julilili42/papers huggingface dataset:
Surgery for primary CNS lymphoma? Challenging a paradigm
2012-09-14

The standard of care for primary central nervous system lymphoma (PCNSL) is systemic chemotherapy with or without whole brain radiotherapy or intrathecal chemotherapy. In contrast to treatment for other brain tumors, efforts at resection are discouraged. This is a secondary analysis of the German PCNSL Study Group-1 trial, a large randomized phase III study comprising 526 patients with PCNSL. Progression-free survival (hazard ratio [HR]: 1.39; 95% confidence interval [CI]: 1.10-1.74; P = .005) and overall survival (HR: 1.33; 95% CI: 1.04-1.70; P = .024) were significantly shorter in biopsied patients compared with patients with subtotal or gross total resections. This difference in outcome was not due to age or Karnofsky performance status (KPS). When controlled for the number of lesions, the HR of biopsy versus subtotal or gross total resection remained unchanged for progression-free survival (HR = 1.37; P = .009) but was smaller for overall survival (HR = 1.27; P = .085). This analysis of the largest PCNSL trial ever performed challenges the traditional view that the extent of resection has no prognostic impact on this disease. Therefore, we propose to reconsider the statement that efforts at resection should be discouraged, at least if resection seems safe, as is often the case in treatment of single PCNSL lesions.
The use of motion information in multiple object tracking
2012-09-14

In multiple-object tracking participants track several moving target objects among identical distractor objects (Pylyshyn & Storm, 1988). Recently it was shown, that the human visual system uses motion information for keeping track of targets. A texture on an object that moved in the opposite direction than the object impaired tracking performance (St. Clair, Huff, & Seiffert, 2010). In this study, we examined the temporal interval at which motion information is integrated in dynamic scenes.
Moonlighting osteoclasts as undertakers of apoptotic cells
2012-09-15

Rapid clearance of apoptotic cells, frequently referred to as efferocytosis, is crucial for the maintenance of tissue homeostasis and the prevention of autoimmunity. The common model of apoptotic cell clearance involves a system of released "Find me" and exposed "Eat me" signals on apoptotic cells, detected and recognized by matching receptors on macrophages or dendritic cells (DC), referred to as the phagocytic synapse. Osteoclasts share the monocyte lineage with these professional mononuclear phagocytes, thus raising the question if, in addition to bone resorption, osteoclasts can act as scavengers for apoptotic cells. Our qPCR data clearly show that osteoclasts express most of the genes required for dying cell clearance at mRNA levels similar to or even higher than those observed in M1-macrophages, M2-macrophages or DC. Our microscopical analyses reveal that osteoclasts in fact can bind and/or engulf apoptotic cells in an essentially serum-independent fashion. Together with our data on the abundance of the respective mRNAs, these results identify the vitronectin receptor (integrin α(ν)β(3))/milk fat globule-EGF factor 8 protein (MFG-E8) axis, the scavenger receptors (CD36, CD68 and class A macrophage scavenger receptor (SR-A)), the complement/complement receptor axis, the Mer/Tyro3/Protein S axis, and the phosphatidylserine (PS) receptor brain-specific angiogenesis inhibitor 1 (BAI1) as the most promising candidates to be involved in osteoclast-mediated efferocytosis.
Contributors to individual quality of life after liver transplantation
2012-09-15

Eur J Clin Invest 2012 Abstract Background With increasing improvements of patient survival after liver transplantation, the focus on outcome measures shifts from survival rate to quality of life. Individual quality of life is crucial to rehabilitate patients after transplantation. Therefore, it is important to identify specific issues that contribute to high individual quality of life. In contrast to the Short form 36 Health Survey (SF‐36), the Schedule for the Evaluation of Individual aspects of Quality of Life‐direct weighting (SEIQoL‐DW) allows patients to name the areas of life, which are important to them. Design In a semi‐structured interview style, 71 patients following liver transplant were asked to complete the SEIQoL‐DW and the SF‐36 in a cross‐sectional design. Results We found five quality of life areas that were chosen by more than half of the patients: family, friends, sports, partnership and profession/occupation. Health was only mentioned by 45% of all patients. Individual quality of life did not differ from healthy population. In the SF‐36, patients showed normal mental health parameters but reduced physical components. A strong correlation between SEIQoL‐DW‐Index and the mental component summary of the SF‐36 was observed. Conclusion In addition to the widely used standardized SF‐36, the individual measure SEIQoL‐DW shows new aspects concerning the areas of quality of life, which are personally important to the participants. Less than half of our patients mentioned health and the five most nominated areas are not related to health. By focusing on health, the importance of health‐related factors is overrated, and the impact of non‐medical effects is underrepresented.
Sleep-dependency of episodic-like memory consolidation in rats
2012-09-16

Episodic memory refers to the recollection of a representation that binds together into a unique past experience "what" happened, "where" and "when". Sleep has been identified as a state that optimizes the consolidation of newly acquired memory. To determine if sleep is important for the consolidation of episodic-like memory, we tested rats on an episodic-like memory task requiring the binding of an object memory into a spatio-temporal context, as well as retention of its individual components, using separate tests of novel-object recognition ("what"), object-place recognition ("where") and temporal memory ("when"), respectively. The 80-min retention interval between encoding of the task and retrieval testing covered either a period of regular morning sleep or sleep deprivation or a period of evening wakefulness. Sleep during the retention interval, compared with the other two retention conditions, significantly enhanced retrieval in the episodic-like memory task as well as in the object-place recognition and temporal memory tasks. In fact, when the rats stayed awake during the retention interval, there was no significant memory left at retrieval testing for the learnt object place and temporal memory. Sleep did not benefit novel-object recognition memory which unlike the other components of episodic-like memory is considered not to critically rely on the hippocampus. In an additional delayed sleep condition, episodic-like memory in rats which had stayed awake during the first 80-min interval after encoding, was not recovered when they were allowed to sleep during a subsequent 80-min interval. Our results suggest that sleep specifically supports the aspects in episodic memory most closely linked to hippocampal function, i.e., the binding of an event into spatio-temporal context as well as the spatio-temporal context itself. Sleep is particularly effective when it occurs shortly after encoding.
Factorial, convergent, and discriminant validity of timss math and science motivation measures: A comparison of Arab and Anglo-Saxon countries.
2012-09-17

For the international Trends in International Mathematics and Science Study (TIMSS2007) math and science motivation scales (self-concept, positive affect, and value), we evaluated the psychometric properties (factor structure, method effects, gender differences, and convergent and discriminant validity) in 4 Arab-speaking countries (Saudi Arabia, Jordan, Oman, and Egypt) and 4 English-speaking Anglo-Saxon countries (United States, England, Australia, and Scotland). In this article, we also highlight methodological weaknesses in the TIMSS approach to these motivation measures. We found reasonable support for within-group invariance across the math and science domains and between-group invariance across countries for full factor loading invariance and partial item intercept invariance. However, the factor structure is complicated by strong negative-item method effects and correlated unique characteristics associated with the use of math and science items with parallel wording. Correlations involving the motivation factors were reasonably similar across countries, supporting both discriminant and convergent validity in relation to achievement, plans to take more coursework in math and science, and long-term educational aspirations. However, gender differences largely favor girls in the Arab countries (with strong single-sex education systems) relative to Anglo countries (and international norms). The juxtapositions of latent mean differences in achievement and motivation factors are perplexing; students from Anglo countries had substantially higher achievement than students from Arab countries but had substantially lower motivation across all 8 math and science factors.
Radiative properties of magnetic neutron stars with metallic surfaces and thin atmospheres
2012-09-17

The goal of this work is to develop a simple analytic description of the emission properties (spectrum and polarization) of the condensed, strongly magnetized surface of neutron stars. We have improved the method of van Adelsberg et al. (2005) (arXiv:astro-ph/0406001) for calculating the spectral properties of condensed magnetized surfaces. Using the improved method, we calculate the reflectivity of an iron surface at magnetic field strengths B \\sim (10^{12} - 10^{14}) G, with various inclinations of the magnetic field lines and radiation beam with respect to the surface and each other. We construct analytic expressions for the emissivity of this surface as functions of the photon energy, magnetic field strength, and the three angles that determine the geometry of the local problem. Using these expressions, we calculate X-ray spectra for neutron stars with condensed iron surfaces covered by thin partially ionized hydrogen atmospheres. We develop simple analytic descriptions of the intensity and polarization of radiation emitted or reflected by condensed iron surfaces of neutron stars with strong magnetic fields typical for isolated neutron stars. This description provides boundary conditions at the bottom of a thin atmosphere, which are more accurate than previously used approximations. The spectra calculated with this improvement show absorption features different from those in simplified models. The approach developed in this paper yields results that can facilitate modeling and interpretation of the X-ray spectra of isolated, strongly magnetized, thermally emitting neutron stars.
Coding of Melodic Gestalt in Human Auditory Cortex
2012-09-17

The perception of a melody is invariant to the absolute properties of its constituting notes, but depends on the relation between them-the melody's relative pitch profile. In fact, a melody's "Gestalt" is recognized regardless of the instrument or key used to play it. Pitch processing in general is assumed to occur at the level of the auditory cortex. However, it is unknown whether early auditory regions are able to encode pitch sequences integrated over time (i.e., melodies) and whether the resulting representations are invariant to specific keys. Here, we presented participants different melodies composed of the same 4 harmonic pitches during functional magnetic resonance imaging recordings. Additionally, we played the same melodies transposed in different keys and on different instruments. We found that melodies were invariantly represented by their blood oxygen level-dependent activation patterns in primary and secondary auditory cortices across instruments, and also across keys. Our findings extend common hierarchical models of auditory processing by showing that melodies are encoded independent of absolute pitch and based on their relative pitch profile as early as the primary auditory cortex.
The development of standard samples with a defined number of antigen-specific T cells to harmonize T cell assays: a proof-of-principle study
2012-09-17

The validation of assays that quantify antigen-specific T cell responses is critically dependent on cell samples that contain clearly defined measurable numbers of antigen-specific T cells. An important requirement is that such cell samples are handled and analyzed in a comparable fashion to peripheral blood mononuclear cells (PBMC). We performed a proof-of-principle study to show that retrovirally TCR-transduced T cells spiked at defined numbers in autologous PBMC can be used as standard samples for HLA/peptide multimer staining. NY-ESO-1157-165-specific, TCR-transduced CD8+ T cell batches were successfully generated from PBMC of several HLA-A*0201 healthy donors, purified by magnetic cell sorting on the basis of HLA tetramer (TM) staining and expanded with specific antigen in vitro. When subsequently spiked into autologous PBMC, the detection of these CD3+CD8+TM+ T cells was highly accurate with a mean accuracy of 91.6 %. The standard cells can be preserved for a substantial period of time in liquid nitrogen. Furthermore, TM staining of fresh and cryopreserved standard samples diluted at decreasing concentrations into autologous cryopreserved unspiked PBMC revealed that the spiked CD3+CD8+TM+ T cells could be accurately detected at all dilutions in a linear fashion with a goodness-of-fit of over 0.99 at a frequency of at least 0.02 % among the CD3+CD8+ T cell population. Notably, the CD3+CD8+TM+ cells of the standard samples were located exactly within the gates used to analyze patient samples and displayed a similar scatter pattern. The performance of the cryopreserved standard samples in the hands of 5 external investigators was good with an inter-laboratory variation of 32.9 % and the doubtless identification of one outlier.
Multifunctional silica nanoparticles for optical and magnetic resonance imaging
2012-09-17

Abstract The surface of spherical, nonporous silica nanoparticles (SiO 2 -NPs) was modified with gadolinium (Gd) complexes, fluorophores, and cell-penetrating peptides to achieve multifunctionality on a single particle. The Gd surface concentrations were 9–16 μmol/g resulting in nanomaterials with high local longitudinal and transversal relaxivities (~1×10 5 and ~5×10 5 /mm/s/NP, respectively). Rapid cellular uptake was observed in vitro ; however, larger extracellular agglomerates were also formed. In vivo administration revealed a fast distribution throughout the body followed by a nearly complete disappearance of fluorescence in all organs except the lungs, liver, and spleen after 24 h. Such NPs have the potential to serve as efficient multimodal probes in molecular imaging.
Assyria At War: Strategy and Conduct
2012-09-18

Abstract This article examines Assyria's military strategy and conduct of war. It argues that the rise of Assyria can be explained by the peculiar historical setting of the later tenth century and the developments leading to it. It explains that the Assyrian kings used their armies cautiously and successfully, giving their troops a lead in numbers, experience, and competence, and they maintained these advantages for no less than three centuries. It describes the sources and the ideal image of the king at war and comments on the battle reports of kings.
Increased Apoptosis Induction in Hepatocellular Carcinoma by a Novel Tumor-Targeted TRAIL Fusion Protein Combined With Bortezomib
2012-09-18

As the result of an increasing incidence and a prevalent therapy resistance of hepatocellular carcinoma (HCC), there is a strong need for novel strategies to enhance treatment responses in HCC. Tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) has been proposed as a promising anticancer drug because it can selectively induce apoptosis in cancer cells, but not in healthy cells. Nevertheless, most tumor cells show TRAIL resistance, emphasizing the requirement for apoptosis-sensitizing agents and TRAIL molecules with improved tumor specificity. In this study, we employed a recombinant TRAIL molecule, in which three TRAIL protomers were expressed as a single polypeptide chain (scTRAIL), and a novel TRAIL variant, in which scTRAIL was additionally fused to an antibody fragment recognizing epidermal growth factor receptor (EGFR) to improve its HCC-targeting properties. We analyzed the proapoptotic effects of both TRAIL versions in combination with the proteasome inhibitor bortezomib (BZB) in hepatoma cells and primary human hepatocytes as well as in intact explants from HCC and healthy liver tissue. We demonstrate that EGFR-targeted TRAIL in combination with BZB induced significantly higher caspase activation and cell death in hepatoma cells, but not in primary hepatocytes. Importantly, when incubated with fresh liver explants, the combination of EGFR-targeted TRAIL and BZB displayed selective cytotoxicity for HCC, but not for tumor-free liver tissue, which could even be verified in liver explants from the same individuals. Unlike nontargeted TRAIL, EGFR-targeted TRAIL combined with BZB exerted no toxicity in liver tissues from nonalcoholic fatty liver disease patients. Conclusion: EGFR-targeted TRAIL reveals increased antitumor activity toward HCC without inducing toxicity to tumor-free liver tissue and might therefore represent a promising novel strategy for HCC treatment.
Toward a Brain-Computer Interface for Alzheimer's Disease Patients by Combining Classical Conditioning and Brain State Classification
2012-09-18

Brain-computer interfaces (BCIs) provide alternative methods for communicating and acting on the world, since messages or commands are conveyed from the brain to an external device without using the normal output pathways of peripheral nerves and muscles. Alzheimer's disease (AD) patients in the most advanced stages, who have lost the ability to communicate verbally, could benefit from a BCI that may allow them to convey basic thoughts (e.g., "yes" and "no") and emotions. There is currently no report of such research, mostly because the cognitive deficits in AD patients pose serious limitations to the use of traditional BCIs, which are normally based on instrumental learning and require users to self-regulate their brain activation. Recent studies suggest that not only self-regulated brain signals, but also involuntary signals, for instance related to emotional states, may provide useful information about the user, opening up the path for so-called "affective BCIs". These interfaces do not necessarily require users to actively perform a cognitive task, and may therefore be used with patients who are cognitively challenged. In the present hypothesis paper, we propose a paradigm shift from instrumental learning to classical conditioning, with the aim of discriminating "yes" and "no" thoughts after associating them to positive and negative emotional stimuli respectively. This would represent a first step in the development of a BCI that could be used by AD patients, lending a new direction not only for communication, but also for rehabilitation and diagnosis.
Recurrent nodules in a periauricular plaque‐type blue nevus with fatal outcome
2012-09-18

Plaque‐type blue nevus is a rare variant of blue nevus characterized by grouped nodules displaying histomorphological features of a cellular blue nevus. We report the clinical, histopathologic and immunohistologic features of a patient with recurrent nodules in a periauricular plaque‐type blue nevus with malignant transformation and fatal outcome. The nevus was characterized clinically by childhood onset, with slow enlargement during adolescence. At age 16, the patient presented with nodules located retroauricularly. Several surgical excisions with the intent of complete removal of the nodules and the nevus were performed. Histopathological, dermal and subcutaneous proliferations of pigmented melanocytes with melanophages were detected. The nodules showed some cellular atypia and few mitotic figures, (Ki67 estimated &lt;1%). At age 20, the patient developed new nodules retroauricular, with histopathology similar to previous lesions; however, the proliferation rate was higher. A comparative genomic hybridization (CGH) showed chromosomal changes indicative of melanoma. At age 25, the patient developed multiple liver metastases and died after 4 weeks. A sequencing of the tumor DNA revealed a GNAQ Q209P mutation, whereas mutations of GNA11 , BRAF , NRAS and cKIT were not detected. This case shows that nodules in plaque‐type blue nevus may have malignant potential which may be uncovered by CGH.
Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation
2012-09-19

Abstract We conducted a genome-wide association study to identify novel associations between genetic variants and circulating plasminogen activator inhibitor-1 (PAI-1) concentration, and examined functional implications of variants and genes that were discovered. A discovery meta-analysis was performed in 19 599 subjects, followed by replication analysis of genome-wide significant (P &lt; 5 × 10−8) single nucleotide polymorphisms (SNPs) in 10 796 independent samples. We further examined associations with type 2 diabetes and coronary artery disease, assessed the functional significance of the SNPs for gene expression in human tissues, and conducted RNA-silencing experiments for one novel association. We confirmed the association of the 4G/5G proxy SNP rs2227631 in the promoter region of SERPINE1 (7q22.1) and discovered genome-wide significant associations at 3 additional loci: chromosome 7q22.1 close to SERPINE1 (rs6976053, discovery P = 3.4 × 10−10); chromosome 11p15.2 within ARNTL (rs6486122, discovery P = 3.0 × 10−8); and chromosome 3p25.2 within PPARG (rs11128603, discovery P = 2.9 × 10−8). Replication was achieved for the 7q22.1 and 11p15.2 loci. There was nominal association with type 2 diabetes and coronary artery disease at ARNTL (P &lt; .05). Functional studies identified MUC3 as a candidate gene for the second association signal on 7q22.1. In summary, SNPs in SERPINE1 and ARNTL and an SNP associated with the expression of MUC3 were robustly associated with circulating levels of PAI-1.
Pronounced Peramorphosis in Lissamphibians—Aviturus exsecratus (Urodela, Cryptobranchidae) from the Paleocene–Eocene Thermal Maximum of Mongolia
2012-09-19

The presence of these characteristics indicates a peramorphic developmental pattern for Aviturus exsecratus. Our results from Av. exsecratus indicate for the first time pronounced peramorphosis within a crown-group lissamphibian. Av. exsecratus represents a new developmental trajectory within both fossil and recent lissamphibian clades characterized by extended ontogeny and large body size, resembling the pattern known from late Paleozoic eryopines. Moreover, Av. exsecratus is not only a cryptobranchid with distinctive peramorphic characters, but also the first giant salamander with partially terrestrial (amphibious) lifestyle. The morphology of the vomers and dentaries suggests the ability of both underwater and terrestrial feeding.