Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungal and Bacterial Diversity Isolated from Aquilaria malaccensis Tree and Soil, Induces Agarospirol Formation within 3 Months after Artificial Infection

Aquilaria malaccensis Lam, commonly known as Agarwood, is a highly valuable species used in production of agar oil from its infected wood, which is utilized in pharmaceutical and perfumery industry. Agar oil formation in agarwood takes years through the natural process which is induced by natural or artificial injury or microbial infection. The role of soil fungi and bacteria in artificial induction is still an unexplored area. In the present study, we isolated the fungal and bacterial community residing inside the stem of A. malaccensis tree and circumventing soil, samples collected from 21 different sites of the north-eastern state Assam of India and explored their potential in induction of Agarospirol (2-(6,10-Dimethylspiro[4,5]dec-6-en-2-yl)-2-propanol) production by artificially infecting the trees with these microorganisms. A total 340 fungi and 131 bacteria were isolated from 50 stem samples, and 188 fungi and 148 bacteria were isolated from 50 soil samples. Highest Shannon (H′ = 2.43) and Fisher (α = 5.57) diversity index was observed in the stem isolates. The dominant fungal genus was Trichoderma in stem with Pi value of 0.18; while in soil, Aspergillus showed dominance with Pi value 0.73. In bacteria, Bacillus genera showed dominance in both stem and soil samples with Pi = 0.62 and 0.51, respectively. Forty fungal and bacterial isolates were used to assess their potential to induce formation of agarwood in A. malaccensis by artificial infection method. Gas chromatography mass spectroscopy (GC-MS) analysis confirmed development of Agarwood by the presence of Agarospirol compound in samples collected after 3 months of the artificial infection. Only 31% of bacterial and 23% of fungal isolates showed their ability in production of Agarospirol by artificial infection method. Bacteria Pantoea dispersa and fungi Penicillium polonicum showed the highest production in comparison to other isolates.
The importance of drought–pathogen interactions in driving oak mortality events in the Ozark Border Region

Forests are expected to become more vulnerable to drought-induced tree mortality owing to rising temperatures and changing precipitation patterns that amplify drought lethality. There is a crucial knowledge gap regarding drought–pathogen interactions and their effects on tree mortality. The objectives of this research were to examine whether stand dynamics and ‘background’ mortality rates were affected by a severe drought in 2012; and to evaluate the importance of drought–pathogen interactions within the context of a mortality event that killed 10.0% and 26.5% of white (Quercus alba L.) and black (Q. velutina Lam.) oak stems, respectively, in a single year. We synthesized (i) forest inventory data (24 years), (ii) 11 years of ecosystem flux data with supporting biological data including predawn leaf water potential and annual forest inventories, (iii) tree-ring analyses of individual white oaks that were alive and ones that died in 2013, and (iv) documentation of a pathogen infection. This forest displayed stand dynamics consistent with expected patterns of decreasing tree density and increasing basal area. Continued basal area growth outpaced mortality implying a net accumulation of live biomass, which was supported by eddy covariance ecosystem carbon flux observations. Individual white and black oaks that died in 2013 displayed historically lower growth with the majority of dead trees exhibiting Biscogniauxia cankers. Our observations point to the importance of event-based oak mortality and that drought–Biscogniauxia interactions are important in shaping oak stand dynamics in this region. Although forest function has not been significantly impaired, these drought–pathogen interactions could amplify mortality under future climate conditions and thus warrant further investigation.
Effect of Lumbar Disc Degeneration and Low-Back Pain on the Lumbar Lordosis in Supine and Standing: A Cross-Sectional MRI Study

Study Design. Cross-sectional study. Objective. To examine the influence of low-back pain (LBP) and lumbar disc degeneration (LDD) on the lumbar lordosis in weight-bearing positional magnetic resonance imaging (pMRI). Summary of Background Data. The lumbar lordosis increases with a change of position from supine to standing and is known as an essential contributor to dynamic changes. However, the lordosis may be affected by disc degeneration and pain. Methods. Patients with LBP >40 on a 0 to 100 mm Visual Analog Scale (VAS) both during activity and rest and a sex and age-decade matching control group without LBP were scanned in the supine and standing position in a 0.25-T open MRI unit. LDD was graded using Pfirrmann's grading-scale. Subsequently, the L2-to-S1 lumbar lordosis angle (LA) was measured. Results. Thirty-eight patients with an average VAS of 58 (±13.8) mm during rest and 75 (±5.0) mm during activities, and 38 healthy controls were included. MRI findings were common in both groups, whereas, the summation of the Pfirrmann's grades (LDD-score) was significantly higher in the patients [(MD 1.44; 95% confidence intervals (CI) 0.80 to 2.10; P < 0.001]. The patients were less lordotic than the controls in both the supine (MD −6.4°; 95% CI −11.4 to −1.3), and standing position (MD −5.6°; 95% CI −10.7 to −0.7); however, the changes between the positions (&Dgr;LA) were the same (MD 0.8°; 95% CI −1.8 to 3.3). Using generalized linear model the LDD-score was associated with age (P < 0.001) for both groups. The LDD-score and &Dgr;LA were negatively associated in the control group (P < 0.001), also after adjustments for gender and age (&bgr;-coefficient: −2.66; 95% CI −4.3 to −1.0; P = 0.002). Conclusion. Patients may be less lordotic in both the supine and standing position, whereas, change in the lordosis between the positions may be independent of pain. Decreasing lordosis change seems to be associated with age-related increasing disc degeneration in healthy individuals. Level of Evidence: 2
Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic

Staphylococcus aureus USA300 represents the dominant community-associated methicillin-resistant S. aureus lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical S. aureus isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program. Isolates were collected at 12 healthcare centres across nine USA states in 2004, 2009 or 2010. Reconstruction of evolutionary relationships revealed that CC8 was dominated by USA300 isolates (154/191, 81 %), which were heterogeneous and demonstrated limited phylogeographic clustering. Analysis of the USA300 core genomes revealed an increase in median pairwise SNP distance from 62 to 98 between 2004 and 2010, with a stable pattern of above average dN/dS ratios. The phylogeny of the USA300 population indicated that early diversification events led to the formation of nested clades, which arose through cumulative acquisition of predominantly non-synonymous SNPs in various coding sequences. The accessory genome of USA300 was largely homogenous and consisted of elements previously associated with this lineage. We observed an emergence of SCCmec negative and ACME negative USA300 isolates amongst more recent samples, and an increase in the prevalence of ϕSa5 prophage. Together, the analysed S. aureus USA300 collection revealed an evolving pan-genome through increased core genome heterogeneity and temporal variation in the frequency of certain accessory elements.
Two Variable vs. Linear Temporal Logic in Model Checking and Games

Verification tasks have non-elementary complexity for properties of linear traces specified in first-order logic, and thus various limited logical languages are employed. In this paper we consider two restricted specification logics, linear temporal logic (LTL) and two-variable first-order logic (FO2). LTL is more expressive, but FO2 is often more succinct, and hence it is not clear which should be easier to verify. In this paper we take a comprehensive look at the issue, giving a comparison of verification problems for FO2, LTL, and the subset of LTL expressively equivalent to FO2, unary temporal logic (UTL). We give two logic-to-automata translations which can be used to give upper bounds for FO2 and UTL; we apply these to get new bounds for both nondeterministic systems (hierarchical and recursive state machines, games) and for probabilistic systems (Markov chains, recursive Markov chains, and Markov decision processes). We couple this with lower-bound arguments for FO2 and UTL. Our results give both a unified approach to understanding the behavior of FO2 and UTL, along with a nearly comprehensive picture of the complexity of verification for these logics.
Variation in fistula use across dialysis facilities: is it explained by case-mix?

BACKGROUND AND OBJECTIVES Arteriovenous fistulas (AVFs) remain the preferred vascular access for hemodialysis patients. Dialysis facilities that fail to meet Centers for Medicare & Medicaid Services goals cite patient case-mix as a reason for low AVF prevalence. This study aimed to determine the magnitude of the variability in AVF usage across dialysis facilities and the extent to which patient case-mix explains it. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS The vascular access used in 10,112 patients dialyzed at 173 Dialysis Clinic Inc. facilities from October 1 to December 31, 2004, was evaluated. The access in use was considered to be an AVF if it was used for >70% of hemodialysis treatments. Mixed-effects models with a random intercept for dialysis facilities evaluated the effect of facilities on AVF usage. Sequentially adjusted multivariate models measured the extent to which patient factors (case-mix) explain variation across facilities in AVF rates. RESULTS 3787 patients (38%) were dialyzed using AVFs. There was a significant facility effect: 7.6% of variation in AVF use was attributable to facility. This was reduced to 7.1% after case-mix adjustment. There were no identified specific facility-level factors that explained the interfacility variation. CONCLUSIONS AVF usage varies across dialysis facilities, and patient case-mix did not reduce this variation. In this study, 92% of the total variation in AVF usage was due to patient factors, but most were not measurable. A combination of patient factors and process indicators should be considered in adjudicating facility performance for this quality indicator.
Changes in the EEG during castration in horses and ponies anaesthetized with halothane.

OBJECTIVE To identify changes in the amplitude spectrum of the electroencephalogram (EEG) during a standardized surgical model of nociception in horses. ANIMALS Thirteen entire male horses and ponies referred to Division of Clinical Veterinary Science, Bristol (n = 9) and Department of Clinical Veterinary Medicine (n = 4) for castration. MATERIALS AND METHODS Following pre-anaesthetic medication with acepromazine, anaesthesia was induced with guaiphenesin and thiopental and maintained with halothane in oxygen. The EEG was recorded continuously using subcutaneous needle electrodes. Additional monitoring comprised ECG, arterial blood pressure, blood gas analysis, airway gases, and body temperature. All animals were castrated using a closed technique. The raw EEG was analysed after completion of each investigation and the EEG variables median frequency (F50), spectral edge frequency (SEF) 95% and total amplitude were derived from the spectra using standard techniques. The mean values of EEG variables recorded during a baseline time period (recorded before the start of surgery) and castration of each testicle were compared using analysis of variance for repeated measures. RESULTS Total amplitude (Atot) decreased and F50 increased during castration of each testicle compared to the baseline time period [(89.0 +/- 7.8% testicle 1, 87.0 +/- 7.8% testicle 2) and (110.0 +/- 15.0% testicle 1, 109.0 +/- 15.0% testicle 2), respectively]. Changes in SEF 95% were not significant. CONCLUSIONS De-synchronization was identified in the EEG during the nociceptive stimulus of castration. The results suggest that an increase in F50 may be a specific marker for nociception in the horse. CLINICAL RELEVANCE Studies investigating the efficacy of analgesic agents in horses are limited by difficulties in peri-operative pain assessment. This model, using EEG changes associated with nociceptive stimulation, can be used to investigate the anti-nociceptive efficacy of different anaesthetic agents in the horse.
Comparing implicit and synaesthetic number-space associations: visuospatial and verbal SNARC effects

In Dehaene’s (1992) theory of the mental number line, number and space are implicitly associated, giving rise to the spatial-numerical association of response codes (SNARC) effect, in which smaller numbers are more readily associated with the left side of space, larger numbers with the right, during a parity judgement task. Others, however, have argued that the SNARC effect is flexible (e.g. Bachtold, Baumuller, & Brugger, 1998) and better explained by verbal rather than spatial associations (Proctor & Cho, 2006). A few single-case studies on the SNARC effect have tested number-space synaesthetes, who make explicit associations between number and space. Here, we present data from experiments conducted on groups of synaesthetes and non-synaesthetes on the classic SNARC parity judgement task with lateralised response keys and a modified version in which they responded to labels appearing on-screen (Gevers et al., 2010). Synaesthetes’ behaviour was expected to differ from non-synaesthetes’ due to the explicit, fixed nature of their number-space associations, but both experiments show the two groups behaving in the same way, indicating that parity judgement tasks may not be tapping the same representation of number that gives rise to synaesthetic number-space experiences.
High developmental competence of cattle oocytes maintained at the germinal vesicle stage for 24 hours in culture by specific inhibition of MPF kinase activity

Roscovitine, a potent inhibitor of M‐phase Promoting Factor (MPF) kinase activity, was used to maintain cattle oocytes at the germinal vesicle stage for a 24‐hr culture period. A concentration of 25 μM of roscovitine was sufficient to reach the maximum level of meiotic resumption inhibition with 83 ± 6% of the oocytes remaining at the germinal vesicle stage after the 24 hr of culture. The histone H1 kinase activity was maintained at a basal level after culture under roscovitine inhibition at any of the concentrations tested (12.5, 25, 50, and 100 μM). This inhibitory effect of roscovitine was fully reversible since 89 ± 4% of the oocytes cultured for 24 hr in the presence of 25 μM of roscovitine reached the metaphase II stage after a further culture of 24 hr in permissive medium (TCM199 supplemented with 10 ng/ml EGF). The cleavage rate as well as the development to the blastocyst stage was not different for oocytes cultured for 24 hr under roscovitine (25 μM) inhibition and then matured for 24 hr in the presence of EGF as compared to oocytes not submitted to prematuration culture (82 ± 8% cleavage and 41 ± 4% blastocysts at 8 days post insemination for control oocytes compared to 90 ± 7% and 36 ± 7% respectively for roscovitine‐treated oocytes). Roscovitine meiotic inhibition was also effective in the presence of EGF, and the final developmental potential as well as the kinetics of blastocyst formation were not affected after such prematuration treatment. The EGF induced cumulus expansion was also inhibited by roscovitine. These results indicate for the first time the feasibility of culturing cattle oocytes under meiotic inhibition without decreasing their resulting developmental potential. Mol. Reprod. Dev. 55:89–95, 2000. © 2000 Wiley‐Liss, Inc.
Passivity preserving model reduction via a structured Lanczos method

Nowadays, modeling dynamical systems often yields state-space models of very high order (that is, 10,000 or more equations). In order to guarantee a numerical simulation in reasonable time, the dynamical system is reduced to one of the same form which allows simulation of and control-design for the reduced-order state-space model in much less computing time. Usually one would like to obtain a reduced-order system that has the same properties as the original system. In this paper, we will consider stable and passive systems. Antoulas suggests in [1] an approach based on positive real interpolation which is modified by Sorensen [36]. The algorithm is based upon interpolation at selected spectral zeros of the original transfer function to produce a reduced-order transfer function that has the specified roots as its spectral zeros. These interpolation conditions are satisfied through the computation of a basis for a selected invariant subspace of a Hamiltonian matrix which has the spectral zeros as its spectrum. Here we propose to employ a structure-preserving Lanczos algorithm for this part of the computation in order to make use of the underlying structure and physical properties of the problem.
How Are You Feeling? Revisiting the Quantification of Emotional Qualia

Numerous emotion researchers have asked their study participants to attend to the distinct feelings of arousal and valence, and self-report and physiological data have supported the independence of the two. We examined whether this dissociation reflects introspection about distinct emotional qualia or the way in which valence is measured. With either valence (Experiment 1) or arousal (Experiment 2) as the primary focus, when valence was measured using a bipolar scale (ranging from negative to positive), it was largely dissociable from arousal. By contrast, when two separate unipolar scales of pleasant and unpleasant valence were used, their sum was equivalent to feelings of arousal and its autonomic correlates. The association (or dissociation) of valence and arousal was related to the estimation (or nonestimation) of mixed-valence experiences, which suggests that the distinction between valence and arousal may reflect less the nature of emotional experience and more how it is measured. These findings further encourage use of unipolar valence scales in psychological measurement.
Identification of multimodal control behavior in pursuit tracking tasks

In manual control, a pursuit display may support the use of a multimodal “pursuit” control strategy by the human operator. This paper evaluates two methods that may be used to directly estimate describing functions for such multimodal human operator control dynamics in pursuit tracking. The first is a previously developed frequency-domain method based on Fourier coefficients. The second method makes use of linear-time invariant ARMAX models. An experiment is described in which participants performed tracking tasks with quasi-random multisine target and disturbance forcing functions, for single and double integrator controlled elements and with compensatory and pursuit displays. The experiment data confirms the findings from previous experiments, where it was found that multimodal pursuit control dynamics are adopted in control of systems with double integrator dynamics, but not for single integrator control tasks. Furthermore, the direct multimodal identification methods were found to give improved insight into the internal organization and dynamics of the human operator in pursuit tracking.
Valuation Effects and External Adjustment: A Review

This paper surveys the recent empirical and theoretical literature on valuation effects. The increase in cross-border holdings of financial assets opens the door to significant adjustments in a country's external position in response to fluctuations in asset and currency prices. Access to better data on net and gross international investment positions for a broad range of countries permits careful measurement of these “valuation effects”. We distinguish between predictable and unpredictable valuation effects, and argue that they play separate roles in the adjustment process (for better or for worse). Finally, we discuss theoretical conditions under which predictable valuation effects can arise in equilibrium
Towards automatic closed captioning : low latency real time broadcast news transcription

In this paper, we present a low latency real-time Broadcast News recognition system capable of transcribing live television newscasts with reasonable accuracy. We describe our recent modeling and efficiency improvements that yield a 22% word error rate on the Hub4e98 test set while running faster than real-time. These include the discriminative training of a feature transform and the acoustic model, and the optimization of the likelihood computation. We give experimental results that show the accuracy of the system at different speeds. We also explain how we achieved low latency, presenting measurements that show the typical system latency is less than 1 second.
Inhibitory and blocking monoclonal antibody epitopes on merozoite surface protein 1 of the malaria parasite Plasmodium falciparum.

Merozoite surface protein 1 (MSP-1) is a precursor to major antigens on the surface of Plasmodium spp. merozoites, which are involved in erythrocyte binding and invasion. MSP-1 is initially processed into smaller fragments; and at the time of erythrocyte invasion one of these of 42 kDa (MSP-1(42)) is subjected to a second processing, producing 33 kDa and 19 kDa fragments (MSP-1(33) and MSP-1(19)). Certain MSP-1-specific monoclonal antibodies (mAbs) react with conformational epitopes contained within the two epidermal growth factor domains that comprise MSP-1(19), and are classified as either inhibitory (inhibit processing of MSP-1(42) and erythrocyte invasion), blocking (block the binding and function of the inhibitory mAb), or neutral (neither inhibitory nor blocking). We have mapped the epitopes for inhibitory mAbs 12.8 and 12.10, and blocking mAbs such as 1E1 and 7.5 by using site-directed mutagenesis to change specific amino acid residues in MSP-1(19) and abolish antibody binding, and by using PEPSCAN to measure the reaction of the antibodies with every octapeptide within MSP-1(42). Twenty-six individual amino acid residue changes were made and the effect of each on the binding of mAbs was assessed by Western blotting and BIAcore analysis. Individual changes had either no effect, or reduced, or completely abolished the binding of individual mAbs. No two antibodies had an identical pattern of reactivity with the modified proteins. Using PEPSCAN each mAb reacted with a number of octapeptides, most of which were derived from within the first epidermal growth factor domain, although 1E1 also reacted with peptides spanning the processing site. When the single amino acid changes and the reactive peptides were mapped onto the three-dimensional structure of MSP-1(19), it was apparent that the epitopes for the mAbs could be defined more fully by using a combination of both mutagenesis and PEPSCAN than by either method alone, and differences in the fine specificity of binding for all the different antibodies could be distinguished. The incorporation of several specific amino acid changes enabled the design of proteins that bound inhibitory but not blocking antibodies. These may be suitable for the development of MSP-1-based vaccines against malaria.