Miracle-dz/UniFAR-FTUs huggingface dataset:
Eukaryotic diversity at pH extremes

Extremely acidic (pH < 3) and extremely alkaline (pH > 9) environments support a diversity of single-cell and to a lesser extent, multicellular eukaryotic life. This study compared alpha and beta diversity in eukaryotic communities from seven diverse aquatic environments with pH values ranging from 2 to 11 using massively-parallel pyrotag sequencing targeting the V9 hypervariable region of the 18S ribosomal RNA (rRNA) gene. A total of 946 operational taxonomic units (OTUs) were recovered at a 6% cut-off level (94% similarity) across the sampled environments. Hierarchical clustering of the samples segregated the communities into acidic and alkaline groups. Similarity percentage (SIMPER) analysis followed by indicator OTU analysis (IOA) and non-metric multidimensional scaling (NMDS) were used to determine which characteristic groups of eukaryotic taxa typify acidic or alkaline extremes and the extent to which pH explains eukaryotic community structure in these environments. Spain's Rio Tinto yielded the fewest observed OTUs while Nebraska Sandhills alkaline lakes yielded the most. Distinct OTUs, including metazoan OTUs, numerically dominated pH extreme sites. Indicator OTUs included the diatom Pinnularia and unidentified opisthokonts (Fungi and Filasterea) in the extremely acidic environments, and the ciliate Frontonia across the extremely alkaline sites. Inferred from NMDS, pH explained only a modest fraction of the variation across the datasets, indicating that other factors influence the underlying community structure in these environments. The findings from this study suggest that the ability for eukaryotes to adapt to pH extremes over a broad range of values may be rare, but further study of taxa that can broadly adapt across diverse acidic and alkaline environments, respectively present good models for understanding adaptation and should be targeted for future investigations.
B-Cell Dysregulation in Crohn's Disease Is Partially Restored with Infliximab Therapy

Background B-cell depletion can improve a variety of chronic inflammatory diseases, but does not appear beneficial for patients with Crohn’s disease. Objective To elucidate the involvement of B cells in Crohn’s disease, we here performed an ‘in depth’ analysis of intestinal and blood B-cells in this chronic inflammatory disease. Methods Patients with Crohn’s disease were recruited to study B-cell infiltrates in intestinal biopsies (n = 5), serum immunoglobulin levels and the phenotype and molecular characteristics of blood B-cell subsets (n = 21). The effects of infliximab treatment were studied in 9 patients. Results Granulomatous tissue showed infiltrates of B lymphocytes rather than Ig-secreting plasma cells. Circulating transitional B cells and CD21low B cells were elevated. IgM memory B cells were reduced and natural effector cells showed decreased replication histories and somatic hypermutation (SHM) levels. In contrast, IgG and IgA memory B cells were normally present and their Ig gene transcripts carried increased SHM levels. The numbers of transitional and natural effector cells were normal in patients who responded clinically well to infliximab. Conclusions B cells in patients with Crohn’s disease showed signs of chronic stimulation with localization to granulomatous tissue and increased molecular maturation of IgA and IgG. Therapy with TNFα-blockers restored the defect in IgM memory B-cell generation and normalized transitional B-cell levels, making these subsets candidate markers for treatment monitoring. Together, these results suggest a chronic, aberrant B-cell response in patients with Crohn’s disease, which could be targeted with new therapeutics that specifically regulate B-cell function.
Geometric control of mechanical systems : modeling, analysis, and design for simple mechanical control systems

Part I: Modeling of mechanical systems Introductory examples and problems Linear and multilinear algebra Differential geometry Simple mechanical control systems Lie groups, systems on groups, and symmetries. - Part II: Analysis of mechanical control systems Stability Controllability Low-order controllability and kinematic reduction Perturbation analysis. - Part III: A sampling of design methodologies Linear and nonlinear potential shaping for stabilization Stabilization and tracking for fully actuated systems Stabilization and tracking using oscillatory controls Motion planning for underactuated systems Appendices Time-dependent vector fields Some proofs.
The Dynamics of Semigroups of Rational Functions I

This paper is concerned with a generalisation of the classical theory of the dynamics associated to the iteration of a rational mapping of the Riemann sphere, to the more general setting of the dynamics associated to an arbitrary semigroup of rational mappings. We are partly motivated by results of Gehring and Martin which show that certain parameter spaces for KJeinian groups are essentially the stable basins of infinity for certain polynomial semigroups. Here we discuss the structure of the Fatou and Julia sets and their basic properties. We investigate to what extent Sullivan's 'no wandering domains' theorem remains valid. We obtain a complete generalisation of the classical results concerning classification of basins and their associated dynamics under an algebraic hypothesis analogous to the group-theoretical notion of 'virtually abelian'. We show that, in general, polynomial semigroups can have wandering domains. We put forward some conjectures regarding what we believe might be true. We also prove a theorem about the existence of filled in Julia sets for certain polynomial semigroups with specific applications to the theory of Kleinian groups in mind.
Online readers between the camps: A Text World Theory analysis of ethical positioning in We Need to Talk About Kevin

Recent investigations into ethical experiences of fictional narratives have discussed the ‘positions’ that readers adopt in relation to the author, narrator and characters . This article applies Text World Theory as a means of accounting for the ethical experience of Lionel Shriver’s We Need to Talk About Kevin. Qualitative analysis of a sample of 150 online reader responses on the reading-based social network Goodreads reveals a range of ethical responses to the novel positioned between two interpretative ‘camps’ and the nature/nurture debate they reflect with regards to the character, Kevin. Drawing from this dataset, I explore how stylistic features of Shriver’s epistolary novel could be seen to influence readers’ ethical positioning in relation to the multiple perspectives presented at different levels of its narrative structure. As a result of the analysis, I propose that an account of ethical experience using Text World Theory may benefit from the concept of ‘construal’ in Langacker’s Cognitive Grammar. By modeling readers’ variable attention to multiple minds, including their own, a cognitive grammatical model of construal may support an understanding of ethical interpretation as an interpersonal experience within particular reading contexts.
The new intermediate long-bursting source XTE J1701-407

Aims. XTE J1701-407 is a newly discovered X-ray transient source. We investigate its flux variability and study the intermediate long- and short-bursts discovered by Swift on July 17, and 27, 2008, respectively. Methods. Only one intermediate long-burst, of duration ≈18 min and ten days later a short burst, have been recorded from XTE J1701407. We analyzed the public available data from Swift and RXTE, and compared the observed properties of the intermediate long-burst with theoretical ignition condition and light curves to investigate the possible nuclear-burning processes. Results. The intermediate long-burst may have exhibited a photospheric radius expansion, allowing us to derive the source distance at 6.2 kpc, assuming the empirically derived Eddington luminosity for pure helium. The intermediate long-burst decay was described most accurately by using two exponential functions with e-folding times of τ1 = 40 ± 3sa ndτ2 = 221 ± 9 s. The bursts occurred at a persistent luminosity of Lper = 8.3 × 10 36 erg s −1 (≈2.2% of the Eddington luminosity). For the intermediate long-burst, the mass accretion rate per unit area onto the neutron star was u m ≈ 4 × 10 3 gc m −2 s −1 , and the total energy released was Eburst ≈ 3.5 × 10 40 erg. This corresponds to an ignition column depth of yign ≈ 1.8 × 10 9 gc m −2 , for a pure helium burning. We find that the energetics of this burst can be modeled in different ways, as (i) pure helium ignition, as the result of either pure helium accretion or depletion of hydrogen by steady burning during accumulation; or (ii) as ignition of a thick layer of hydrogen-rich material in a source of low metallicity. However, comparison of the burst duration with model light curves suggests that hydrogen burning plays an important role during the burst, and therefore that this source is a low accretion-rate burster with a low metallicity in the accreted material.
Characterisation and Carriage Ratio of Clostridium difficile Strains Isolated from a Community-Dwelling Elderly Population in the United Kingdom

Background Community-associated Clostridium difficile infection (CDI) appears to be an increasing problem. Reported carriage rates by C.difficile are debatable with suggestions that primary asymptomatic carriage is associated with decreased risk of subsequent diarrhoea. However, knowledge of potential reservoirs and intestinal carriage rates in the community, particularly in the elderly, the most susceptible group, is limited. We have determined the presence of C.difficile in the faeces of a healthy elderly cohort living outside of long-term care facilities (LCFs) in the United Kingdom. Methods Faecal samples from 149 community-based healthy elderly volunteers (median age 81 years) were screened for C.difficile using direct (Brazier's CCEY) and enrichment (Cooked Meat broth) culture methods and a glutamate dehydrogenase (GDH) immunoassay. Isolates were PCR-ribotyped and analysed for toxin production and the presence of toxin genes. Results Of 149 faecal samples submitted, six (4%) were found to contain C.difficile. One particular sample was positive by both the GDH immunoassay and direct culture, and concurrently produced two distinct strain types: one toxigenic and the other non-toxigenic. The other five samples were only positive by enrichment culture method. Overall, four C.difficile isolates were non-toxigenic (PCR-ribotypes 009, 026 (n = 2) and 039), while three were toxigenic (PCR-ribotypes 003, 005 and 106). All individuals who had a positive culture were symptom-free and none of them had a history of CDI and/or antibiotics use in the 3 month period preceding recruitment. Conclusions To our knowledge, this is the first study of the presence of C.difficile in healthy elderly community-dwelling individuals residing outside of LCFs. The observed carriage rate is lower than that reported for individuals in LCFs and interestingly no individual carried the common epidemic strain PCR-ribotype 027 (NAP1/BI). Further follow-up of asymptomatic carriers in the community, is required to evaluate host susceptibility to CDI and identify dynamic changes in the host and microbial environment that are associated with pathogenicity.
Invariant Generation through Strategy Iteration in Succinctly Represented Control Flow Graphs

We consider the problem of computing numerical invariants of programs, for instance bounds on the values of numerical program variables. More specifically, we study the problem of performing static analysis by abstract interpretation using template linear constraint domains. Such invariants can be obtained by Kleene iterations that are, in order to guarantee termination, accelerated by widening operators. In many cases, however, applying this form of extrapolation leads to invariants that are weaker than the strongest inductive invariant that can be expressed within the abstract domain in use. Another well-known source of imprecision of traditional abstract interpretation techniques stems from their use of join operators at merge nodes in the control flow graph. The mentioned weaknesses may prevent these methods from proving safety properties. The technique we develop in this article addresses both of these issues: contrary to Kleene iterations accelerated by widening operators, it is guaranteed to yield the strongest inductive invariant that can be expressed within the template linear constraint domain in use. It also eschews join operators by distinguishing all paths of loop-free code segments. Formally speaking, our technique computes the least fixpoint within a given template linear constraint domain of a transition relation that is succinctly expressed as an existentially quantified linear real arithmetic formula. In contrast to previously published techniques that rely on quantifier elimination, our algorithm is proved to have optimal complexity: we prove that the decision problem associated with our fixpoint problem is in the second level of the polynomial-time hierarchy.
Information gathering during Enterprise System selection - insight from practice

Purpose – The purpose of this paper is to examine the information gathering methods used during enterprise system (ES) selection among Polish organizations and to have IT consulting experts evaluate these methods, which will result in identification of the preferred approach for the information‐gathering task during system selection.Design/methodology/approach – The research has a qualitative exploratory design with grounded theory being the main research method. A mixed quantitative‐qualitative approach to data collection was used: an e‐mail‐based survey was used as an introductory stage to gather data on information‐gathering methods. The results of the survey were evaluated by ES experts during unstructured interviews. The interviews were then transcribed and coded according to the grounded theory coding techniques.Findings – The evaluation of selection approaches revealed that the approach to information gathering should depend on the level of configurability of the systems subject to selection. Two g.
Wind farm power maximization based on a cooperative static game approach

The objective of this study is to improve the cost-effectiveness and production efficiency of wind farms using cooperative control. The key factors in determining the power production and the loading for a wind turbine are the nacelle yaw and blade pitch angles. However, the nacelle and blade angles may adjust the wake direction and intensity in a way that may adversely affect the performance of other wind turbines in the wind farm. Conventional wind-turbine control methods maximize the power production of a single turbine, but can lower the overall wind-farm power efficiency due to wake interference. This paper introduces a cooperative game concept to derive the power production of individual wind turbine so that the total wind-farm power efficiency is optimized. Based on a wake interaction model relating the yaw offset angles and the induction factors of wind turbines to the wind speeds experienced by the wind turbines, an optimization problem is formulated with the objective of maximizing the sum of the power production of a wind farm. A steepest descent algorithm is applied to find the optimal combination of yaw offset angles and the induction factors that increases the total wind farm power production. Numerical simulations show that the cooperative control strategy can increase the power productions in a wind farm.
Examining public acquisition of science knowledge from social media in Singapore: an extension of the cognitive mediation model

ABSTRACT This study extends the cognitive mediation model (CMM) by examining the role of social media in cultivating public science knowledge. A sample of 901 Singaporeans was collected through an online survey panel. The results showed that the CMM could be applied to a social media context with a focus on science literacy. Specifically, the findings indicated that people with higher levels of surveillance gratification and social utility motivations tended to pay more attention and to elaborate more about science news that they encounter on social media. Likewise, people with greater social utility motivation tended to engage in greater interpersonal discussions on social media. Notably, attention to news on social media had an indirect association with science knowledge through news elaboration and interpersonal discussion on social media. Implications for theory and practice for science communication were discussed.
Summarising and validating test accuracy results across multiple studies for use in clinical practice

Following a meta‐analysis of test accuracy studies, the translation of summary results into clinical practice is potentially problematic. The sensitivity, specificity and positive (PPV) and negative (NPV) predictive values of a test may differ substantially from the average meta‐analysis findings, because of heterogeneity. Clinicians thus need more guidance: given the meta‐analysis, is a test likely to be useful in new populations, and if so, how should test results inform the probability of existing disease (for a diagnostic test) or future adverse outcome (for a prognostic test)? We propose ways to address this. Firstly, following a meta‐analysis, we suggest deriving prediction intervals and probability statements about the potential accuracy of a test in a new population. Secondly, we suggest strategies on how clinicians should derive post‐test probabilities (PPV and NPV) in a new population based on existing meta‐analysis results and propose a cross‐validation approach for examining and comparing their calibration performance. Application is made to two clinical examples. In the first example, the joint probability that both sensitivity and specificity will be >80% in a new population is just 0.19, because of a low sensitivity. However, the summary PPV of 0.97 is high and calibrates well in new populations, with a probability of 0.78 that the true PPV will be at least 0.95. In the second example, post‐test probabilities calibrate better when tailored to the prevalence in the new population, with cross‐validation revealing a probability of 0.97 that the observed NPV will be within 10% of the predicted NPV. © 2015 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.
Novel parathyroid hormone (1-84) assay as basis for parathyroid hormone monitoring in renal hyperparathyroidism.

HYPOTHESIS Cross-reactivity of parathyroid hormone (PTH) fragments with immunometric "intact" PTH assays limited the use of intraoperative PTH monitoring in renal hyperparathyroidism. A new assay generation measuring whole PTH (1-84) should be able to predict complete or incomplete resection of hyperfunctioning parathyroid tissue. DESIGN Consecutive series for evaluation of intraoperative PTH monitoring using a second-generation assay. SETTING University hospital section of endocrine surgery. PATIENTS Twenty-two patients received hemodialysis; 9 patients showed good and 4 patients reduced graft function after kidney transplantation. INTERVENTIONS Total parathyroidectomy, central neck dissection, bilateral thymectomy, and immediate autotransplantation was the standardized approach in 35 consecutive patients. Blood samples were drawn before incision and at 5-minute intervals after excision of the last gland. Stored samples were analyzed using a "second-generation" assay (Bio-Intact PTH [1-84]; Nichols Institute Diagnostics, San Clemente, Calif). Parathyroidectomy was classified as total, subtotal, or insufficient according to first-generation intact PTH values in the first postoperative week. MAIN OUTCOME MEASURES Intraoperative ability to predict total, subtotal, or incomplete parathyroidectomy. RESULTS Independent of renal function, Bio-Intact PTH dropped into the normal range in all patients with total and subtotal resections after a maximum of 20 minutes. It indicated insufficient parathyroidectomy in 4 (80%) of 5 patients. One failure was caused by devascularization of remaining parathyroid tissue. An intraoperative differentiation between total and subtotal resection was not possible. CONCLUSIONS Intraoperative monitoring with quick, second-generation assays for PTH (1-84) seems to be a valuable new tool in surgery for renal hyperparathyroidism because a more accurate differentiation between sufficient and insufficient parathyroidectomy may be achieved. An intraoperative decision about the need for immediate or delayed autotransplantation seems impossible because a differentiation between total or subtotal parathyroidectomy cannot be made. Because of possible devascularization of parathyroid tissue, Bio-Intact PTH monitoring can only be interpreted in the context of the operative findings.
Wimpy Nodes with 10GbE: Leveraging One-Sided Operations in Soft-RDMA to Boost Memcached

Recently, various key/value stores have been proposed targeting clusters built from low-power CPUs. The typical network configuration is that the nodes in those clusters are connected using 1 Gigabit Ethernet. During the last couple of years, 10 Gigabit Ethernet has become commodity and is increasingly used within the data centers providing cloud computing services. The boost in network link speed, however, poses a challenge to the cluster nodes because filling the network link can be a CPU-intensive task. In particular for CPUs running in low-power mode, it is therefore important to spend CPU cycles used for networking as efficiently as possible. In this paper, we propose a modified Memcached architecture to leverage the one-side semantics of RDMA. We show how the modified Memcached is more CPU efficient and can serve up to 20% more GET operations than the standard Memcached implementation on low-power CPUs. While RDMA is a networking technology typically associated with specialized hardware, our solution uses soft-RDMA which runs on standard Ethernet and does not require special hardware.
Elevation-dependent responses of tree mast seeding to climate change over 45 years

We use seed count data from a New Zealand mono-specific mountain beech forest to test for decadal trends in seed production along an elevation gradient in relation to changes in climate. Seedfall was collected (1965 to 2009) from seed trays located on transect lines at fixed elevations along an elevation gradient (1020 to 1370 m). We counted the number of seeds in the catch of each tray, for each year, and determined the number of viable seeds. Climate variables were obtained from a nearby (<2 km) climate station (914-m elevation). Variables were the sum or mean of daily measurements, using periods within each year known to correlate with subsequent interannual variation in seed production. To determine trends in mean seed production, at each elevation, and climate variables, we used generalized least squares (GLS) regression. We demonstrate a trend of increasing total and viable seed production, particularly at higher elevations, which emerged from marked interannual variation. Significant changes in four seasonal climate variables had GLS regression coefficients consistent with predictions of increased seed production. These variables subsumed the effect of year in GLS regressions with a greater influence on seed production with increasing elevation. Regression models enforce a view that the sequence of climate variables was additive in their influence on seed production throughout a reproductive cycle spanning more than 2 years and including three summers. Models with the most support always included summer precipitation as the earliest variable in the sequence followed by summer maximum daily temperatures. We interpret this as reflecting precipitation driven increases in soil nutrient availability enhancing seed production at higher elevations rather than the direct effects of climate, stand development or rising atmospheric CO2 partial pressures. Greater sensitivity of tree seeding at higher elevations to changes in climate reveals how ecosystem responses to climate change will be spatially variable.