hippoboscoidea, Nycterophiliinae)

ABSTRACT We investigated previously unknown associations between bacterial endosymbionts and bat flies of the subfamily Nycterophiliinae (Diptera, Streblidae). Molecular analyses revealed a novel clade of Gammaproteobacteria in Nycterophilia bat flies. This clade was not closely related to Arsenophonus-like microbes found in its sister genus Phalconomus and other bat flies. High population infection rates in Nycterophilia across a wide geographic area, the presence of the symbionts in pupae, the general codivergence between hosts and symbionts, and high AT composition bias in symbiont genes together suggest that this host-symbiont association is obligate in nature and ancient in origin. Some Nycterophilia samples (14.8%) also contained Wolbachia supergroup F (Alphaproteobacteria), suggesting a facultative symbiosis. Likelihood-based ancestral character mapping revealed that, initially, obligate symbionts exhibited association with host-specific Nycterophilia bat flies that use a broad temperature range of cave environments for pupal development. As this mutualism evolved, the temperature range of bat flies narrowed to an exclusive use of hot caves, which was followed by a secondary broadening of the bat flies' host associations. These results suggest that the symbiosis has influenced the environmental tolerance of parasite life history stages. Furthermore, the contingent change to an expanded host range of Nycterophilia bat flies upon narrowing the ecological niche of their developmental stages suggests that altered environmental tolerance across life history stages may be a crucial factor in shaping parasite-host relationships.
Measuring the degree of non-stationarity by using the Wigner-Ville spectrum

The Wigner-Ville spectrum is the only conjoint time-frequency representation of the second order properties of non-stationary random signals which is real-valued and compatible with linear filtering and modulation. Pseudo Wigner estimators are known to form a class of estimators being more flexible than short time periodograms: They give uncorrelated estimates for appropriately spaced neighboured frequencies allowing separately to measure the degree of non-stationarity for each band of frequencies. Using the model of quasi stationary processes, their stability and precision are defined as a measure of their character of non-stationarity. The performances are then tested on simulated data and successfully applied to the problem of classifying biological time-keeping facilties.
Improved hidden Markov modeling of phonemes for continuous speech recognition

This paper discusses the use of the Hidden Markov Model (HMM) in phonetic recognition. In particular, we present improvements that deal with the problems of modeling the effect of phonetic context and the problem of robust pdf estimation. The effect of phonetic context is taken into account by conditioning the probability density functions (pdfs) of the acoustic parameters on the adjacent phonemes, only to the extent that there are sufficient tokens of the phoneme in that context. This partial conditioning is achieved by combining the conditioned and unconditioned pdfs models with weights that depend on the confidence in each pdf estimate. This combination is shown to result in better performance than either model by itself. We also show that it is possible to obtain the computational advantages of using discrete probability densities without the usual requirement for large amounts of training data.
A new approach for accurate mass assignment on a multi-turn time-of-flight mass spectrometer

A simple, effective accurate mass assignment procedure for a time-of-flight mass spectrometer is desirable. External mass calibration using a mass calibration standard together with an internal mass reference (lock mass) is a common technique for mass assignment, however, using polynomial fitting can result in mass-dependent errors. By using the multi-turn time-of-flight mass spectrometer infiTOF-UHV, we were able to obtain multiple time-of-flight data from an ion monitored under several different numbers of laps that was then used to calculate a mass calibration equation. We have developed a data acquisition system that simultaneously monitors spectra at several different lap conditions with on-the-fly centroid determination and scan law estimation, which is a function of acceleration voltage, flight path, and instrumental time delay. Less than 0.9 mDa mass errors were observed for assigned mass to charge ratios (m/z) ranging between 4 and 134 using only 40Ar+ as a reference. It was also observed that estimating the scan law on-the-fly provides excellent mass drift compensation.
The Regulation of Plant Communities by the Food Chains Exploiting Them

In 1960, three ecologists at the University of Michigan proposed a "balance of nature" hypothesis: N. Hairston, F. Smith, and L. Slobodkin [1], hereafter denoted HSS. Basically, they argued that most plant material had some sort of grazer which potentially could reduce that part of the plant community to rarity or worse. Since this did not happen ("The world is green," they observed), they supposed that something was keeping these grazers in check. The something was probably a predator population. These arguments led the theorists to conclude that the predators, as a group, were limited in abundance by the amount of food they could find and capture; grazers as a group were predator limited, with their abundance held so low by predators that the plants they fed on, being free of too much grazer pressure, were, as a group, limited in abundance by the amount of resources (mostly water or nitrogen) they could find.
Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities

ABSTRACT Orange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange Beggiatoa (“Candidatus Maribeggiatoa”) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC–MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated.
Effects of enalapril or nifedipine on muscle strength or functional capacity in elderly subjects. A double blind trial

Introduction. The inhibition of angiotensin-converting enzyme could be useful to avoid sarcopenia in the elderly. Materials and methods. We compared in a prospective double blind trial, the effects of treatment with enalapril or nifedipine on muscle performance in hypertensive elderly subjects. Patients were followed for nine months, and at baseline, 4.5 months and the end of follow-up, quadriceps and hand grip muscle strength, walking capacity, timed up and go and the short physical performance test were measured. Results. During follow-up, more subjects on nifedipine than on enalapril discontinued the medication due to side-effects. No differences in the evolution of muscle strength, walking capacity or functional measures were observed. At nine months, plasma angiotensin-converting enzyme activity decreased by 6.0±2.5 U/L among patients on enalapril and increased by 8.5±4.2 U/L (p<0.001) among patients on nifedipine. Conclusion. In this group of elderly subjects, enalapril was not superior to nifedipine with regard to the age-related decline of muscle performance.
Polymorphisms of renin-angiotensin system genes as a risk factor for high-altitude pulmonary oedema

The genes of the renin—angiotensin system (RAS) play an important role in the regulation of pulmonary vascular tone. Although studies on individual genes polymorphisms have reported association with high-altitude pulmonary oedema (HAPE), studies on multiple genes or epistasis are lacking. We therefore investigated the association of the RAS polymorphisms with HAPE. In a case-control design, we screened 163 HAPE-resistant/controls (HAPE-r) and 160 HAPEpatients (HAPE-p) of Indian origin for eight polymorphisms of four RAS genes, ACE, AGT, AGTR1 and AGTR2. Significant difference in genotype and allele frequencies of the ACE I/D and AGT M235T polymorphisms was observed between HAPE-p and HAPE-r (p < 0.05). In three-locus haplotype analysis of AGT the haplotype GTM was significantly higher in HAPE-p (29%) and haplotype GTT in HAPE-r (27%) after Bonferroni correction (p < 0.006). The differences were insignificant for polymorphisms from AGTR1 and AGTR2. The MDR (multifactor dimensional reduction) approach for gene—gene interaction depicted individual polymorphism M235T as the best disease predicting model (cross validation consistency, CVC = 10/10). We found a significant association of D allele of ACE and M allele of AGT with HAPE. The findings are supported at the haplotypic level as well as through nested genetic interaction between the RAS gene polymorphisms using the MDR approach.
Iron Response Regulator Protein IrrB in Magnetospirillum gryphiswaldense MSR-1 Helps Control the Iron/Oxygen Balance, Oxidative Stress Tolerance, and Magnetosome Formation

ABSTRACT Magnetotactic bacteria are capable of forming nanosized, membrane-enclosed magnetosomes under iron-rich and oxygen-limited conditions. The complete genomic sequence of Magnetospirillum gryphiswaldense strain MSR-1 has been analyzed and found to contain five fur homologue genes whose protein products are predicted to be involved in iron homeostasis and the response to oxidative stress. Of these, only the MGMSRv2_3149 gene (irrB) was significantly downregulated under high-iron and low-oxygen conditions, during the transition of cell growth from the logarithmic to the stationary phase. The encoded protein, IrrB, containing the conserved HHH motif, was identified as an iron response regulator (Irr) protein belonging to the Fur superfamily. To investigate the function of IrrB, we constructed an irrB deletion mutant (ΔirrB). The levels of cell growth and magnetosome formation were lower in the ΔirrB strain than in the wild type (WT) under both high-iron and low-iron conditions. The ΔirrB strain also showed lower levels of iron uptake and H2O2 tolerance than the WT. Quantitative real-time reverse transcription-PCR analysis indicated that the irrB mutation reduced the expression of numerous genes involved in iron transport, iron storage, heme biosynthesis, and Fe-S cluster assembly. Transcription studies of the other fur homologue genes in the ΔirrB strain indicated complementary functions of the Fur proteins in MSR-1. IrrB appears to be directly responsible for iron metabolism and homeostasis and to be indirectly involved in magnetosome formation. We propose two IrrB-regulated networks (under high- and low-iron conditions) in MSR-1 cells that control the balance of iron and oxygen metabolism and account for the coexistence of five Fur homologues.
Stress of caring and nurses' beliefs in the stroke rehabilitation environment: a cross-sectional study

Background:Part of the multidisciplinary stroke unit team nurses report their role as complex and demanding. Aims:To explore stress of caring in nursing nurses'and its relationship with perception of the work environment and beliefs about stroke. Methods:This cross sectional study recruited a convenience sample of nursing staff from stroke units (n=44), 99% female; mean age 39 years (s.d. 9.6). The Stress of Caring Scale (SCS) and an adapted Illness Perception Questionnaire (IPQ-R: HP) were completed. The responses on the IPQ-R: HP were compared to stroke survivors (n=106) responses to the original IPQ-R completed in an earlier study. Results:Nurses' stress was positively correlated with perceptions of demand, strain and effort, and reward imbalance (P<.001) and negatively correlated with decisional control and helpfulness of support (P<05). Nurses believed stroke to incur greater symptoms, consequences, emotional impact, and a longer duration (P<.01) and that the patient's role and their treatment (P<. 05.