julilili42/papers huggingface dataset:
Nephroblastoma: does the decrease in tumor volume under preoperative chemotherapy predict the lymph nodes status at surgery?
2011-04-29

Abstract Background Partial nephrectomy (NSS) for unilateral nephroblastoma may be beneficial, although in case of regional lymph node (LN) involvement, radiotherapy counteracts the functional benefit of NSS. The aim is to verify whether decrease of tumor volume under preoperative chemotherapy implies clearance of regional LN. Procedure SIOP 9301 (1993–2001) collected 1,450 localized nephroblastoma patients of whom 1,360 (93%) had sufficiently available data and were retrospectively reviewed. Results Histologic subtypes were classically distributed. Patients were divided in those with tumor positive LN (76, 5.5%) and those with tumor negative LN (1,284, 94.5%) at surgery. In the LN(+) group, the tumor volume changed from a median of 554 (318–772) to 192 (63–458) ml = 67% (27–88%) during preoperative ChT. In the LN(−) group—377 (200–612) to 130 (44–294) ml = 62% (28–83%) (NS). Increase of tumor volume was observed in 16% of patients with LN(+), and 11% of those with LN(−) (NS); ranges are interquartile. Initial tumor volume was significantly larger in the LN(+) patients ( P = 0.00091) but not different (NS) at surgery; patients with initial tumor volume under 318 ml had the regional LN involved significantly less frequently ( P = 0.00751). Conclusions Change in tumor volume under preoperative chemotherapy is not a predictor for LN status at surgery, although larger initial volume is associated with a higher risk of LN invasion. The decrease of tumor volume is not a good criterion for the safety of NSS. The low rate of LN(+) (5.5%) indicates that this risk is low. Pediatr Blood Cancer 2011; 57: 1266–1269. © 2011 Wiley Periodicals, Inc.
Degeneration of the mouse retina upon dysregulated activity of serum response factor.
2011-04-29

This is the first report suggesting an influence of the transcription factor SRF on the development and function of the murine retina. Ectopic SRF-VP16 mRNA expression in the retinas of young animals is correlated with photoreceptor layer mislamination and impaired retinal function. At an advanced age of six months, degenerative processes are detected in SRF-VP16 transgenic retinas accompanied by impaired retinal function. The Gt(ROSA)26Sor(tm1(SRF-VP16)Antu) mouse strain represents a genetic SRF gain-of-function mouse model that will complement the current SRF loss-of-function models. It promises to provide new insight into the hitherto poorly defined role of SRF in retinal development and function, including potential contributions to ophthalmologic disorders. Furthermore, using conditional Cre-mediated activation of SRF-VP16, the described mouse strain will enable assessment of the impact of dysregulated SRF activity on the physiologic functions of various other organs.
Alternative (non-animal) methods for cosmetics testing: current status and future prospects—2010
2011-04-30

The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take at least another 7-9 years for the replacement of the current in vivo animal tests used for the safety assessment of cosmetic ingredients for skin sensitisation. However, the experts were also of the opinion that alternative methods may be able to give hazard information, i.e. to differentiate between sensitisers and non-sensitisers, ahead of 2017. This would, however, not provide the complete picture of what is a safe exposure because the relative potency of a sensitiser would not be known. For toxicokinetics, the timeframe was 5-7 years to develop the models still lacking to predict lung absorption and renal/biliary excretion, and even longer to integrate the methods to fully replace the animal toxicokinetic models. For the systemic toxicological endpoints of repeated dose toxicity, carcinogenicity and reproductive toxicity, the time horizon for full replacement could not be estimated.
Language Effects on Children’s Nonverbal Number Line Estimations
2011-05-01

The mental number line of children is usually assumed to be language-independent; however, this independency has not yet been studied. In this cross-cultural study, we examined the influence of language properties on a nonverbal version of the number line task in Italian- and German-speaking first graders. The essential difference between the two languages concerns the inversion property of most German multi-digit numbers (e.g., 48 → “eight-and-forty”), whereas in Italian number-words no inversion is found. The analyses revealed two language-specific differences in the number line task: (a) Generally, the estimates of Italian children were more accurate than those of Austrian children, even when controlling for general cognitive abilities. (b) Italian children performed particularly better when inversion errors led to large estimation errors. In conclusion, these findings indicate that the organization of children’s mental number line is indeed influenced by language properties even in nonverbal settings.
Does Staphylococcus Aureus Nasal Colonization Involve Biofilm Formation?
2011-05-01

The human anterior nares are used by Staphylococcus aureus as the major colonization site in 20-30% of the human population. Eradication of S. aureus carriage can significantly reduce the numbers of nosocomial infections. However, the interactions governing the colonization process have remained elusive and it has been debated whether S. aureus adopts a biofilm-like state in the nose. We summarize recent studies on staphylococcal living conditions during nasal colonization, which favour a dispersed rather than a biofilm-related mode of growth during S. aureus nasal colonization. This notion is of major importance for future directions in the development of new decolonization strategies.
Extending SILAC to Proteomics of Plant Cell Lines
2011-05-01

Abstract Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) is a widespread method for metabolic labeling of cells and tissues in quantitative proteomics; however, incomplete incorporation of the label has so far restricted its wider use in plants. Here, we argue that differential labeling by two different versions of the labeled amino acids renders SILAC fully applicable to dark-grown plant cell lines. By comparing Arabidopsis thaliana cell cultures labeled with two versions of heavy Lys (Lys-4 and Lys-8), we show that this simple modification of the SILAC protocol enables similar quantitation accuracy, precision, and reproducibility as conventional SILAC in animal cells.
Endoluminal full-thickness resection of GI lesions: A new device and technique
2011-05-01

Full-thickness resection techniques are of growing interest in the field of endoscopic removal of tumors or their precursors in the digestive tract. A new dedicated full-thickness resection device has been developed based on the combination of the OTSC clip, an enlarged resection cap and an integrated snare. The device prototype allows combined resection of all gastrointestinal organ wall layers in one maneuver, up to a size of 3 x 3 cm. The device has been pre-clinically tested to demonstrate feasibility of full-thickness resection in the colon. Two clinical cases have been performed successfully to date.
New material ofGilmoremys lancensisnov. comb. (Testudines: Trionychidae) from the Hell Creek Formation and the diagnosis of plastomenid turtles
2011-05-01

Plastomenidae is a poorly diagnosed clade of extinct soft-shelled turtles (Trionychidae) known from the Campanian to Eocene of North America. Five skulls, a mandible, two carapaces, and numerous plastral remains from the Hell Creek Formation (Late Cretaceous, Maastrichtian) of North Dakota and Montana are referable to Gilmoremys lancensis nov. comb., a taxon previously known from a carapace and xiphiplastron only. Gilmoremys lancensis is diagnosed by a carapace that is covered by elongate sinusoidal grooves, distally expanded second costals, hyoplastral shoulders, an extensive secondary palate with accessory ridges, an extremely elongate mandible, a contribution of the parietal to the wall of the orbit, and a posterior ossified narial canal. A phylogenetic analysis of all well-known plastomenid turtles establishes Gilmoremys lancensis as the most basal known plastomenid and reveals that cranial characters are more reliable in diagnosing plastomenid turtles, in particular the contribution of the parietal to the orbit wall and the extensive secondary palate. All plastomenid turtles with a locked entoplastron are placed in Hutchemys. Assuming that all taxa are monophyletic, the phylogenetic analysis implies that the G. lancensis lineage is the only one to go extinct at the K/T boundary, whereas the four remaining plastomenid lineages survive. Extensive ghost ranges are nevertheless apparent. Taphonomic considerations indicate that G. lancensis was a riverine turtle, whereas more derived plastomenids preferred swampy habitats.
Milestones in magnetic resonance imaging and transcranial sonography of movement disorders
2011-05-01

Abstract Twenty‐five years ago, when this journal was initiated, imaging of movement disorders was in its infancy. Since that time, magnetic resonance imaging has become a standard technique that is routinely performed in patients with movement disorders in order to exclude secondary causes and in some instances to provide specific information that aids in making the diagnosis of a neurodegenerative condition. Transcranial sonography is a more recent advance and is now widely employed to aid in the diagnosis of Parkinson's disease and possibly in detecting individuals in the premotor phases of the disease. Investigations are currently under way to evaluate the value of this technique in other movement disorders. © 2011 Movement Disorder Society
Anatomy of the human cochlea – implications for cochlear implantation
2011-05-01

Since the classical description by Retzius in 1884, many extensive studies of the micro-anatomy of the human cochlea have been presented. The human cochlea is one of the most difficult tissues to study due to the bony capsule and its delicate contents. Most preparations suffer from post-mortem changes caused by the delay between demise and fixation. For over a decade, we have analyzed human inner-ear tissue obtained at surgery using transmission electron microscopy, scanning electron microscopy, in vitro culture, and immunohistochemistry. These studies show the value of these techniques for fine structural and molecular analyses. Modern cochlear implant surgery requires that ear surgeons are familiar with the intricate anatomy of the human cochlea and its variations. The classical technique to insert electrode arrays through a drilled cochleostomy has been abandoned by some surgeons today. Instead a round-window approach can be used as originally implemented by William House for short electrodes. This so-called 'hook' region of the cochlea presents extensive anatomical variations that can be difficult to foresee on pre-operative computed tomography. CI depends on the functional status of remaining spiral ganglion neurons. These cells are more or less preserved in CI patients but how the conservation influences the outcome of CI is debatable. Notwithstanding their preservation is crucial and more information should be attained about their deterioration and how it can be prevented. Better understanding of structure, function, and regenerative capability is needed to comprehend the nature of electrical stimulation of the peripheral and central nervous system to improve the design of future implant systems.
Differential Language Effects on Numerical Skills in Second Grade
2011-05-01

Little is known about the causes of cross-cultural specifics of numerical development. The authors examined effects of inversion (a linguistic effect) on three different numerical tasks in 220 second graders from France, Wallonia, Flanders, Germany, and Austria tested for the standardization of the dyscalculia test TEDI-MATH. Results revealed that performance differences between countries are only partly attributable to language effects, but group differences in recognition of unit- and decade-digits and subtraction are more likely due to curricular effects. As expected, language effects due to the inversion principle could be observed in writing Arabic numbers to dictation affecting performance both specifically as well as in a generalized way being present in different error types. These results clearly show that numerical skills do not develop in a unitary fashion and that cross-cultural differences can be due to several factors.
Modeling the long‐term and transient evolution of biogeochemical and isotopic signatures in coal tar–contaminated aquifers
2011-05-01

Reactive transport modeling is a critical element in assessing the potential of natural attenuation of groundwater pollutants. In the present study, we developed a comprehensive quantitative model that incorporates the key processes affecting the long‐term fate of complex organic compound mixtures released from coal tar–type dense nonaqueous phase liquid sources. The model framework addresses the simulation of the long‐term dynamics of source zone depletion, the fate of the released compounds during reactive transport in the groundwater, the evolution of the aquifer's biogeochemical response, in particular its redox conditions, and the redox‐dependent carbon isotope fractionation of selected organic compounds. The modeling framework was applied for the interpretation of observed biogeochemical and isotopic data from a well‐characterized coal tar–contaminated site in northern Germany. The simulations highlight the diversity of fates of the individual compounds, which result from their widely varying physicochemical characteristics, and also how complex interactions develop over the lifetime of the contamination. The highly transient release of contaminants from the coal tar as pool and as heterogeneously distributed blobs in the source zone triggers continuously changing biogeochemical conditions and isotope signatures. The modeling results illustrate how difficult and uncertain the assessment of contaminant fate can be if the collected data cover only a small time window relative to the transport time scale. This emphasizes the need for a holistic understanding of the governing processes that control the effectiveness of monitored natural attenuation before it is implemented as a passive remediation strategy at nonaqueous phase liquid–contaminated sites.
EFFECTIVE HAMILTONIANS FOR THIN DIRICHLET TUBES WITH VARYING CROSS-SECTION
2011-05-01

We show how to translate recent results on effective Hamiltonians for quantum\\nsystems constrained to a submanifold by a sharply peaked potential to quantum\\nsystems on thin Dirichlet tubes. While the structure of the problem and the\\nform of the effective Hamiltonian stays the same, the difficulties in the\\nproofs are different.\\n
Mapping of specific sentinel node locations for skin cancer of the head
2011-05-01

In current dermatological practice lymphatic mapping and sentinel lymph node biopsy (SLNB) are frequently used in patients with cutaneous cancers, like malignant melanoma, squamous cell carcinoma and Merkel cell carcinoma. However, those tumors are often located on the head and neck, regions with notoriously variable lymphatic drainage patterns. Consequently, the incidence of successful SLNB in the head and neck is considerably lower compared to the SLNB on the trunk and extremities. Thus, there is a need to improve the hit rate of SLNB in this special area. Therefore, in the current study we analyzed SLNB of 149 patients treated for cutaneous tumors at the Department of Dermatology, University of Tuebingen, Germany. By mapping SLN (sentinel lymph node) locations to their specific tumor sites on the head and neck, we were able to calculate the frequency of SLN distribution to defined tumor locations. Furthermore, our analysis revealed that approximately 7% of tumors on the head and neck drain to contralateral SLN, which is of relevance for the classification in the current cancer TNM system. Thus, our mapping can predict SLN location in patients with cutaneous head and neck tumors and might help to further increase the rate of successful SLNB.
Field-portable Mössbauer spectroscopy on Earth, the Moon, Mars, and beyond
2011-05-01

Iron occurs naturally as Fe2+, Fe3+, and, to a lesser extent, as Fe0. Many fundamental (bio)geochemical processes are based on redox cycling between these oxidation states. M&amp;ouml;ssbauer spectroscopy provides quantitative information about the distribution of Fe among its oxidation states, identification of Fe-bearing phases, and relative distribution of Fe among those phases. Portable, miniaturised M&amp;ouml;ssbauer spectrometers were developed for NASA&amp;rsquo;s Mars Exploration Rovers (in operation since 2004) and provide a means for non-destructive, in-situ field investigations. On Mars, these instruments provided evidence for aqueous activity with implications for habitability, were applied in geological mapping of the landing sites, and helped to identify meteorites, for example. On Earth, they were used in field studies of green rust, the identification of air pollution sources, or the study of archaeological artefacts. Their application to in-situ resource utilisation (ISRU) on the Moon has been demonstrated in a recent NASA field test of hardware for oxygen production. A new detector system in an advanced version of these instruments is based on Si Drift Detectors and permits the simultaneous acquisition of X-ray fluorescence spectra to determine elemental compositions.
Vertical structure of the outer accretion disk in persistent low-mass X-ray binaries
2011-05-01

We have investigated the influence of X-ray irradiation on the vertical structure of the outer accretion disk in low-mass X-ray binaries by performing a self-consistent calculation of the vertical structure and X-ray radiation transfer in the disk. Penetrating deep into the disk, the field of scattered X-ray photons with energy \\,keV exerts a significant influence on the vertical structure of the accretion disk at a distance \\,cm from the neutron star. At a distance \\,cm, where the total surface density in the disk reaches \\,g\\,cm , X-ray heating affects all layers of an optically thick disk. The X-ray heating effect is enhanced significantly in the presence of an extended atmospheric layer with a temperature \\,K above the accretion disk. We have derived simple analytic formulas for the disk heating by scattered X-ray photons using an approximate solution of the transfer equation by the Sobolev method. This approximation has a \\,% accuracy in the range of X-ray photon energies \\,keV.
Cooperative visual mapping in a heterogeneous team of mobile robots
2011-05-01

Mapping is regarded as one of the most fundamental tasks for mobile robots. In this work, we present an approach that enables multiple resource-limited mobile robots to cooperatively build an image-based map of the environment and to afterwards localize in it. To achieve this, we deploy a hierarchical team of mobile robots. A parent robot possesses state-of-the-art sensors, computation power and acts as a leader. It teleoperates small child robots within its line-of-sight. In contrast to other approaches and due to the cooperation among the robots, we can relax the requirement that every robot must be able to self-localize to take part in multi-robot mapping. Additionally, our algorithm ensures the mapping of the entire area in an efficient way, i.e., it fulfills the requirements of area coverage. To test our approach, extensive experiments have been performed both in simulation and real-world. In the latter case, a team of four heterogeneous mobile robots was deployed. Besides the successful cooperation in the robot team, localization results are presented to validate the applicability of the proposed mapping procedure.
Animations of Medical Training Scenarios in Immersive Virtual Environments
2011-05-01

Medical training centers often provide various simulations for students and professionals. Their goal is not only to make trainees practice specific scenarios but also to help them effectively transfer the acquired skills to the real world. Having in mind that virtual environments have already been acknowledged for their potential to improve the medical training process, we propose an approach for rapid generation of animated medical scenarios, which can be used as an additional training tool that fits into the time frame of a semester training program.
Novel regulatory SNPs in the promoter region of the TNFRSF18 gene in a Gabonese population
2011-05-01

Parasites are accountable for driving diversity within immune gene families. We identified and investigated regulatory single nucleotide polymorphisms (SNPs) in the promoter regions of the tumor necrosis factor receptor superfamily member 18 (TNFRSF18) gene by direct sequencing in a group of male Gabonese individuals exposed to a wide array of parasitic diseases such as malaria, filariasis and schistosomiasis. Two new promoter variants were identified in 40 individuals. Both novel variants were heterozygous and were linked to SNP #rs3753344 (C/T), which has been described. One of the SNP variants (ss2080581728) was close to the general transcription factor site, the TATA box. We further validated these new promoter variants for their allelic gene expression using transient transfection assays. One new promoter variant with two base changes (C/T - ss2080581728/rs3753344) displayed an altered expression of the marker gene. Both novel variants remained less active at the non-induced state in comparison to the major allele. The allele frequencies observed in this study were consistent with data for other African populations. The detection and analysis of these human immune gene polymorphisms contribute to a better understanding of the interaction between host-parasite and expression of Treg activity.
Imidazolium Dicyanoargentates
2011-05-01

New imidazolium dicyanoargentate salts were synthesized by treatment of 2-chloro-1,3-diisopropyl-4,5-dimethylimidazolium chloride (2a) with an excess of silver cyanide in acetonitrile to afford 2-chloro-1,3-diisopropyl-4,5-dimethylimidazolium dicyanoargentate (3) and its conversion into the corresponding 2-cyano-1,3-diisopropyl-4,5-dimethylimidazolium dicyanoargentate (4) by reaction with an excess amount of potassium cyanide. The crystal structures of 3 and 4 are reported
6DoF Registration of 2D Laser Scans
2011-05-01

We address the problem of registering a set of 2D laser scans in 3D space with regard to six degrees of freedom. Registering single 2D scans is only possible when making strong assumptions on the structure of the scene or on the acquisition process, since only a slice of the 3D environment is captured and the information content is very limited. With a combination of two differently oriented laser scanners, however, the registration problem becomes feasible. We present a method that is based on the idea of preserving the free space represented in each of these combined scans. On realistically simulated laser range data we show that, given a sufficient sampling density, the proposed algorithm is capable to recover from large translational and moderate rotational errors in the initial configuration.