Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of dental development in Homo, Australopithecus, Pan, and Gorilla.

Smith ([1986] Nature 323:327-330) distinguished patterns of development of teeth of juvenile fossil hominids as being "more like humans" or "more like apes" based on statistical similarity to group standards. Here, this central tendency discrimination (CTD) is tested for its ability to recognize ape and human patterns of dental development in 789 subadult hominoids. Tooth development of a modern human sample (665 black southern Africans) was scored entirely by an outside investigator; pongid and fossil hominid samples (59 Pan, 50 Gorilla, and 14 fossil hominids) were scored by the author. The claim of Lampl et al. ([1993] Am. J. Phys. Anthropol. 90:113-127) that Smith's 1986 method succeeds in only 8% of human cases was not sustained. Figures for overall success of classification (87% humans, 68% apes) mask important effects of teeth sampled and age class. For humans, the power of CTD varied between 53% and 92% depending on the number and kind of teeth available--nearly that of a coin toss when data described only two nearby teeth, but quite successful with more teeth or distant teeth. For apes, only age class affected accuracy: "Infant" apes (M1 development < or = root cleft complete, unemerged) were usually classed as humans, probably because the present developmental standard for great apes is in substantial error under 3 years of age. "Juvenile" apes (M1 > or = root 1/4), however, were correctly discriminated in 87% of cases. Overall, CTD can be considered reliable (accuracy of 92% for humans and 88% for apes) when data contrast development of distant dental fields and subjects are juveniles (not infants). Restricting analysis of fossils to specimens satisfying these criteria, patterns of dental development of gracile australopithecines and Homo habilis remain classified with African apes. Those of Homo erectus and Neanderthals are classified with humans, suggesting that patterns of growth evolved substantially in the Hominidae. To standardize future research, the computer program that operationalizes CTD is now available.
Correlation-enhanced electron-phonon coupling: Applications of GW and screened hybrid functional to bismuthates, chloronitrides, and other high-Tc superconductors

We show that the electron-phonon coupling (EPC) in many materials can be significantly underestimated by the standard density-functional theory (DFT) in the local-density approximation (LDA) due to large nonlocal correlation effects. We present a simple yet efficient methodology to evaluate the realistic EPC, going beyond the LDA by using more advanced and accurate GW and screened-hybridfunctional DFT approaches. The corrections that we propose explain the extraordinarily high superconducting temperatures that are observed in two distinct classes of compounds—the bismuthates and the transition-metal chloronitrides—thus solving a 30-year-old puzzle. Our work calls for the critical reevaluation of the EPC of certain phonon modes in many other materials, such as cuprates and ironbased superconductors. The proposed methodology can be used to design new correlation-enhanced hightemperature superconductors and other functional materials that involve electron-phonon interaction. DOI: 10.1103/PhysRevX.3. 021011 Subject Areas: Computational Physics, Materials Science, Superconductivity
Data Mining on Symbolic Knowledge Extracted from the Web

Information extractors and classifiers operating on unrestricted, unstructured texts are an errorful source of large amounts of potentially useful information, especially when combined with a crawler which automatically augments the knowledge base from the world-wide web. At the same time, there is much structured information on the World Wide Web. Wrapping the web-sites which provide this kind of information provide us with a second source of information; possibly less up-to-date, but reliable as facts. We give a case study of combining information from these two kinds of sources in the context of learning facts about companies. We provide results of association rules, propositional and relational learning, which demonstrate that data-mining can help us improve our extractors, and that using information from two kinds of sources improves the reliability of data-mined rules.
A 25-year study of the clinical and histologic outcomes of hepatitis C virus infection and its modes of transmission in a cohort of initially asymptomatic blood donors.

BACKGROUND A total of 738 volunteer blood donors who were positive for anti-hepatitis C virus (HCV) were assessed for risk factors and outcomes for up to 15 years within the study and up to 54 years from the estimated onset of infection. METHODS A third-generation recombinant immunoblot assay (RIBA) was performed to distinguish true from false anti-HCV reactivity. Findings of HCV polymerase chain reaction classified subjects as having chronic HCV infection or as having recovered. Liver biopsy specimens were staged by Ishak fibrosis score and graded by histologic activity index. RESULTS Of 738 anti-HCV-positive subjects, 469 (64%) had positive RIBA results, 217 (29%) had negative results, and 52 (7%) had indeterminate results. Primary independent risk factors were injection drug use (odds ratio [OR], 35.0; P < .0001), blood transfusion (OR, 9.9; P < .0001), and intranasal cocaine use, including 79 "snorters" who repeatedly denied injection drug use or blood transfusion (OR, 8.5; P < .0001). Classification and regression tree and random forest analyses confirmed these risk factors. A total of 384 RIBA-positive donors (82%) were HCV RNA positive; of these, liver biopsy specimens from 185 (48%) showed no fibrosis in 33%, mild fibrosis in 52%, bridging fibrosis in 12%, and cirrhosis in 2% a mean duration of 25 years after infection. Analysis of 63 repeat biopsy specimens showed that 8% progressed ≥2 Ishak stages over 5 years (mean progression, 0.06 Ishak stages/year). CONCLUSIONS Injection drug use and blood transfusion before 1990 are dominant risk factors for HCV acquisition; intranasal cocaine use may be a surreptitious route of parenteral spread. After a mean of 25 years of HCV infection, histologic outcomes were relatively mild: 85% had no or mild fibrosis, and only 2% had cirrhosis. Nearly one-fifth spontaneously recovered.
Sickle cell disease in the United States: Looking back and forward at 100 years of progress in management and survival

The past 100 years since James Herrick's first description of sickle cell disease in the United States have been characterized by the gradual development of management strategies. We review the progress in sickle cell disease management in the United States over the past 100 years, with emphasis on the diverse forces surrounding advances in disease management. Mortality and survival data are presented chronologically, with an attempt to highlight improvements in survival associated with specific advancements for pediatric and adult care. Finally, the future course for sickle cell disease management is explored, given the continued work in advancing the field. Am. J. Hematol. 2010. © 2010 Wiley‐Liss, Inc.
Monetary Policy Analysis with Potentially Misspecified Models

The paper proposes a novel method for conducting policy analysis with potentially misspecified dynamic stochastic general equilibrium (DSGE) models and applies it to a New Keynesian DSGE model along the lines of Christiano, Eichenbaum, and Evans (JPE2005) and Smets and Wouters (JEEA2003). We first quantify the degree of model misspecification and then illustrate its implications for the performance of different interest-rate feedback rules. We find that many of the prescriptions derived from the DSGE model are robust to model misspecification.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

MOTIVATION ChIP-chip and ChIP-seq technologies provide genome-wide measurements of various types of chromatin marks at an unprecedented resolution. With ChIP samples collected from different tissue types and/or individuals, we can now begin to characterize stochastic or systematic changes in epigenetic patterns during development (intra-individual) or at the population level (inter-individual). This requires statistical methods that permit a simultaneous comparison of multiple ChIP samples on a global as well as locus-specific scale. Current analytical approaches are mainly geared toward single sample investigations, and therefore have limited applicability in this comparative setting. This shortcoming presents a bottleneck in biological interpretations of multiple sample data. RESULTS To address this limitation, we introduce a parametric classification approach for the simultaneous analysis of two (or more) ChIP samples. We consider several competing models that reflect alternative biological assumptions about the global distribution of the data. Inferences about locus-specific and genome-wide chromatin differences are reached through the estimation of multivariate mixtures. Parameter estimates are obtained using an incremental version of the Expectation-Maximization algorithm (IEM). We demonstrate efficient scalability and application to three very diverse ChIP-chip and ChIP-seq experiments. The proposed approach is evaluated against several published ChIP-chip and ChIP-seq software packages. We recommend its use as a first-pass algorithm to identify candidate regions in the epigenome, possibly followed by some type of second-pass algorithm to fine-tune detected peaks in accordance with biological or technological criteria. AVAILABILITY R source code is available at http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/. Access to Chip-seq data: GEO repository GSE17937.
Plant–Aphid Interactions Under Elevated CO2: Some Cues from Aphid Feeding Behavior

Although the increasing concentration of atmospheric carbon dioxide (CO2) accelerates the accumulation of carbohydrates and increases the biomass and yield of C3 crop plants, it also reduces their nitrogen concentration. The consequent changes in primary and secondary metabolites affect the palatability of host plants and the feeding of herbivorous insects. Aphids are phloem feeders and are considered the only feeding guild that positively responds to elevated CO2. In this review, we consider how elevated CO2 modifies host defenses, nutrients, and water-use efficiency by altering concentrations of the phytohormones jasmonic acid, salicylic acid, ethylene, and abscisic acid. We will describe how these elevated CO2-induced changes in defenses, nutrients, and water statusfacilitate specific stages of aphid feeding, including penetration, phloem-feeding, and xylem absorption. We conclude that a better understanding of the effects of elevated CO2 on aphids and on aphid damage to crop plants will require research on the molecular aspects of the interaction between plant and aphid but also research on aphid interactions with their intra- and inter-specific competitors and with their natural enemies.
The molecular machinery of myelin gene transcription in Schwann cells

During late fetal life, Schwann cells in the peripheral nerves singled out by the larger axons will transit through a promyelinating stage before exiting the cell cycle and initiating myelin formation. A network of extra‐ and intracellular signaling pathways, regulating a transcriptional program of cell differentiation, governs this progression of cellular changes, culminating in a highly differentiated cell. In this review, we focus on the roles of a number of transcription factors not only in myelination, during normal development, but also in demyelination, following nerve trauma. These factors include specification factors involved in early development of Schwann cells from neural crest (Sox10) as well as factors specifically required for transitions into the promyelinating and myelinating stages (Oct6/Scip and Krox20/Egr2). From this description, we can glean the first, still very incomplete, contours of a gene regulatory network that governs myelination and demyelination during development and regeneration. © 2008 Wiley‐Liss, Inc.
Mental Equilibrium and Rational Emotions

We model emotions as part of an equilibrium notion. In a mental equilibrium each player \selects" an emotional state that determines the player’s preferences over the outcomes of the game. These preferences typically dier from the players’ material preferences. The emotional states interact to play a Nash equilibrium and in addition each player’s emotional state must be a best response to the emotional states of the others (in the sense of maximazing material payos). We discuss the concept behind the denition of mental equilibrium and examine it in the context of some of the most popular games discussed in the experimental economics literature. We shall demonstrate the role of mental equilibrium in incentive mechanisms and discuss the concept of collective emotions, which is based on the idea that players can coordinate their emotional states.
Fabry-Perot laser diode modeling

A model of a single-mode Fabry-Perot semiconductor laser that predicts laser performance in analog transmission has been developed. The model is based on a time domain simulation of the rate equations for a semiconductor laser. The model can be used to simulate laser characteristics such as light versus current, step response, harmonic and intermodulation distortion. Simulated distortion results agree with experimentally measured results. <<ETX>>
Elasto-plastic impact of fine particles and fragmentation of small agglomerates

Surface deposition of dense aerosol particles is of major concern in the nuclear industry for safety assessment. This study presents theoretical investigations and computer simulations of single gas-born U3O8 particles impacting with the in-reactor surface and the fragmentation of small agglomerates. A theoretical model for elasto-plastic spheres has been developed and used to analyse the force-displacement and force-time relationships. The impulse equations, based on Newton's second law, are applied to govern the tangential bouncing behaviour. The theoretical model is then incorporated into the Distinct Element Method code TRUBAL in order to perform computer simulated tests of particle collisions. A comparison of simulated results with both theoretical predictions and experimental measurements is provided. For oblique impacts, the results in terms of the force-displacement relationship, coefficients of restitution, trajectory of the impacting particle, and distribution of kinetic energy and work done during the process of impact are presented. The effects of Poisson's ratio, friction, plastic deformation and initial particle rotation on the bouncing behaviour are also discussed. In the presence of adhesion an elasto-plastic collision model, which is an extension to the JKR theory, is developed. Based on an energy balance equation the critical sticking velocity is obtained. For oblique collisions computer simulated results are used to establish a set of criteria determining whether or not the particle bounces off the target plate. For impact velocities above the critical sticking value, computer simulated results for the coefficients of restitution and rebound angles of the particle are presented. Computer simulations of fracture/fragmentation resulting from agglomerate-wall impact have also been performed, where two randomly generated agglomerates (one monodisperse, the other polydisperse), each consisting of 50 primary particles are used. The effects of impact angle, local structural arrangements close to the impact point, and plastic deformation at the contacts on agglomerate damage are examined. The simulated results show a significant difference in agglomerate strength between the two assemblies. The computer data also shows that agglomerate damage resulting from an oblique impact is determined by the normal velocity component rather than the impact speed.
Selective Accumulation of Raft-Associated Membrane Protein Lat in T Cell Receptor Signaling Assemblies

Activation of T cell antigen receptor (TCR) induces tyrosine phosphorylations that mediate the assembly of signaling protein complexes. Moreover, cholesterol-sphingolipid raft membrane domains have been implicated to play a role in TCR signal transduction. Here, we studied the assembly of TCR with signal transduction proteins and raft markers in plasma membrane subdomains of Jurkat T leukemic cells. We employed a novel method to immunoisolate plasma membrane subfragments that were highly concentrated in activated TCR–CD3 complexes and associated signaling proteins. We found that the raft transmembrane protein linker for activation of T cells (LAT), but not a palmitoylation-deficient non-raft LAT mutant, strongly accumulated in TCR-enriched immunoisolates in a tyrosine phosphorylation–dependent manner. In contrast, other raft-associated molecules, including protein tyrosine kinases Lck and Fyn, GM1, and cholesterol, were not highly concentrated in TCR-enriched plasma membrane immunoisolates. Many downstream signaling proteins coisolated with the TCR/LAT-enriched plasma membrane fragments, suggesting that LAT/TCR assemblies form a structural scaffold for TCR signal transduction proteins. Our results indicate that TCR signaling assemblies in plasma membrane subdomains, rather than generally concentrating raft-associated membrane proteins and lipids, form by a selective protein-mediated anchoring of the raft membrane protein LAT in vicinity of TCR.
Divergence and gene flow in the globally distributed blue‐winged ducks

The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence-with-gene-flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue-winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub-lineages, the globally-distributed shoveler group and the New World blue-winged/cinnamon teal group. The blue-winged/cinnamon sub-lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler A. clypeata and the more sedentary, African Cape shoveler A. smithii into the Australasian shoveler A. rhynchotis, although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue-winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.
The Salmonella effector protein SpvC, a phosphothreonine lyase is functional in plant cells

Salmonella is one of the most prominent causes of food poisoning and growing evidence indicates that contaminated fruits and vegetables are an increasing concern for human health. Successful infection demands the suppression of the host immune system, which is often achieved via injection of bacterial effector proteins into host cells. In this report we present the function of Salmonella effector protein in plant cell, supporting the new concept of trans-kingdom competence of this bacterium. We screened a range of Salmonella Typhimurium effector proteins for interference with plant immunity. Among these, the phosphothreonine lyase SpvC attenuated the induction of immunity-related genes when present in plant cells. Using in vitro and in vivo systems we show that this effector protein interacts with and dephosphorylates activated Arabidopsis Mitogen-activated Protein Kinase 6 (MPK6), thereby inhibiting defense signaling. Moreover, the requirement of Salmonella SpvC was shown by the decreased proliferation of the ΔspvC mutant in Arabidopsis plants. These results suggest that some Salmonella effector proteins could have a conserved function during proliferation in different hosts. The fact that Salmonella and other Enterobacteriaceae use plants as hosts strongly suggests that plants represent a much larger reservoir for animal pathogens than so far estimated.
Urodynamics in women from menopause to oldest age: what motive? What diagnosis?

PURPOSE To analyze age-associated changes as a motive for urodynamics and urodynamic diagnosis in community-dwelling menopausal women and to discuss the role of menopause and ageing. MATERIALS AND METHODS Four hundred and forty nine consecutive menopausal women referred for urodynamic evaluation of lower urinary tract (LUT) symptoms, met the inclusion criteria and were stratified into 3 age groups: 55-64 years (A), 65-74 years (B), and 75-93 years (C). Comprehensive assessment included previous medical history and clinical examination. Studied items were motive for urodynamics, results of uroflows (free flow and intubated flow) and cystometry, urethral pressure profilometry, and final urodynamic diagnosis. RESULTS The main motive was incontinence (66.3%) with significant increase of mixed incontinence in group C (p = 0.028). Detrusor function significantly deteriorated in the oldest group, mainly in absence of neurological disease (overactivity p = 0.019; impaired contractility p = 0.028). In the entire population, underactivity predominated in group C (p = 0.0024). A progressive decrease of maximum urethral closure pressure occurred with ageing. In subjects with no detrusor overactivity there was a decrease with age of detrusor pressure at opening and at maximum flow, and of maximum flow while post void residual increased only in the C group. CONCLUSION In our population of community-dwelling menopausal women, incontinence was the main motive for urodynamics increasing with ageing. A brisk change in LUT function of women older than 75 years underlined deterioration in bladder function with a high incidence of detrusor hyperactivity with or without impaired contractility while change in urethral function was progressive. Effect of ageing appears to be predominant compared to menopause.
An algorithm for the extraction of static features from 3D Flash LADAR datasets: Supporting navigation in GPS challenged environments

3D Flash LADAR cameras provide ranging information at a high frame rate, offering the opportunity to navigate from imaged features. This requires the identification of common features from multiple images acquired from different positions. It is necessary to determine if the features exhibit a static condition, such that moving elements in the imageries are not utilized as part of the navigation solution. Extending previous research (ION April 2006, ION September 2006) in the utilization of implicit polynomials for feature extraction, a new algorithmic approach for the extraction of static and non-static features is exhibited.