julilili42/papers huggingface dataset:
The four-population model: a new classification scheme for pre-planetesimal collisions
2011-07-07

\\n Context. Within the collision growth scenario for planetesimal formation, the growth step from centimetre-sized pre-planetesimals to kilometre-sized planetesimals remains unclear. The formation of larger objects from the highly porous pre-planetesimals may be halted by a combination of fragmentation in disruptive collisions and mutual rebound with compaction. However, the right amount of fragmentation is necessary to explain the observed dust features in late T Tauri discs. Therefore, detailed data on the outcome of pre-planetesimal collisions is required and has to be presented in a suitable and precise format.\\n Aims. We wish to develop a new classification scheme broad enough to encompass all events with sticking, bouncing, and fragmentation contributions, accurate enough to capture the important collision outcome nuances, and at the same time simple enough to be implementable in global dust coagulation simulations. We furthermore wish to demonstrate the reliability of our numerical smoothed particle hydrodynamics (SPH) model and the applicability of our new collision outcome classification to previous results as well as our simulation results.\\n Methods. We propose and apply a scheme based on the quantitative aspects of four fragment populations: the largest and second largest fragment, a power-law population, and a sub-resolution population. For the simulations of pre-planetesimal collisions, we adopt the SPH numerical scheme with extensions for the simulation of porous solid bodies. On the basis of laboratory benchmark experiments, this model was previously calibrated and tested for the correct simulation of the compaction, bouncing, and fragmentation behaviour of macroscopic highly porous SiO2 dust aggregates.\\n Results. We demonstrate that previous attempts to map collision data were much too oriented on qualitatively categorising into sticking, bouncing, and fragmentation events. Intermediate categories are found in our simulations that are difficult to map to existing qualitative categorisations. We show that the four-population model encompasses all previous categorisations and in addition allows for transitions. This is because it is based on quantitative characteristic attributes of each population such as the mass, kinetic energy, and filling factor. In addition, the numerical porosity model successfully passes another benchmark test: the correct simulation of the entire list of collision outcome types yielded by laboratory experiments. As a demonstration of the applicability and the power of the four-population model, we utilise it to present the results of a study on the influence of collision velocity in head-on collisions of intermediate porosity aggregates.\\n
Opposite Effects of Cortisol on Consolidation of Temporal Sequence Memory during Waking and Sleep
2011-07-07

Abstract Memory functions involve three stages: encoding, consolidation, and retrieval. Modulating effects of glucocorticoids (GCs) have been consistently observed for declarative memory with GCs enhancing encoding and impairing retrieval, but surprisingly, little is known on how GCs affect memory consolidation. Studies in rats suggest a beneficial effect of GCs that were administered during postlearning wake periods, whereas in humans, cortisol impaired memory consolidation when administered during postlearning sleep. These inconsistent results raise the question whether effects of GCs critically depend on the brain state during consolidation (sleep vs. wake). Here, we compare for the first time directly the effects of cortisol on memory consolidation during postlearning sleep and wakefulness in different measures of declarative memory. Cortisol (13 mg vs. placebo) was intravenously infused during a postlearning nap or a time-matched period of wakefulness after participants had encoded neutral and emotional text material. Memory for the texts was tested (a) by asking for the contents of the texts (“item” memory) and (b) for the temporal order of the contents within the texts (“relational” memory). Neither postlearning infusion of cortisol during sleep nor during wakefulness affected retention of content words of emotional or neutral texts. Critically, however, the retention of temporal order within the texts, known to rely most specifically on the hippocampus proper within the medial-temporal lobe memory system, was distinctly improved by cortisol infusion during the wake phase but impaired by cortisol during sleep. These results point toward fundamentally different mechanisms of hippocampal memory consolidation, depending on the brain state.
WAVE INTERACTIONS IN LOCALIZING MEDIA — A COIN WITH MANY FACES
2011-07-08

A variety of heterogeneous potentials are capable of localizing linear noninteracting waves. In this work, we review different examples of heterogeneous localizing potentials which were realized in experiments. We then discuss the impact of nonlinearity induced by wave interactions, in particular, its destructive effect on the localizing properties of the heterogeneous potentials.
PRESERVATIVE-FREE TRIAMCINOLONE ACETONIDE INJECTABLE SUSPENSION VERSUS “TRADITIONAL” TRIAMCINOLONE PREPARATIONS
2011-07-09

Retinal cytotoxicity of TA seems only to occur when there is intimate contact of TA crystals with the cellular membrane. Cytotoxicity depends on the number and size of TA crystal aggregates-with larger conglomerates being more harmful. Of the TA formulations tested, triamcinolone acetonide injectable suspension had the strongest tendency to form large TA crystal conglomerates and to gravitate downward.
Quasinormal modes of black holes: From astrophysics to string theory
2011-07-11

Perturbations of black holes, initially considered in the context of possible\\nobservations of astrophysical effects, have been studied for the past ten years\\nin string theory, brane-world models and quantum gravity. Through the famous\\ngauge/gravity duality, proper oscillations of perturbed black holes, called\\nquasinormal modes (QNMs), allow for the description of the hydrodynamic regime\\nin the dual finite temperature field theory at strong coupling, which can be\\nused to predict the behavior of quark-gluon plasmas in the nonperturbative\\nregime. On the other hand, the brane-world scenarios assume the existence of\\nextra dimensions in nature, so that multidimensional black holes can be formed\\nin a laboratory experiment. All this stimulated active research in the field of\\nperturbations of higher-dimensional black holes and branes during recent years.\\nIn this review recent achievements on various aspects of black hole\\nperturbations are discussed such as decoupling of variables in the perturbation\\nequations, quasinormal modes (with special emphasis on various numerical and\\nanalytical methods of calculations), late-time tails, gravitational stability,\\nAdS/CFT interpretation of quasinormal modes, and holographic superconductors.\\nWe also touch on state-of-the-art observational possibilities for detecting\\nquasinormal modes of black holes.\\n
Nonlinear waves in disordered chains: Probing the limits of chaos and spreading
2011-07-11

We probe the limits of nonlinear wave spreading in disordered chains which are known to localize linear waves. We particularly extend recent studies on the regimes of strong and weak chaos during subdiffusive spreading of wave packets [Europhys. Lett. 91, 30001 (2010)] and consider strong disorder, which favors Anderson localization. We probe the limit of infinite disorder strength and study Fröhlich-Spencer-Wayne models. We find that the assumption of chaotic wave packet dynamics and its impact on spreading is in accord with all studied cases. Spreading appears to be asymptotic, without any observable slowing down. We also consider chains with spatially inhomogeneous nonlinearity, which give further support to our findings and conclusions.
Male Mating Rate Is Constrained by Seminal Fluid Availability in Bedbugs, Cimex lectularius
2011-07-11

Sexual selection, differences in reproductive success between individuals, continues beyond acquiring a mating partner and affects ejaculate size and composition (sperm competition). Sperm and seminal fluid have very different roles in sperm competition but both components encompass production costs for the male. Theoretical models predict that males should spend ejaculate components prudently and differently for sperm and seminal fluid but empirical evidence for independent variation of sperm number and seminal fluid volume is scarce. It is also largely unknown how sperm and seminal fluid variation affect future mating rate. In bedbugs we developed a protocol to examine the role of seminal fluids in ejaculate allocation and its effect on future male mating rate. Using age-related changes in sperm and seminal fluid volume we estimated the lowest capacity at which mating activity started. We then showed that sexually active males allocate 12% of their sperm and 19% of their seminal fluid volume per mating and predicted that males would be depleted of seminal fluid but not of sperm. We tested (and confirmed) this prediction empirically. Finally, the slightly faster replenishment of seminal fluid compared to sperm did not outweigh the faster decrease during mating. Our results suggest that male mating rate can be constrained by the availability of seminal fluids. Our protocol might be applicable to a range of other organisms. We discuss the idea that economic considerations in sexual conflict research might benefit from distinguishing between costs and benefits that are ejaculate dose-dependent and those that are frequency-dependent on the mating rate per se.
Prospective evaluation of serum tissue inhibitor of metalloproteinase 1 and carbonic anhydrase IX in correlation to circulating tumor cells in patients with metastatic breast cancer
2011-07-11

Abstract Introduction Circulating tumor cells (CTCs) reflect aggressive tumor behavior by hematogenous tumor cell dissemination. The tissue inhibitor of metalloproteinase 1 (TIMP-1) plays a role in tissue invasion and is also involved in angiogenesis, abrogation of apoptosis and in chemoresistance. Carbonic anhydrase IX (CAIX) is a metalloenzyme involved in cell adhesion, growth and survival of tumor cells. The aim of the study was to investigate whether serum concentrations of TIMP-1 and CAIX are associated with the detection of CTC in metastatic breast cancer. Methods Blood was obtained in a prospective multicenter setting from 253 patients with metastatic breast cancer at the time of disease progression. Serum TIMP-1 and CAIX were determined using commercial ELISA-kits (Oncogene Science). CTC were detected with the CellSearchTM system (Veridex). Results Five or more CTCs were detected in 122 patients out of 245 evaluable patients (49.8%). Out of 253 metastatic patients 70 (28%) had serum TIMP-1 levels above 454 ng/mL. Serum CAIX was elevated above 506 ng/mL in 90 (35%) patients. Both serum markers had prognostic significance. Median progression free survival (PFS) was 7.2 months with elevated TIMP-1 vs. 11.4 months with non-elevated levels (p &lt; 0.01). OS was 11.5 vs. 19.1 months (p &lt; 0.01). Median PFS was 7.5 months with elevated CAIX vs. 11.7 months with non-elevated levels (p &lt; 0.01), overall survival (OS) was 13.4 months vs. 19.1 months (p &lt; 0.01). In patients with five or more CTCs, serum levels were above the cut-off for CAIX in 47% vs. 25% in those with less than five CTCs (p = 0.01). For TIMP-1, 37% patients with five or more CTCs had elevated serum levels and 17% of patients with less than five CTCs (p = 0.01). Including TIMP-1, CAIX, CTC and established prognostic factors in the multivariate analysis, the presence of CTCs, the therapy line and elevated CAIX remained independent predictors of OS. Conclusions Elevated serum levels of the invasion markers TIMP-1 and CAIX in metastatic breast cancer are prognostic markers and are associated with the presence of CTCs. Whether increased secretion of TIMP-1 and/or CAIX might directly contribute to tumor cell dissemination remains to be elucidated in further investigations. Trial registration Current Controlled Trials: ISRCTN59722891
Acetazolamide-responsive exercise-induced episodic ataxia associated with a novel homozygous DARS2 mutation: Figure 1
2011-07-11

Background Leukoencephalopathy with brain stem and spinal cord involvement and brain lactate elevation (LBSL) was recently shown to be caused by mutations in the DARS2 gene, encoding a mitochondrial aspartyl-tRNA synthetase. So far, affected individuals were invariably compound heterozygous for two mutations in DARS2 , and drug treatments have remained elusive. Methods Prospective 2-year follow-up of the natural history of the main presenting symptoms in a homozygous DARS2 mutation carrier, followed by a 60 day treatment with acetazolamide in two different doses and with two random treatment interruptions. Results The patient presented with exercise-induced paroxysmal gait ataxia and areflexia as an atypical phenotype associated with a novel homozygous DARS2 mutation. These features showed an excellent dose-dependent, sustained treatment response to a carbonic anhydrase inhibitor. Pathogenic mutations in episodic ataxia genes were excluded, thus making it highly unlikely that this phenotype was because of episodic ataxia as a second disorder besides LBSL. Conclusions This case demonstrates that DARS2 mutation homozygosity is not lethal, as suggested earlier, but compatible with a rather benign disease course. More importantly, it extends the phenotypic spectrum of LBSL and reveals that at least some DARS2 -associated phenotypic features might be readily treatable. However, future observations of paroxsymal ataxia and, possibly, areflexia in other DARS2 -mutated patients are warranted to further corroborate our finding that DARS2 mutations can lead to a paroxsymal ataxia phenotype.
Efficient Colonization and Therapy of Human Hepatocellular Carcinoma (HCC) Using the Oncolytic Vaccinia Virus Strain GLV-1h68
2011-07-11

Virotherapy using oncolytic vaccinia virus strains is one of the most promising new strategies for cancer therapy. In this study, we analyzed for the first time the therapeutic efficacy of the oncolytic vaccinia virus GLV-1h68 in two human hepatocellular carcinoma cell lines HuH7 and PLC/PRF/5 (PLC) in cell culture and in tumor xenograft models. By viral proliferation assays and cell survival tests, we demonstrated that GLV-1h68 efficiently colonized, replicated in, and did lyse these cancer cells in culture. Experiments with HuH7 and PLC xenografts have revealed that a single intravenous injection (i.v.) of mice with GLV-1h68 resulted in a significant reduction of primary tumor sizes compared to uninjected controls. In addition, replication of GLV-1h68 in tumor cells led to strong inflammatory and oncolytic effects resulting in intense infiltration of MHC class II-positive cells like neutrophils, macrophages, B cells and dendritic cells and in up-regulation of 13 pro-inflammatory cytokines. Furthermore, GLV-1h68 infection of PLC tumors inhibited the formation of hemorrhagic structures which occur naturally in PLC tumors. Interestingly, we found a strongly reduced vascular density in infected PLC tumors only, but not in the non-hemorrhagic HuH7 tumor model. These data demonstrate that the GLV-1h68 vaccinia virus may have an enormous potential for treatment of human hepatocellular carcinoma in man.
Who Took the “×” out of Expectancy-Value Theory?
2011-07-12

Expectancy-value theory (EVT) is a dominant theory of human motivation. Historically, the Expectancy × Value interaction, in which motivation is high only if both expectancy and value are high, was central to EVT. However, the Expectancy × Value interaction mysteriously disappeared from published research more than 25 years ago. Using large representative samples of 15-year-olds ( N = 398,750) from 57 diverse countries, we attempted to solve this mystery by testing Expectancy × Value interactions using latent-variable models with interactions. Expectancy (science self-concept), value (enjoyment of science), and the Expectancy × Value interaction all had statistically significant positive effects on both engagement in science activities and intentions of pursuing scientific careers; these results were similar for the total sample and for nearly all of the 57 countries considered separately. This study, apparently the strongest cross-national test of EVT ever undertaken, supports the generalizability of EVT predictions—including the “lost” Expectancy × Value interaction.
Calpain and PARP Activation during Photoreceptor Cell Death in P23H and S334ter Rhodopsin Mutant Rats
2011-07-12

Retinitis pigmentosa (RP) is a heterogeneous group of inherited neurodegenerative diseases affecting photoreceptors and causing blindness. Many human cases are caused by mutations in the rhodopsin gene. An important question regarding RP pathology is whether different genetic defects trigger the same or different cell death mechanisms. To answer this question, we analysed photoreceptor degeneration in P23H and S334ter transgenic rats carrying rhodopsin mutations that affect protein folding and sorting respectively. We found strong activation of calpain and poly(ADP-ribose) polymerase (PARP) in both mutants, concomitant with calpastatin down-regulation, increased oxidative DNA damage and accumulation of PAR polymers. These parameters were strictly correlated with the temporal progression of photoreceptor degeneration, mirroring earlier findings in the phosphodiesterase-6 mutant rd1 mouse, and suggesting execution of non-apoptotic cell death mechanisms. Interestingly, activation of caspases-3 and -9 and cytochrome c leakage-key events in apoptotic cell death--were observed only in the S334ter mutant, which also showed increased expression of PARP-1. The identification of the same metabolic markers triggered by different mutations in two different species suggests the existence of common cell death mechanisms, which is a major consideration for any mutation independent treatment.
In Vitro Activity against Staphylococcus aureus of a Novel Antimicrobial Agent, PRF-119, a Recombinant Chimeric Bacteriophage Endolysin
2011-07-12

ABSTRACT Antistaphylococcal activity of the novel chimeric endolysin PRF-119 was evaluated with the microdilution method. The MIC 50 and MIC 90 of 398 methicillin-susceptible Staphylococcus aureus isolates were 0.098 μg/ml and 0.391 μg/ml, respectively (range, 0.024 to 0.780 μg/ml). Both the MIC 50 and MIC 90 values of 776 methicillin-resistant S. aureus isolates were 0.391 μg/ml (range, 0.024 to 1.563 μg/ml). All 192 clinical isolates of coagulase-negative staphylococci exhibited MIC values of &gt;50 μg/ml. In conclusion, PRF-119 exhibited very good activity specifically against S. aureus .
Cortical processing of near-threshold tactile stimuli in a paired-stimulus paradigm - an MEG study
2011-07-12

In the present magnetoencephalography study, we applied a paired-stimulus paradigm to study the weak cortical responses evoked by near-threshold tactile prime stimuli by means of their attenuating effect on the cortical responses evoked by subsequently applied above-threshold test stimuli. In stimulus pairs with adequate interstimulus intervals (ISIs), the extent of test stimulus response attenuation is related to the amplitude of prime stimulus responses, and the duration of the attenuating effect indicates how long memory traces of a prime stimulus reside in cortical areas. We hypothesized that the attenuation of test stimulus responses, studied for ISIs of 30, 60 and 150 ms, would provide insight into the temporal dynamics of near-threshold stimulus processing in primary (SI) and secondary somatosensory cortex (SII), and reveal differences in response amplitude due to conscious perception. Attenuation of test stimulus responses in SI was observed for ISIs up to 60 ms, whereas in SII the effect outlasted the ISI of 150 ms. Differences due to conscious perception of the near-threshold stimuli were only observed in SII with stronger attenuation for perceived than for missed near-threshold stimuli. Applying this indirect approach to near-threshold stimulus processing, we could show that the extent and duration of response attenuation is related to prime stimulus processing and differential temporal and functional characteristics of near-threshold stimulus information processing in SI and SII: transient processing of basic stimulus information not sufficient for conscious perception in SI and long-lasting activations involving conscious perception in SII.
A Screening Assay Based on Host-Pathogen Interaction Models Identifies a Set of Novel Antifungal Benzimidazole Derivatives
2011-07-12

ABSTRACT Fungal infections are a serious health problem in clinics, especially in the immune-compromised patient. Disease ranges from widespread superficial infections like vulvovaginal infections to life-threatening systemic candidiasis. Especially for systemic mycoses, only a limited arsenal of antifungals is available. The most commonly used classes of antifungal compounds used include azoles, polyenes, and echinocandins. Due to emerging resistance to standard therapy, significant side effects, and high costs for several antifungals, there is a medical need for new antifungals in the clinic and general practice. In order to expand the arsenal of compounds with antifungal activities, we screened a compound library including more than 35,000 individual compounds derived from organic synthesis as well as combinatorial compound collections representing mixtures of compounds for antimycotic activity. In total, more than 100,000 compounds were screened using a new type of activity-selectivity assay, analyzing both the antifungal activity and the compatibility with human cells at the same time. One promising hit, an ( S )-2-aminoalkyl benzimidazole derivative, was developed among a series of lead compounds showing potent antifungal activity. ( S )-2-(1-Aminoisobutyl)-1-(3-chlorobenzyl) benzimidazole showed the highest antifungal activity and the best compatibility with human cells in several cell culture models and against a number of clinical isolates of several species of pathogenic Candida yeasts. Transcriptional profiling indicates that the newly discovered compound is a potential inhibitor of the ergosterol pathway, in contrast to other benzimidazole derivatives, which target microtubules.
Rapid inward migration of planets formed by gravitational instability
2011-07-13

The observation of massive exoplanets at large separation from their host star, like in the HR 8799 system, challenges theories of planet formation. A possible formation mechanism involves the fragmentation of massive self-gravitating discs into clumps. While the conditions for fragmentation have been extensively studied, little is known of the subsequent evolution of these giant planet embryos, in particular their expected orbital migration. Assuming a single planet has formed by fragmentation, we investigate its interaction with the gravitoturbulent disc it is embedded in. Two-dimensional hydrodynamical simulations are used with a simple prescription for the disc cooling. A steady gravitoturbulent disc is first set up, after which simulations are restarted including a planet with a range of masses approximately equal to the clump's initial mass expected in fragmenting discs. Planets rapidly migrate inwards, despite the stochastic kicks due to the turbulent density fluctuations. We show that the migration timescale is essentially that of type I migration, with the planets having no time to open a gap. In discs with aspect ratio ~ 0.1 at their forming location, planets with a mass comparable to, or larger than Jupiter's can migrate in as short as 10000 years, that is, about 10 orbits at 100 AU. Massive planets formed at large separation from their star by gravitational instability are thus unlikely to stay in place, and should rapidly migrate towards the inner parts of protoplanetary discs, regardless of the planet mass.