julilili42/papers huggingface dataset:
New Tumor Biomarkers in Ovarian Cancer and Its Prognostic and Clinical Relevance
2012-02-17

In Europe and the United States, ovarian cancer is currently the major cause of death from gynecological malignancy. Up to 60% ovarian cancer patients die from locally advanced disease. Nonetheless, even patients treated with optimal cytoreduction may subsequently suffer from metastatic disease. Since treatment strategies are developed to control locoregional cancer growth, it may be anticipated that more patients will die of distant metastases. The lack of early disease signals further contributes to the fact that only onefourth of ovarian cancers are identified at stage I. Ovarian cancer remains thus undetected due to late symptoms and the lack of reliable and clinically applicable screening tools. Further, the identification of new biomarkers could optimize prediction and monitoring of anticancer therapies and provide insights into ovarian cancer progression. Presence of disseminated tumor cells (DTC) in bone marrow is a common phenomenon observed in solid epithelial tumors. As shown by a multi-center analysis of bone marrow (BM) specimens from more than 4,700 patients, DTC detection at the time of breast cancer diagnosis is strongly correlated with poor clinical outcome (level-I-evidence) [1]. There is growing evidence that hematogenous tumor cell dissemination may occur in other tumors, such as prostate, colon and gynecologic malignancies. DTC, as surrogate parameter for occult hematogenous spread, are routinely detected in 22-51% ovarian cancer patients. Interestingly, ovarian metastases to the bone are only rarely observed [2], [3], [4]. Whether bone marrow serves in these patients as a temporary compartment from where persistent DTC are able to migrate, remains unclear. It has been demonstrated that dissemination of isolated tumor cells to secondary sites occurs as early as in FIGO stage I disease [4]. Single tumor cells acquire thus the potential to disseminate to extraperitoneal compartments early in the process of the disease. Of all prognostic factors, monitoring of minimal residual disease is the only one available after the tumor has been removed. Beside monitoring of tumor markers, there is currently a major effort to identify other biological markers which can be assessed with minimally invasive methods and persist beyond surgery. We previously reported on a significant correlation of positive bone marrow status with shortened relapse-free survival in ovarian cancer patients [5]. DTC persistence after completion of platinum-based chemotherapy was also found to be prognostically relevant [6]. Further, the identification of molecular biomarkers may represent excellent targets for new treatment strategies for chemoresistant
Therapeutic Potential of Small Molecules Modulating the Cyclooxygenase–5‐Lipoxygenase Pathway
2012-02-17

This chapter contains sections titled: Introduction Targets of the Eicosanoid Pathway Rationale for Development of Dual Inhibitors of the Cyclooxygenase–5-Lipoxygenase Pathway Dual Inhibitors of the Cyclooxygenase–5-Lipoxygenase Pathway Development of Licofelone Conclusions References
Chitosan oligosaccharide as prospective cross-linking agent for naproxen-loaded Ca-alginate microparticles with improved pH sensitivity
2012-02-18

The obtained findings proved that COS could be used as an effective cross-linking agent for improvement of Ca-alginate microparticles stability in SIF, allowing prolonged release of the encapsulated drug after oral administration.
Models, forests and trees of York English: Was/were variation as a case study for statistical practice
2012-02-19

What is the explanation for vigorous variation between was and were in plural existential constructions and what is the optimal tool for analyzing it? The standard variationist tool — the variable rule program — is a generalized linear model; however, recent developments in statistics have introduced new tools, including mixed-effects models, random forests and conditional inference trees. In a step-by-step demonstration, we show how this well known variable benefits from these complementary techniques. Mixed-effects models provide a principled way of assessing the importance of random-effect factors such as the individuals in the sample. Random forests provide information about the importance of predictors, whether factorial or continuous, and do so also for unbalanced designs with high multicollinearity, cases for which the family of linear models is less appropriate. Conditional inference trees straightforwardly visualize how multiple predictors operate in tandem. Taken together the results confirm that polarity, distance from verb to plural element and the nature of the DP are significant predictors. Ongoing linguistic change and social reallocation via morphologization are operational. Furthermore, the results make predictions that can be tested in future research. We conclude that variationist research can be substantially enriched by an expanded tool kit
XMMU J0541.8-6659, a new supernova remnant in the Large Magellanic Cloud
2012-02-20

\\n Context. The high sensitivity of the XMM-Newton instrumentation offers the opportunity to study faint and extended sources in the Milky Way and nearby galaxies such as the Large Magellanic Cloud (LMC) in detail. The ROSAT PSPC survey of the LMC has revealed more than 700 X-ray sources, among which there are 46 supernova remnants (SNRs) and candidates.\\n Aims. We have observed the field around one of the most promising SNR candidates in the ROSAT PSPC catalogue, labelled [HP99] 456 with XMM-Newton, to determine its nature.\\n Methods. We investigated the XMM-Newton data along with new radio-continuum, near infrared and optical data. In particular, spectral and morphological studies of the X-ray and radio data were performed.\\n Results. The X-ray images obtained in different energy bands reveal two different structures. Below 1.0 keV the X-ray emission shows the shell-like morphology of an SNR with a diameter of ~73 pc, one of the largest known in the LMC. For its thermal spectrum we estimate an electron temperature of (0.49 ± 0.12) keV assuming non-equilibrium ionisation. The X-ray images above 1.0 keV reveal a less extended source within the SNR emission, located 1′ west of the centre of the SNR and coincident with bright point sources detected in radio-continuum. This hard component has an extent of 0.9′ (i.e. ~13 pc at a distance of ~50 kpc) and a non-thermal spectrum. The hard source coincides in position with the ROSAT source [HP99] 456 and shows an indication for substructure. \\n Conclusions. We firmly identify a new SNR in the LMC with a shell-like morphology and a thermal spectrum. Assuming the SNR to be in the Sedov phase yields an age of ~23 kyr. We explore possible associations of the hard non-thermal emitting component with a pulsar wind nebula (PWN) or background active galactic nucleus (AGN). \\n
In memoriam Antonio Prevosti (1919-2011), a pioneer of genetics of natural populations
2012-02-20

Prof. Dr. Antonio Prevosti was born on the 15th of February, 1919, at Barcelona where he grew up and lived with his wife Maria Monclús and his family until his death. Between the years 1939 and 1942 he registered at the University of Barcelona and finished his studies there with the"University Degree in Natural Science" obtaining the extraordinary award of his promotion. Immediately afterwards he started his research about the growth rate of Barcelona school children from two very different social groups at the Anthropology Laboratory of the University of Barcelona. The obtained results were published in his Doctoral Thesis (1948). Further investigations on quantitative traits in human populations improved his knowledge of statistical analyses and provided the basis for a scholarship from the Italian Ministry of Foreign Affairs to work at the Institute of Statistical and Demographical Sciences in Rome directed by Prof. C. Gini.
Cell-cycle-regulated expression of STIL controls centriole number in human cells
2012-02-21

Control of centriole number is crucial for genome stability and ciliogenesis. Here, we characterize the role of human STIL, a protein that displays distant sequence similarity to the centriole duplication factors Ana2 in Drosophila and SAS-5 in Caenorhabditis elegans. Using RNA interference, we show that STIL is required for centriole duplication in human cells. Conversely, overexpression of STIL triggers the near-simultaneous formation of multiple daughter centrioles surrounding each mother, which is highly reminiscent of the phenotype produced by overexpression of the polo-like kinase PLK4 or the spindle assembly abnormal protein 6 homolog (SAS-6). We further show, by fluorescence and immunoelectron microscopy, that STIL is recruited to nascent daughter centrioles at the onset of centriole duplication and degraded, in an APC/CCdc20–Cdh1-dependent manner, upon passage through mitosis. We did not detect a stable complex between STIL and SAS-6, but the two proteins resemble each other with regard to both localization and cell cycle control of expression. Thus, STIL cooperates with SAS-6 and PLK4 in the control of centriole number and represents a key centriole duplication factor in human cells.
The Cerebro-Morphological Fingerprint of a Progeroid Syndrome: White Matter Changes Correlate with Neurological Symptoms in Xeroderma Pigmentosum
2012-02-21

The most prominent feature was the white matter affectation, as assessed by DTI, with volume and directionality reductions of the fiber projections involving both the craniocaudal fibers and the interhemispheric connections. These findings, although heterogeneous among the study sample, could be correlated with the clinico-neurological symptoms. The imaging findings support the position that myelin structures degrade prematurely in the brain of XP patients.
Leaf surface structures enable the endemic Namib desert grass Stipagrostis sabulicola to irrigate itself with fog water
2012-02-22

The Namib grass Stipagrostis sabulicola relies, to a large degree, upon fog for its water supply and is able to guide collected water towards the plant base. This directed irrigation of the plant base allows an efficient and rapid uptake of the fog water by the shallow roots. In this contribution, the mechanisms for this directed water flow are analysed. Stipagrostis sabulicola has a highly irregular surface. Advancing contact angle is 98° ± 5° and the receding angle is 56° ± 9°, with a mean of both values of approximately 77°. The surface is thus not hydrophobic, shows a substantial contact angle hysteresis and therefore, allows the development of pinned drops of a substantial size. The key factor for the water conduction is the presence of grooves within the leaf surface that run parallel to the long axis of the plant. These grooves provide a guided downslide of drops that have exceeded the maximum size for attachment. It also leads to a minimum of inefficient drop scattering around the plant. The combination of these surface traits together with the tall and upright stature of S. sabulicola contributes to a highly efficient natural fog-collecting system that enables this species to thrive in a hyperarid environment.
Perioperative Outcome of Patients with Congenital Diaphragmatic Hernia Undergoing Open Versus Minimally Invasive Surgery
2012-02-22

Median values of pCO(2 max) in the postoperative course were significantly lower in the minimally invasive surgery group. In addition, postoperative ventilation time was shorter when children underwent minimally invasive surgery. In conclusion, minimally invasive surgery seems to offer advantages for selected patients with CDH.
miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases
2012-02-22

Abstract Background Expression profiling provides new insights into regulatory and metabolic processes and in particular into pathogenic mechanisms associated with diseases. Besides genes, non-coding transcripts as microRNAs (miRNAs) gained increasing relevance in the last decade. To understand the regulatory processes of miRNAs on genes, integrative computer-aided approaches are essential, especially in the light of complex human diseases as cancer. Results Here, we present miRTrail, an integrative tool that allows for performing comprehensive analyses of interactions of genes and miRNAs based on expression profiles. The integrated analysis of mRNA and miRNA data should generate more robust and reliable results on deregulated pathogenic processes and may also offer novel insights into the regulatory interactions between miRNAs and genes. Our web-server excels in carrying out gene sets analysis, analysis of miRNA sets as well as the combination of both in a systems biology approach. To this end, miRTrail integrates information on 20.000 genes, almost 1.000 miRNAs, and roughly 280.000 putative interactions, for Homo sapiens and accordingly for Mus musculus and Danio rerio. The well-established, classical Chi-squared test is one of the central techniques of our tool for the joint consideration of miRNAs and their targets. For interactively visualizing obtained results, it relies on the network analyzers and viewers BiNA or Cytoscape-web, also enabling direct access to relevant literature. We demonstrated the potential of miRTrail by applying our tool to mRNA and miRNA data of malignant melanoma. MiRTrail identified several deregulated miRNAs that target deregulated mRNAs including miRNAs hsa-miR-23b and hsa-miR-223, which target the highest numbers of deregulated mRNAs and regulate the pathway "basal cell carcinoma". In addition, both miRNAs target genes like PTCH1 and RASA1 that are involved in many oncogenic processes. Conclusions The application on melanoma samples demonstrates that the miRTrail platform may open avenues for investigating the regulatory interactions between genes and miRNAs for a wide range of human diseases. Moreover, miRTrail cannot only be applied to microarray based expression profiles, but also to NGS-based transcriptomic data. The program is freely available as web-server at mirtrail.bioinf.uni-sb.de.
Mood Modulates Auditory Laterality of Hemodynamic Mismatch Responses during Dichotic Listening
2012-02-22

Hemodynamic mismatch responses can be elicited by deviant stimuli in a sequence of standard stimuli even during cognitive demanding tasks. Emotional context is known to modulate lateralized processing. Right-hemispheric negative emotion processing may bias attention to the right and enhance processing of right-ear stimuli. The present study examined the influence of induced mood on lateralized pre-attentive auditory processing of dichotic stimuli using functional magnetic resonance imaging (fMRI). Faces expressing emotions (sad/happy/neutral) were presented in a blocked design while a dichotic oddball sequence with consonant-vowel (CV) syllables in an event-related design was simultaneously administered. Twenty healthy participants were instructed to feel the emotion perceived on the images and to ignore the syllables. Deviant sounds reliably activated bilateral auditory cortices and confirmed attention effects by modulation of visual activity. Sad mood induction activated visual, limbic and right prefrontal areas. A lateralization effect of emotion-attention interaction was reflected in a stronger response to right-ear deviants in the right auditory cortex during sad mood. This imbalance of resources may be a neurophysiological correlate of laterality in sad mood and depression. Conceivably, the compensatory right-hemispheric enhancement of resources elicits increased ipsilateral processing.
Cover Picture: The Alzheimer’s Disease Related Tau Protein as a New Target for Chemical Protein Engineering (Chem. Eur. J. 9/2012)
2012-02-22

The first semisynthesis of the tau protein is illustrated on the cover picture. This protein is known to aggregate upon phosphorylation, which makes it a key player in neurodegenerative diseases, such as Alzheimer's disease. In their Communication on page 2488 ff., C. P. R. Hackenberger, D. Schwarzer, et al. describe the chemical synthesis of the C-terminal phosphorylated part of tau, which they subsequently ligated to the N-terminal fragment of the protein produced in bacteria. Probably not as easy, but nevertheless similar to putting the final brick on a very popular childrens' game...︁ (printed with kind permission from Lego®). Polyoxometalates In their Communication on page 2503 ff., Y. Wei et al. report on the synthesis and characterization of an organoimido-substituted, monovacant hexamolybdate containing additional multidentate ligands and its phenylphosphonate derivative. Considering these two derivatives were synthesized from a general protocol, this work realizes an extension of the domain on the covalent modification of polyoxometalates (POMs) with organoimido ligands from saturated homo POMs to lacunary and hetero POMs.1 Ion-Pair Receptors A new calix[4]pyrrole with a directly appended crown-6 strap acts as a ditopic ion-pair receptor for a variety of alkali-cation salts under different conditions. This receptor can control cation traffic and transport chloride anions through membranes. For more details, see the Full Paper by C.-H. Lee, J. L. Sessler, P. A. Gale et al. on page 2514 ff.1 Heterogeneous Catalysis In their Full Paper on page 2639 ff., X. Wang et al. demonstrate the highly selective synthesis of Pd nanocrystals with three different shapes (cluster nanowires, icosahedra, and nanocubes) in an environmentally benign solvent by using a one-pot method. In particular, the cluster nanowire was synthesized for the first time. By immobilization of Pd nanocrystals on carbon nanotubes and γ-Al2O3, the catalytic activity and stability of Pd nanocrystals were greatly enhanced in the liquid-phase hydrogenation of cinnamaldehyde and gas-phase hydrogenation of 1,3-butadiene.1
Peritoneal Carcinomatosis: Cytoreductive Surgery and HIPEC–-Overview and Basics
2012-02-23

Tumor involvement of the peritoneum-peritoneal carcinomatosis-is a heterogeneous form of cancer that had been generally regarded as a sign of systemic tumor disease and as a terminal condition. The multimodal treatment approach for patients with peritoneal carcinomatosis, which had been conceived and developed, consists of what is known as cytoreductive surgery, followed by hyperthermic intraperitoneal chemotherapy (HIPEC). Depending on the tumor mass as assessed intraoperatively and the histopathological differentiation, patients who undergo cytoreductive surgery and HIPEC have a significant survival benefit. Mean increases in the survival period ranging from six months to up to four years have now been reported. In view of the substantial logistic effort and the extent of the surgery involved, this treatment approach represents a major challenge both for patients and for surgical oncologists, as well as for the members of the overall interdisciplinary structure required, which includes oncology, anesthesiology and intensive care, psycho-oncology, and patient management. The surgical procedures alone may take 8-14 hr. The present paper provides an overview of the basis for the approach and the use of specialized classifications and quantitative prognostic indicators.
Depletion of Dendritic Cells Enhances Innate Anti-Bacterial Host Defense through Modulation of Phagocyte Homeostasis
2012-02-23

Dendritic cells (DCs) as professional antigen-presenting cells play an important role in the initiation and modulation of the adaptive immune response. However, their role in the innate immune response against bacterial infections is not completely defined. Here we have analyzed the role of DCs and their impact on the innate anti-bacterial host defense in an experimental infection model of Yersinia enterocolitica (Ye). We used CD11c-diphtheria toxin (DT) mice to deplete DCs prior to severe infection with Ye. DC depletion significantly increased animal survival after Ye infection. The bacterial load in the spleen of DC-depleted mice was significantly lower than that of control mice throughout the infection. DC depletion was accompanied by an increase in the serum levels of CXCL1, G-CSF, IL-1α, and CCL2 and an increase in the numbers of splenic phagocytes. Functionally, splenocytes from DC-depleted mice exhibited an increased bacterial killing capacity compared to splenocytes from control mice. Cellular studies further showed that this was due to an increased production of reactive oxygen species (ROS) by neutrophils. Adoptive transfer of neutrophils from DC-depleted mice into control mice prior to Ye infection reduced the bacterial load to the level of Ye-infected DC-depleted mice, suggesting that the increased number of phagocytes with additional ROS production account for the decreased bacterial load. Furthermore, after incubation with serum from DC-depleted mice splenocytes from control mice increased their bacterial killing capacity, most likely due to enhanced ROS production by neutrophils, indicating that serum factors from DC-depleted mice account for this effect. In summary, we could show that DC depletion triggers phagocyte accumulation in the spleen and enhances their anti-bacterial killing capacity upon bacterial infection.
Multiple retinal arterial macroaneurysms associated with submacular hemorrhage
2012-02-23

Purpose To present the unusual case of multiple retinal arterial macroaneurysms (RAMs) associated with an extensive submacular hemorrhage. Methods A 64-year-old hypertensive woman is presented including the clinical findings, fluorescein angiography, and optical coherence tomography. Results The patient presented with 20/200 vision due to a dense submacular hemorrhage in the right eye. Fluorescein angiography revealed 4 hyperfluorescent lesions along the inferotemporal arteriole corresponding to RAMs. Optical coherence tomography confirmed RAM rupture with no choroidal abnormality. The patient refused surgical intervention. At 3-month follow-up, vision had improved to 20/70 with partial resolution of the hemorrhage. However, vitreoretinal traction with neurosensory retinal detachment involving the macula had developed. Conclusions Acquired RAMs are typically found as unilateral solitary lesions in older hypertensive women. The presence of 4 RAMs along the same arteriole has not been reported previously. Hypertensive patients should be examined regularly in order to detect potential RAMs early enough to permit treatment and prevent vision loss.