Miracle-dz/UniFAR-FTUs huggingface dataset:
The rise and fall of species: implications for macroevolutionary and macroecological studies

Knowing the geographic extents of species is crucial for understanding the causes of diversity distributions and modes of speciation and extinction. Species geographic ranges are often viewed as approximately constant in size in geological time, even though climate change studies have shown that historical and modern species geographic distributions are not static. Here, we use an extensive global microfossil database to explore the temporal trajectories of geographic extents over the entire lifespan of marine nannoplankton, diatom, planktic foraminifer and radiolarian species. We show that geographic extents are not static over geological time-scales. Temporal trajectories of species geographic ranges are asymmetric: the rise is quicker than the fall. We propose that once a species has overcome its initial difficulties in geographic establishment, it rises to its peak geographic extent. However, once this peak value is reached, it will also have a maximal number of species to interact with. The negative of these biotic interactions could then cause a gradual geographic decline. We discuss the multiple implications of our findings with reference to macroecological and macroevolutionary studies.
On the entrainment law at the top of the convectively- driven atmospheric boundary layer

We discuss the entrainment processes at the top of the convectively-driven boundary layer. The discussion is based on results from a high-resolution (256 grid points) large-eddy simulation initialized by a commonly used sounding of Day 33 of the Wangara experiment. We find that the mixed-layer turbulence precisely follows the Kolmogorov spectral law for the velocity field, whether two-dimensional (in horizontal planes) or one-dimensional spectra are computed. This behavior also holds for the frequency spectrum, when the Taylor’s frozen turbulence hypothesis is used. As well, the fluctuating virtual potential temperature field follows the Corrsin-Oboukhov spectral law. The multiplicative constants of the power laws, inferred from the compensated spectra, are found to be in good agreement with previous measurements in the atmosphere. We next revisit the entrainment law at the mixed-layer top from two complementary Eulerian and Lagrangian approaches. The Lagrangian approach yields similar results to the eulerian one: the normalized entrainement velocity we/w⋆, where we and w⋆ are the entrainment and convective velocities, is found to vary as a function of the bulk Froude number squared at the interface with a multiplicative constant close to 1.2.
Tumor Necrosis Factor Alpha Is a Key Mediator in the Regulation of Experimental Trypanosoma brucei Infections

ABSTRACT In order to evaluate during experimental Trypanosoma brucei infections the potential role of tumor necrosis factor alpha (TNF-α) in the host-parasite interrelationship, C57BL/6 TNF-α knockout mice (TNF-α−/−) as well as C57BL/6 wild-type mice were infected with pleomorphic T. bruceiAnTat 1.1 E parasites. In the TNF-α−/− mice, the peak levels of parasitemia were strongly increased compared to the peak levels recorded in wild-type mice. The increased parasite burden did not reflect differences in clearance efficacy or in production ofT. brucei-specific immunoglobulin M (IgM) and IgG antibodies. Trypanosome-mediated immunopathological features, such as lymph node-associated immunosuppression and lipopolysaccharide hypersensitivity, were found to be greatly reduced in infected TNF-α−/− mice. These results demonstrate that, during trypanosome infections, TNF-α is a key mediator involved in both parasitemia control and infection-associated pathology.
A Novel Approach using Dual Active Feature Sample Selection and LTS (Learn to Search)

the bug signatures(context of bug) is difficult, as it involves mining the execution traces of the program. The discriminative graph mining algorithm is used to identify the bug signatures. It requires manual labelling of the input set to estimate the discriminative subgraphs. To reduce the tedious work of manual labelling, this paper presents novel framework to identify bug signatures. The proposed algorithm uses hybrid approach of dual active feature sample selection and LTS(Learn to Search). In the hybrid method, the dual active feature sample selection is used to find the query graph and its corresponding discriminative subgraphs, and LTS method is applied to obtain risk free optimal solution. The performance of the combined approach is measured with the parameters (i)runtime, (ii)recall and (iii)precision. The experiment results shows that this hybrid approach has an improved runtime of 60.10% when only 40% of the input graph set is manually labelled. The recall and precision are also improved by 33.33% when compared with dual active feature sample selection without LTS. KeywordsMining, Discriminative subgraph mining, Bug Signatures
Arterial baroreflex control of heart rate during exercise in postural tachycardia syndrome.

Patients with postural tachycardia syndrome (POTS) have excessive tachycardia without hypotension during orthostasis as well as exercise. We tested the hypothesis that excessive tachycardia during exercise in POTS is not related to abnormal baroreflex control of heart rate (HR). Patients (n = 13) and healthy controls (n = 10) performed graded cycle exercise at 25, 50, and 75 W in both supine and upright positions while arterial pressure (arterial catheter) and HR (ECG) were measured. Baroreflex sensitivity of HR was assessed by bolus intravenous infusion of phenylephrine at each workload. In both positions, HR was higher in the patients than the controls during exercise. Supine baroreflex sensitivity (HR/systolic pressure) in POTS patients was -1.3 +/- 0.1 beats.min(-1). mmHg(-1) at rest and decreased to -0.6 +/- 0.1 beats.min(-1). mmHg(-1) during 75-W exercise, neither significantly different from the controls (P > 0.6). In the upright position, baroreflex sensitivity in POTS patients at rest (-1.4 +/- 0.1 beats.min(-1). mmHg(-1)) was higher than the controls (-1.0 +/- 0.1 beats.min(-1). mmHg(-1)) (P < 0.05), and it decreased to -0.1 +/- 0.04 beats.min(-1). mmHg(-1) during 75-W exercise, lower than the controls (-0.3 +/- 0.09 beats.min(-1). mmHg(-1)) (P < 0.05). The reduced arterial baroreflex sensitivity of HR during upright exercise was accompanied by greater fluctuations in systolic and pulse pressure in the patients than in the controls with 56 and 90% higher coefficient of variations, respectively (P < 0.01). However, when baroreflex control of HR was corrected for differences in HR, it was similar between the patients and controls during upright exercise. These results suggest that the tachycardia during exercise in POTS was not due to abnormal baroreflex control of HR.
Parallel Edge Splatting for Scalable Dynamic Graph Visualization

We present a novel dynamic graph visualization technique based on node-link diagrams. The graphs are drawn side-byside from left to right as a sequence of narrow stripes that are placed perpendicular to the horizontal time line. The hierarchically organized vertices of the graphs are arranged on vertical, parallel lines that bound the stripes; directed edges connect these vertices from left to right. To address massive overplotting of edges in huge graphs, we employ a splatting approach that transforms the edges to a pixel-based scalar field. This field represents the edge densities in a scalable way and is depicted by non-linear color mapping. The visualization method is complemented by interaction techniques that support data exploration by aggregation, filtering, brushing, and selective data zooming. Furthermore, we formalize graph patterns so that they can be interactively highlighted on demand. A case study on software releases explores the evolution of call graphs extracted from the JUnit open source software project. In a second application, we demonstrate the scalability of our approach by applying it to a bibliography dataset containing more than 1.5 million paper titles from 60 years of research history producing a vast amount of relations between title words.
A Novel Small-Molecule Inhibitor Targeting the IL-6 Receptor β Subunit, Glycoprotein 130

IL-6 is a major causative factor of inflammatory disease. Although IL-6 and its signaling pathways are promising targets, orally available small-molecule drugs specific for IL-6 have not been developed. To discover IL-6 antagonists, we screened our in-house chemical library and identified LMT-28, a novel synthetic compound, as a candidate IL-6 blocker. The activity, mechanism of action, and direct molecular target of LMT-28 were investigated. A reporter gene assay showed that LMT-28 suppressed activation of STAT3 induced by IL-6, but not activation induced by leukemia inhibitory factor. In addition, LMT-28 downregulated IL-6–stimulated phosphorylation of STAT3, gp130, and JAK2 protein and substantially inhibited IL-6–dependent TF-1 cell proliferation. LMT-28 antagonized IL-6–induced TNF-α production in vivo. In pathologic models, oral administration of LMT-28 alleviated collagen-induced arthritis and acute pancreatitis in mice. Based on the observation of upstream IL-6 signal inhibition by LMT-28, we hypothesized IL-6, IL-6Rα, or gp130 to be putative molecular targets. We subsequently demonstrated direct interaction of LMT-28 with gp130 and specific reduction of IL-6/IL-6Rα complex binding to gp130 in the presence of LMT-28, which was measured by surface plasmon resonance analysis. Taken together, our data suggest that LMT-28 is a novel synthetic IL-6 inhibitor that functions through direct binding to gp130.
Ipratropium bromide versus short acting beta-2 agonists for stable chronic obstructive pulmonary disease.

BACKGROUND Chronic obstructive pulmonary disease (COPD) is a condition associated with high morbidity, mortality and cost to the community. Patients often report symptomatic improvement with short-acting beta-2 agonists (SABA) and anticholinergic bronchodilator medications, and both are recommended in COPD guidelines. These medications have different mechanisms of action and therefore could have an additive effect when combined. OBJECTIVES To compare the relative efficacy and safety of regular long term use (at least four weeks) of ipratropium bromide and short- acting beta-2 agonist therapy in patients with stable COPD. SEARCH STRATEGY The Cochrane Airways Group Specialised Register of Trials was searched. Bibliographies were checked to identify relevant cross-references. Drug companies were contacted for relevant trial data. The searches are current to August 2005. SELECTION CRITERIA All randomised controlled trials comparing at least 4 weeks of treatment with an anticholinergic agent (ipratropium bromide) alone or in combination with a beta-2 agonist (short acting) versus the beta-2 agonist alone, delivered via metered dose inhaler or nebuliser, in non-asthmatic adult subjects with stable COPD. DATA COLLECTION AND ANALYSIS Data extraction and study quality assessment was performed independently by three reviewers. Authors of studies and relevant manufacturers were contacted if data were missing. MAIN RESULTS Eleven studies (3912 participants) met the inclusion criteria of the review. Small benefits of ipratropium over a short-acting beta-2 agonist were demonstrated on lung function outcomes. There were small benefits in favour of ipratropium on quality of life (HRQL), as well as a reduction in the requirement for oral steroids. Combination therapy with ipratropium plus a short-acting beta-2 agonist conferred benefits over a short-acting beta-2 agonist alone in terms of post-bronchodilator lung function. There was no significant benefit of combination therapy in subjective improvements in HRQL, but again there was a reduction in the requirement for oral steroids. AUTHORS' CONCLUSIONS The available data from the trials included in this review suggest that the advantage of regular long term use of ipratropium alone or in combination with a short-acting beta-2 agonist or over a beta-2 agonist alone are small, if the aim is to improve lung function, symptoms and exercise tolerance. Until further data are available, the strategy of providing a short-acting beta-2 agonist on a PRN basis, and then either continuing with the short-acting beta-2 agonist regularly or conducting an "n of 1" trial of regular beta-2 agonist or regular anticholinergic to determine the treatment that gives the best relief of symptoms (and continuing with it), would seem cost effective. This strategy does need formal evaluation. Patient preference is also important, as is the relative importance of avoiding the use of systemic corticosteroids.
Automatic attentional orienting to other people's gaze in schizophrenia

Explicit tests of social cognition have revealed pervasive deficits in schizophrenia. Less is known of automatic social cognition in schizophrenia. We used a spatial orienting task to investigate automatic shifts of attention cued by another person's eye gaze in 29 patients and 28 controls. Central photographic images of a face with eyes shifted left or right, or looking straight ahead, preceded targets that appeared left or right of the cue. To examine automatic effects, cue direction was non-predictive of target location. Cue–target intervals were 100, 300, and 800 ms. In non-social control trials, arrows replaced eye-gaze cues. Both groups showed automatic attentional orienting indexed by faster reaction times (RTs) when arrows were congruent with target location across all cue–target intervals. Similar congruency effects were seen for eye-shift cues at 300 and 800 ms intervals, but patients showed significantly larger congruency effects at 800 ms, which were driven by delayed responses to incongruent target locations. At short 100-ms cue–target intervals, neither group showed faster RTs for congruent than for incongruent eye-shift cues, but patients were significantly slower to detect targets after direct-gaze cues. These findings conflict with previous studies using schematic line drawings of eye-shifts that have found automatic attentional orienting to be reduced in schizophrenia. Instead, our data indicate that patients display abnormalities in responding to gaze direction at various stages of gaze processing—reflected by a stronger preferential capture of attention by another person's direct eye contact at initial stages of gaze processing and difficulties disengaging from a gazed-at location once shared attention is established.
Transients, Metastability, and Neuronal Dynamics

This paper is about neuronal dynamics and how their special complexity can be understood in terms of nonlinear dynamics. There are many aspects of neuronal interactions and connectivity that engender the complexity of brain dynamics. In this paper we consider (i) the nature of this complexity and (ii) how it depends on connections between neuronal systems (e.g., neuronal populations or cortical areas). The main conclusion is that simulated neural systems show complex behaviors, reminiscent of neuronal dynamics, when these extrinsic connections are sparse. The patterns of activity that obtain, under these conditions, show a rich form of intermittency with the recurrent and self-limiting expression of stereotyped transient-like dynamics. Despite the fact that these dynamics conform to a single (complex) attractor this metastability gives the illusion of a dynamically changing attractor manifold (i.e., a changing surface upon which the dynamics unfold). This metastability is characterized using a measure that is based on the entropy of the time series' spectral density.
Automatic generation and analysis of physics-based puzzle games

In this paper we present a method for the automatic generation of content for the physics-based puzzle game Cut The Rope. An evolutionary game generator is implemented which evolves the design of levels based on a context-free grammar. We present various measures for analyzing the expressivity of the generator and visualizing the space of content covered. We further perform an experiment on evolving playable content of the game and present and analyze the results obtained.
Kidney-type Intervertebral Spacers Should be Located Anteriorly in Cantilever Transforaminal Lumbar Interbody Fusion: Analyses of Risk Factors for Spacer Subsidence for a Minimum of 2 Years

Study Design Retrospective analysis of factors related to kidney-type interbody spacer subsidence (SS) in transforaminal interbody fusion (TLIF). Objective To determine the risk factors for SS in TLIF using kidney-type spacers. Summary of Background Data SS into the vertebral body, a major complication of TLIF, has not been studied extensively. Methods Between July 2004 and May 2006, 54 consecutive patients with lumbar dysplastic changes or degenerative disc diseases underwent TLIF using 82 kidney-type spacers with iliac bone grafts. All were followed-up for more than 2 years (mean, 2 y, 11 mo). SS was defined as disc height loss >2 mm. Risk factors analyzed for SS included spacer location in the intervertebral space (IVS, anterior, center, and posterior), sex, age, body mass index, and disease (spondylolisthesis, degenerative disc disease). Clinical outcomes were assessed using the Japanese Orthopedic Associated Score for back pain, as were adjacent segment disorder and nonunion. Results Of the 82 spacers, 66 were located in the center of the IVS and 16 anteriorly. There were 18 SS. Spacer position at the center of the IVS (P<0.001) and older age (P<0.001) were significantly associated with SS, with the first 2 factors having a synergistic effect. Adjacent level disorder (n=5) and nonunion (n=3) were observed only in patients with spacers positioned at the center of the IVS. Conclusions Kidney-type spacers should be located in the anterior portion of the IVS to prevent subsidence of the intervertebral body, especially in patients with elderly age.
The Risk of Colorectal Neoplasia in Patients with Gallbladder Diseases

Cholecystectomy is associated with an increased risk of colorectal cancer, but little is known about the relationship between gallbladder disease and colorectal adenoma. Gallbladder polyps and colorectal neoplasia (CRN) share several risk factors such as obesity, diabetes and metabolic syndrome, which might account for their association. In this study, we investigated whether asymptomatic patients with gallbladder disease are at increased risk of CRN and identified the factors to their association. The study population consisted of 4,626 consecutive, asymptomatic individuals drawn from a prospective health check-up cohort who underwent both ultrasonography and colonoscopy screening. The prevalence of CRNs in patients with gallbladder polyps or gallstones was significantly higher than that in the control group (32.1% vs. 26.8%; P = 0.032, 35.8% vs. 26.9%; P = 0.020). A multivariate regression analysis showed that gallbladder polyps were an independent risk factor for CRN [adjusted odds ratio (OR): 1.29; 95% confidence interval (CI); 1.03-1.62] whereas gallstones were not (adjusted OR: 1.14; 95% CI: 0.79-1.63). The adjusted OR for the risk of CRN was 1.12 for gallbladder polyps < 5 mm (95% CI, 0.85-1.46) and 1.79 for gallbladder polyps ≥ 5 mm (95% CI, 1.15-2.77). The prevalence of CRN increased with increasing polyp size (P trend = 0.022). Our results suggest that colorectal neoplasia is significantly related to gallbladder polyps, especially those ≥ 5 mm. Graphical Abstract
Cell Wall Polysaccharides Are Specifically Involved in the Exclusion of Aluminum from the Rice Root Apex1

Rice (Oryza sativa) is the most aluminum (Al)-resistant crop species among the small-grain cereals, but the mechanisms responsible for this trait are still unclear. Using two rice cultivars differing in Al resistance, rice sp. japonica ‘Nipponbare’ (an Al-resistant cultivar) and rice sp. indica ‘Zhefu802’ (an Al-sensitive cultivar), it was found that Al content in the root apex (0–10 mm) was significantly lower in Al-resistant ‘Nipponbare’ than in sensitive ‘Zhefu802’, with more of the Al localized to cell walls in ‘Zhefu802’, indicating that an Al exclusion mechanism is operating in ‘Nipponbare’. However, neither organic acid efflux nor changes in rhizosphere pH appear to be responsible for the Al exclusion. Interestingly, cell wall polysaccharides (pectin, hemicellulose 1, and hemicellulose 2) in the root apex were found to be significantly higher in ‘Zhefu802’ than in ‘Nipponbare’ in the absence of Al, and Al exposure increased root apex hemicellulose content more significantly in ‘Zhefu802’. Root tip cell wall pectin methylesterase (PME) activity was constitutively higher in ‘Zhefu802’ than in ‘Nipponbare’, although Al treatment resulted in increased PME activity in both cultivars. Immunolocalization of pectins showed a higher proportion of demethylated pectins in ‘Zhefu802’, indicating a higher proportion of free pectic acid residues in the cell walls of ‘Zhefu802’ root tips. Al adsorption and desorption kinetics of root tip cell walls also indicated that more Al was adsorbed and bound Al was retained more tightly in ‘Zhefu802’, which was consistent with Al content, PME activity, and pectin demethylesterification results. These responses were specific to Al compared with other metals (CdCl2, LaCl3, and CuCl2), and the ability of the cell wall to adsorb these metals was also not related to levels of cell wall pectins. All of these results suggest that cell wall polysaccharides may play an important role in excluding Al specifically from the rice root apex.
INTENSITY‐BASED VALUATION OF RESIDENTIAL MORTGAGES: AN ANALYTICALLY TRACTABLE MODEL

This paper presents an analytically tractable valuation model for residential mortgages. The random mortgage prepayment time is assumed to have an intensity process of the form ht=h0(t) +γ (k−rt)+, where h0(t) is a deterministic function of time, rt is the short rate, and γ and k are scalar parameters. The first term models exogenous prepayment independent of interest rates (e.g., a multiple of the PSA prepayment function). The second term models refinancing due to declining interest rates and is proportional to the positive part of the distance between a constant threshold level and the current short rate. When the short rate follows a CIR diffusion, we are able to solve the model analytically and find explicit expressions for the present value of the mortgage contract, its principal‐only and interest‐only parts, as well as their deltas. Mortgage rates at origination are found by solving a non‐linear equation. Our solution method is based on explicitly constructing an eigenfunction expansion of the pricing semigroup, a Feynman‐Kac semigroup of the CIR diffusion killed at an additive functional that is a linear combination of the integral of the CIR process and an area below a constant threshold and above the process sample path (the so‐called area functional). A sensitivity analysis of the term structure of mortgage rates and calibration of the model to market data are presented.