julilili42/papers huggingface dataset:
Disseminated Tumor Cells and Cancer Stem Cells in Ovarian Cancer
2013-02-27

Ovarian cancer is currently the fifth most lethal malignancy of women in Europe and the United States [1, 2]. The prognosis of ovarian cancer patients is limited due to lack of specific early symptoms and a high rate of relapse; more than half of all patients will suffer from disease recurrence, resulting in a poor overall survival [3]. Most cases are di‐ agnosed in advanced stages, and although the initial response to chemotherapy is gener‐ ally good, a significant proportion of patients will suffer from a relapse despite optimal cytoreductive surgery [4]. Since treatment strategies are mainly developed to control lo‐ coregional cancer growth, it may be anticipated that more women will die of distant metastatic disease. The identification of novel molecular markers, reflecting current tu‐ mor activity, may improve prediction and therapy monitoring and provide valuable in‐ sights into process of carcinogenesis. In this regard, oncologic research have increasingly focused on disseminated and circulating tumor cells.
Transmigration of polymorphnuclear neutrophils and monocytes through the human blood-cerebrospinal fluid barrier after bacterial infection in vitro
2013-02-28

Abstract Background Bacterial invasion through the blood-cerebrospinal fluid barrier (BCSFB) during bacterial meningitis causes secretion of proinflammatory cytokines/chemokines followed by the recruitment of leukocytes into the CNS. In this study, we analyzed the cellular and molecular mechanisms of polymorphonuclear neutrophil (PMN) and monocyte transepithelial transmigration (TM) across the BCSFB after bacterial infection. Methods Using an inverted transwell filter system of human choroid plexus papilloma cells (HIBCPP), we studied leukocyte TM rates, the migration route by immunofluorescence, transmission electron microscopy and focused ion beam/scanning electron microscopy, the secretion of cytokines/chemokines by cytokine bead array and posttranslational modification of the signal regulatory protein (SIRP) α via western blot. Results PMNs showed a significantly increased TM across HIBCPP after infection with wild-type Neisseria meningitidis (MC58). In contrast, a significantly decreased monocyte transmigration rate after bacterial infection of HIBCPP could be observed. Interestingly, in co-culture experiments with PMNs and monocytes, TM of monocytes was significantly enhanced. Analysis of paracellular permeability and transepithelial electrical resistance confirmed an intact barrier function during leukocyte TM. With the help of the different imaging techniques we could provide evidence for para- as well as for transcellular migrating leukocytes. Further analysis of secreted cytokines/chemokines showed a distinct pattern after stimulation and transmigration of PMNs and monocytes. Moreover, the transmembrane glycoprotein SIRPα was deglycosylated in monocytes, but not in PMNs, after bacterial infection. Conclusions Our findings demonstrate that PMNs and monoctyes differentially migrate in a human BCSFB model after bacterial infection. Cytokines and chemokines as well as transmembrane proteins such as SIRPα may be involved in this process.
Dedolomitization and reservoir quality: insights from reactive transport modelling
2013-02-28

Abstract Dedolomitization or calcitization, the replacement of dolomite by calcite, modifies the porosity and permeability of carbonate rocks. This study evaluates the effects of dedolomitization on the porosity of carbonates by means of geochemical and reactive transport simulations. The obtained results indicate that dedolomitization is a slow process that may be triggered by cold meteoric water but also by warm groundwater at temperatures of ≤50°C. Dedolomitization is more efficient with fluid fluxes on the order of tens of metres per year. Most of the simulations performed in this study resulted in a loss of porosity due to calcitization. The rate of the dedolomitization reaction increases significantly when calcium‐bearing minerals with faster dissolution kinetics and smaller molar volume than calcite, such as anhydrite, are present in the system. In such situations, the porosity of the rock increases significantly (approximately 10%) during a time span of hundreds of thousands of years. Therefore, depending on its original composition, fluid flow conditions and fluid composition, the porosity of a tight dolostone can be enhanced and reach porosity values of reservoir rocks after being calcitized.
OLEMACH THEOREM: ANGULAR-MOMENTUM CONSERVATION IMPLIES GRAVITATIONAL-REDSHIFT PROPORTIONAL CHANGE OF LENGTH, MASS AND CHARGE
2013-02-28

There is a minor revolution going on in general relativity: a “return to the mothers “ – that is, to the equivalence principle of Einstein. Recently, the Telemach theorem was described. Here now, the completely independent but fully convergent “Olemach theorem ” is introduced. It connects omega (rotation rate), length, mass and charge in a static field. The predictable consequence of the two theorems is a return to the hard core of general relativity at the expense of some peripheral features. A connection to cosmology is mentioned along with a promising technological development.
Chiral symmetry breaking and meson wave functions in soft-wall AdS/QCD
2013-03-01

We consider mesons composed of light and heavy quarks and discuss the\\nconstruction of the corresponding meson wave functions in soft-wall AdS/QCD. We\\nspecifically take care that constraints imposed by chiral symmetry breaking and\\nby the heavy quark limit are fulfilled. The main results are: i) the wave\\nfunctions of light mesons have a nontrivial dependence on the current quark\\nmass, which gives rise to a mass spectrum consistent with the one including\\nexplicit breaking of chiral symmetry; ii) the wave functions of heavy-light\\nmesons generate their correct mass spectrum, the mass splittings of vector and\\npseudoscalar states, and the correct scaling of leptonic decay constants f(Q\\n\\\\bar q) \\\\sim 1/sqrt(mQ); iii) the wave functions of heavy quarkonia produce\\ntheir correct mass spectrum and lead to a scaling behaviour of the leptonic\\ndecay constants f(Q \\\\bar Q) \\\\sim sqrt(mQ) and f(c \\\\bar b) \\\\sim mc/sqrt(mb) at\\nmc &lt;&lt; mb, consistent with potential models and QCD sum rules.\\n
Electrical breakdown in a V 2 O 3 device at the insulator-to-metal transition
2013-03-01

We have measured the electrical properties of a V2O3 thin film micro bridge\\nat the insulator metal transition (IMT). Discontinuous jumps to lower voltages\\nin the current voltage characteristic (IV) followed by an approximately\\nconstant voltage progression for high currents indicate an electrical breakdown\\nof the device. In addition, the IV curve shows hysteresis and a training\\neffect, i.e. the subsequent IV loops are different from the first IV loop after\\nthermal cycling. Low temperature scanning electron microscopy (LTSEM) reveals\\nthat the electrical breakdown over the whole device is caused by the formation\\nof electro-thermal domains (ETDs), i.e. the current and temperature\\nredistribution in the device. On the contrary, at the nanoscale, the electrical\\nbreakdown causes the IMT of individual domains. In a numerical model we\\nconsidered these domains as a network of resistors and we were able to\\nreproduce the electro-thermal breakdown as well as the hysteresis and the\\ntraining effect in the IVs.\\n
A new giant salamander (Urodela, Pancryptobrancha) from the Miocene of Eastern Europe (Grytsiv, Ukraine)
2013-03-01

ABSTRACT We present new and well-preserved giant salamander material from the Miocene of the Grytsiv locality, Ukraine. Disarticulated skull and postcranial bones from two individuals are described as a new taxon, Ukrainurus hypsognathus, gen. et sp. nov. U. hypsognathus is characterized by poorly ossified bone tissues, relatively inflexible mandibles, a high dentary, a crista on the lingual surface of the dentary, a pars dentalis of the dentary that is composed of a dental lamina and a subdental surface, presence of an eminentia dorsalis on the squamosal, a broad pericondylar facet on the occipital, extremely elongated prezygapophyses, and hemal processes with an elongate, oval base. Moreover, U. hypsognathus shows evidence of strong mandibular levator muscles that indicate great biting force. A phylogenetic analysis of all well-understood Tertiary and Recent giant salamanders recovers a monophyletic group of Asian and North American cryptobranchids, but places U. hypsognathus outside crown group Cryptobranchidae. This result suggests that Cryptobranchidae originated in Asia and dispersed to North America. The oldest representative of crown Cryptobranchidae is Aviturus exsecratus from the terminal Paleocene of the Nemegt Basin, Mongolia. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
The Tendinous Framework in the Temporal Skull Region of Turtles and Considerations About Its Morphological Implications in Amniotes: A Review
2013-03-01

In 1926, Tage Lakjer hypothesized a replacement of the infratemporal bar in diapsids by a ligament spanning between quadrate and the upper jaw. As a similar ligament is also present in turtles, he argued for a diapsid origin of this group. Based on recent advances in the homologization of the tendinous framework in the reptile jaw adductor chamber - reviewed in this paper - one could argue for independent origins of the cheek ligaments in sauropsids. The quadratomaxillar ligament of turtles could, with reservation, be homologized with the quadrate aponeurosis of other sauropsids, as well as to the superficial tendon of m. masseter in mammals. These structures have a strong morphogenetic influence to cranial anatomy. Given such an identity, the hypothesis of a structural replacement of the lower temporal arcade in lizards would be refuted. Moreover, such a homology could be correlated to the evolution of the middle ear and to the origin of the chewing mechanism in mammals, which contributed to the evolutionary success of that group. The homologization presented herein is critically discussed and is open for revision. Nevertheless, the value of tendinous structures for fundamental homologisations in the vertebrate head is highlighted.
New Tools for the Identification of Developmentally Regulated Enhancer Regions in Embryonic and Adult Zebrafish
2013-03-01

We have conducted a screen to identify developmentally regulated enhancers that drive tissue-specific Gal4 expression in zebrafish. We obtained 63 stable transgenic lines with expression patterns in embryonic or adult zebrafish. The use of a newly identified minimal promoter from the medaka edar locus resulted in a relatively unbiased set of expression patterns representing many tissue types derived from all germ layers. Subsequent detailed characterization of selected lines showed strong and reproducible Gal4-driven GFP expression in diverse tissues, including neurons from the central and peripheral nervous systems, pigment cells, erythrocytes, and peridermal cells. By screening adults for GFP expression, we also isolated lines expressed in tissues of the adult zebrafish, including scales, fin rays, and joints. The new and efficient minimal promoter and large number of transactivating driver-lines we identified will provide the zebrafish community with a useful resource for further enhancer trap screening, as well as precise investigation of tissue-specific processes in vivo.
Intrahepatic Application of Suicide Gene-Armed Measles Virotherapeutics: A Safety Study in Transgenic Mice and Rhesus Macaques
2013-03-01

Abstract Oncolytic viruses such as measles virus (MV) represent a new class of therapeutic agents that might help to overcome current limitations in cancer therapy. Although MV-based virotherapeutics already have entered clinical testing for various tumor entities, the preclinical safety of MV virotherapeutics so far has not been elucidated for particular regimens with high medical need, such as (1) direct injection into hepatic tumor sites, (2) employing high doses ibidem, and (3) concurrent usage of arming with cytotoxic genes required to further enhance oncolytic efficiency. Here, we assessed the safety and pharmacokinetics of suicide gene-armed vector MV-SCD when administered intrahepatically in two animal models, IFNAR(tm)-CD46(Ge) (interferon-α receptor deficient and CD46 MV receptor knock-in) transgenic mice and rhesus macaques (Macaca mulatta). Clinically, singular direct intrahepatic applications of MV-SCD were found to be well tolerated. Quantitative RT-PCR demonstrated the transient presence of viral RNA in various organs, whereas no shedding of infectious virus particles was observed at any time point. Histological analyses of organs did not exhibit adverse effects attributable to the test article. Blood parameters including liver enzymes revealed no deviations from normal. In both species an antiviral humoral immune response was mounted shortly after virus administration. Surprisingly, daily repeated systemic applications of MV-SCD under concomitant prodrug administration resulted in side effects in IFNAR(tm)-CD46(Ge) mice, but were less pronounced than in a 5-fluorouracil standard therapy control cohort. Taken together, these data indicate that "single shot" direct intrahepatic injections of MV-SCD in conjunction with systemic prodrug administration are safe and could be used in future virotherapeutic treatments of liver cancers.
Editorial: Strategies in tissue engineering and regenerative medicine
2013-03-01

"Strategies in Tissue Engineering": this special issue is edited by Prof. Katja Schenke-Layland and Prof. Heike Walles and covers many salient aspects of tissue engineering and regenerative medicine. The issue includes articles on Raman spectroscopy and its application in tissue engineering; bioreactor design and surface functionalization for tissue culture applications; improved method for RNA isolation from tissue samples and much more.
Subgraph-based Classification of Explicit and Implicit Discourse Relations
2013-03-01

Current approaches to recognizing discourse relations rely on a combination of shallow, surfacebased features (e.g., bigrams, word pairs), and rather specialized hand-crafted features. As a way to avoid both the shallowness of word-based representations and the lack of coverage of specialized linguistic features, we use a graph-based representation of discourse segments, which allows for a more abstract (and hence generalizable) notion of syntactic (and partially of semantic) structure. Empirical evaluation on a hand-annotated corpus of German discourse relations shows that our graphbased approach not only provides a suitable representation for the linguistic factors that are needed in disambiguating discourse relations, but also improves results over a strong state-of-the-art baseline by more accurately identifying Temporal, Comparison and Reporting discourse relations. 1
Neural correlates of sensory preconditioning: A preliminary fMRI investigation
2013-03-01

Sensory preconditioning (SPC; also known as behaviorally silent learning) consists of a combination of two neutral stimuli, none of which elicits an unconditional response. After one of them is later paired with an unconditional stimulus (US), the other neutral stimulus also yields a conditional response although it has never been paired with the US. In this study, an event‐related functional magnetic resonance imaging (fMRI) paradigm was used to specify brain regions involved in SPC. The results demonstrated that SPC was associated with significant changes in activity of several regions, notably, the left amygdala, the left hippocampus, the bilateral thalamus, the bilateral medial globus pallidus, the bilateral cerebellum, the bilateral premotor cortex, and the bilateral middle frontal gyrus. This is a first effort to use fMRI to examine the effects of SPC on brain activation. Our data suggest that there is a distributed network of structures involved in SPC including both cortical and subcortical regions, therefore add to our understanding of the neural mechanisms underlying the ability to associative learning. Hum Brain Mapp 35:1297–1304, 2014 . © 2013 Wiley Periodicals, Inc.
Post-craniotomy blindness in the supine position: Unlikely or ignored?
2013-03-01

Immediate visual loss following craniotomy in the supine position is a disastrous complication in neurosurgical patients. The incidence is unknown and little is known on the definite pathogenesis. Also, preventive or restorative interventions are unclear. We describe the rare case of post-craniotomy optic neuropathy and sudden visual loss after craniotomy in the supine position for an olfactory groove meningioma, discuss the possible pathophysiology and review the literature on the pathogenesis, risk factors, and outcome. Although rare, neurosurgeons, as well as neuroanesthesiologists should be aware of the possibility of this devastating complication in the high-risk group of patients.
Be a robot! Robot navigation patterns in a path crossing scenario
2013-03-01

In this paper we address the question how a human would expect a robot to move when a human is crossing its way. In particular we consider the problem that physical capabilities of robots differ from humans. In order to find out how humans expect a robot, with non humanlike capabilities, to move we designed and conducted a study were the participants steer the robot. We identified four motion patterns and our results show that driving straight towards the goal and stopping when a human might collide with the robot is the favored motion pattern.
The right choice of antihypertensives protects primary human hepatocytes from ethanol- and recombinant human TGF-&beta;1-induced cellular damage
2013-03-01

Our results suggest that antihypertensives may both positively and negatively influence chronic liver disease progression. Therefore, we propose that in future patients with ALD and high blood pressure, they could benefit from an adjusted antihypertensive therapy with additional antifibrotic effects.
Assessing political agency across the Taiwan Strait: The case of the taishang
2013-03-01

The migration of Taiwanese to the Chinese mainland is one of the most striking features of the deepening interaction and integration across the Taiwan Strait. Among these newcomers, Taiwanese businesspeople ( taishang) have long since been considered an important ‘linkage community’ that profoundly affects the dynamics of cross-Strait relations. However, to what extent can and do they exert political agency in cross-Strait relations? Drawing on recent literature, as well as fieldwork conducted between 2006 and 2009 in Taiwan, the Pearl River Delta (Dongguan), and the Kunshan–Shanghai metropolitan area, this article begins by analysing the political mindset of the taishang, most notably with respect to their understanding of themselves as political actors. It then looks at different dimensions of political agency exercised by the taishang in both China and Taiwan. Since little is known about their strategies to politically safeguard their group-specific interests, the findings and assessments presented here can only be preliminary. Nevertheless, the article contributes to a better understanding of the concept of linkage community and provides a useful foundation for further investigations of the taishang’s political role in shaping cross-Strait relations.
Peroxide-induced effects on spontaneous contraction of murine small intestine: Lack of inhibition by antioxidants
2013-03-01

An experimental model of inflammatory reaction in murine small intestine was developed by characterizing the effects of oxidative stress on spontaneous contractions in vitro. The tissue specimen were obtained from wild type mice (C57Bl6) and mounted in an organ bath allowing the registration of contraction forces under isometric conditions (Merkel, Thesis, 2010). Rhythmic spontaneous contractions were observed under normal perfusion conditions with a frequency (F) of approx. 20 ± 3/min and a mean amplitude (A) of 1.8 ± 0.4 mN. In order to induce oxidative stress, hydrogen peroxide was applied (0.05 – 0.6 mM/l) and the effects on contractile behaviour were recorded. Besides a longer lasting, yet transient, increase in contraction force (T), a slow reduction of the spontaneous contractions was found leading to decreased values of F and A, depending on the duration of the application. When, within one hour, the perfusion medium of the organ bath was changed again to normal conditions, all the contractile parameters returned to the initial values which lasted approx. 30 min. Therefore, at the one hand, the parameters of T, A and F, as well as the time needed for significant peroxide-induced changes on A and F can be used to quantify effects related to oxidative stress. On the other hand, they can also be used to recognize protection e.g. by antioxidants applied also to the tissue. Till now, we tested various substances among them vitamin C, rosmarinic acid, trolox and a herbal extract from Melissae folium, all of which were shown to exhibit strong antioxidative properties in different in vitro test systems (Germann et al, 2006). However, none of these revealed any significant protective effect on the changes in contractility, even when applied by preincubation prior to the peroxide.
Deterministic clustering of the available chemical space
2013-03-01

Clustering of compound libraries using 2D binary fingerprints is a fundamental task in chemoinformatics and various methods have been described to solve it [1]. These methods can roughly be grouped into deterministic and non-deterministic approaches with two key-characteristics distinguishing them. First, the algorithmic complexity of deterministic approaches is more demanding whereas the non-deterministic methods often try to overcome this drawback by using heuristics to save time and memory. Second, deterministic clustering algorithms, especially agglomerative hierarchical techniques have been shown to yield good results and often perform better than non-deterministic approaches [2]. As a consequence, clustering of small to medium sized libraries with up to 1 million compounds is regularly performed using deterministic techniques whereas libraries comprising millions of compounds are mostly clustered using heuristics like k-means [3]. Here, we present a deterministic approach for clustering huge compound libraries based on all pairwise compound similarities. For this purpose, we use an extremely fast and flexible algorithm for similarity calculations, which we have developed to be purely CPU-based thus having no need for any specialized hardware. Using this similarity method, we implemented a workflow with the following steps. First, we create a set of unique input fingerprints by filtering duplicates that are then stored and finally remapped onto their representative clusters. Second, we calculate all pairwise similarities to construct a similarity network by applying a fixed Tanimoto threshold to select the edges to be inserted into the network. From this similarity network the connected subgraphs are extracted and forwarded to the last step. Finally, connected subgraphs exceeding a predefined size are hierarchically clustered. As a result, we show that our algorithm for similarity calculation is competitive to recently published CPU-based methods and can perform up to 380 million Tanimoto calculations per second on a current desktop computer. This efficient method allows our workflow to process medium to large libraries on current desktop computers within minutes. To finally demonstrate the power of our clustering workflow, we processed the commercially available chemical space comprising about 17 million compounds [4]. The entire clustering workflow took 63 hours on a compute server using 64 cores and 100 GB main memory to complete.