julilili42/papers huggingface dataset:
The cavum septi pellucidi in euploid and aneuploid fetuses
2013-01-10

ABSTRACT Objective To examine whether the cavum septi pellucidi ( CSP ) is larger in second‐ and third‐trimester fetuses with chromosomal abnormalities than in euploid fetuses. Methods This was a retrospective study utilizing stored two‐dimensional images of second‐ and third‐trimester fetuses between 18 and 40 weeks' gestation from three centers in Germany. The width of the CSP was measured by placing the calipers on the inner portion of its lateral borders. Two operators, both of whom were blinded to the fetal karyotype and to the measurements obtained by the other, measured the CSP width. The normal range in euploid fetuses was computed based on the biparietal diameter ( BPD ) by applying univariate regression analysis. The CSP width in euploid and aneuploid fetuses was transformed into Z ‐scores and compared using Student's t ‐test. Univariate regression analysis was used to determine the dependency of Z ‐score on head biometry. Results The study population consisted of 406 singleton pregnancies, 267 with euploid fetuses, 81 with trisomy 21, 50 with trisomy 18 and eight with trisomy 13. In the euploid group, the mean CSP width was 4.5 (range, 1.8–7.4) mm. Regression analysis showed a significant dependency of CSP width on BPD ( CSP width = 0.658 + (0.064 × BPD ), r = 0.781, P &lt; 0.0001; both parameters in mm). The mean CSP width increased from 3.2 to 7.1 mm for BPD values of 40 to 100 mm, respectively. In the groups of fetuses with trisomy 21, 18 and 13, mean CSP width was 5.7 (range, 2.8–10.5), 7.9 (range, 3.5–12.8) and 5.8 (range, 4.0–9.0) mm, respectively. In 42.0% of the fetuses with trisomy 21, CSP width was above the 95 th centile. In trisomy 18 and 13, CSP width was above the 95 th centile in 92.0% and 37.5% of cases, respectively. Conclusion A large CSP width should prompt a detailed ultrasound examination to further assess the risk for chromosomal abnormalities. Copyright © 2013 ISUOG. Published by John Wiley &amp; Sons Ltd.
Raman spectroscopy as a probe of molecular order, orientation, and stacking of fluorinated copper‐phthalocyanine (F16CuPc) thin films
2013-01-10

We report Raman scattering measurements on azimuthally ordered thin films of F 16 CuPc, prepared by organic molecular beam deposition on A‐plane sapphire substrates. The observed peak frequencies have been compared both to the results of a model calculation for the vibrational modes of the free molecule and to those reported by other authors in related materials. This analysis provides a plausible identification of the modes responsible for the strongest spectral features. Detailed evaluation of the spectra reveals that some observed modes, which correspond to vibrations of the macrocycle inner ring, largely retain the intramolecular character and their polarisation properties can be used to study the orientation and stacking configuration of the molecules. We provide structural parameters deduced either in molecular or crystal symmetry considering the simpler possibilities, i.e. a single column molecular stacking and a herringbone‐like structure. The results suggest that the thicker and most ordered film is structurally close to the recently reported crystal organisation of bulk ribbon samples of this compound. The crystalline quality of the ordered films is mainly reflected in some other Raman peaks which are related to the motion of peripheral atoms and dominate the high wavenumber part of the spectra. These modes are affected by intermolecular interactions inducing Davydov splittings that are unequivocally identified by the observed Raman selection rules. The performed analysis also provides quantitative estimates of the degree of in‐plane ordering. Copyright © 2013 John Wiley &amp; Sons, Ltd.
Dual Routes to Cognitive Flexibility: Learning and Response‐Conflict Resolution in the Dimensional Change Card Sort Task
2013-01-11

Cognitive control, the ability to align our actions with goals or context, is largely absent in children under four. How then are preschoolers able to tailor their behavior to best match the situation? Learning may provide an alternative route to context‐sensitive responding. This study investigated this hypothesis in the Dimensional Change Card Sort (DCCS), a classic test of cognitive control that most under‐fours fail. A training intervention based on learning theoretic principles proved highly effective: Three‐year‐olds who learned about DCCS rules and game contexts in a card‐labeling task, subsequently transferred this knowledge to sorting in the DCCS , passing at more than 3 times the rate of controls ( N = 47). This surprising finding reveals much about the nature of the developing mind.
Emended description of Anomalomyces (Ustilaginales), including Anomalomyces yakirrae sp. nov. on Yakirra pauciflora (Poaceae) from Australia
2013-01-11

An emended description of the genus Anomalomyces is given to accommodate a new species of smut fungus, Anomalomyces yakirrae, on Yakirra paucifl ora (Poaceae) from Australia.Th e systematic placement of the fungus within the genus Anomalomyces is based on morphological characters and molecular data from two loci.
Regulation of T-Type Calcium Channels in Osteoblasts on Micro-Structured Surface Topography
2013-01-11

Micro- and nanotopography as well as the surface chemistry of biomaterials affect cell adhesion, proliferation and cell differentiation. Furthermore, the organization and localization of intracellular adhesion components such as the actin cytoskeleton are also altered dependent on the material surface topography. However, the detailed influence of the material micro-structure on cellular mechanisms on the molecular level is still unknown. This study is intended to elucidate such effects using regular pillar structures to characterize the modulation of cell responses like the regulation of voltage-sensitive calcium channels as well as signaling molecules in human osteoblasts. To analyze cell behavior on defined biomaterial surfaces, human osteoblastic MG 63 cells were cultured on geometrically micro textured titanium coated silicon wafers, as opposed to planar titanium references. Samples were fabricated by a photolithographic process using the negative tone resist SU 8 and sputter-coated with 100 nm titanium. Immunofluorescence staining and flow cytometry are used to detect the expression levels and the function of T type calcium channels. Knowledge about the biocomplexity of cell behavior dependent on topographical characteristics is of clinical relevance for the development of implant designs in tissue engineering.
Establishment of a human in vitro model to investigate inflammatory immune reactions between Kupffer cell activation and hepatocyte damage – an approach to study DILI
2013-01-11

Hepatic tissue damage can occur due to surgical interventions, infections or drug induced liver injury (DILI). Kupffer cells (KC) play an important role in initiating tissue damage but also in regenerative processes. KC activation by LPS, foreign proteins or endogenous proteins can lead to an activation of the NF-κB signaling pathway mediated by reactive oxygen intermediates (ROI). Once activated, KCs release different cytokine patterns that support inflammation or induce tolerance reactions. Aim of the present study was to establish a human in vitro model which enables the detection of cell-cell communication between KCs activated by damaged or stressed hepatocytes.
Age-related differences in the oxidative stress response of primary rat hepatocytes
2013-01-11

Various studies indicate that the accumulation of reactive oxygen species (ROS) and associated cellular damage play an important role in ageing of various organs, including the liver. Especially high concentrations of ROS in the mitochondria lead to oxidative damages, which have been proposed as one major cause of cellular ageing and death. Conceivably, the decrease of cytosolic and/or mitochondrial glutathione (GSH) concentrations as well as altered enzyme activities could be involved in the progressive redox imbalance of the ageing cell. However, the underlying mechanisms have not been clarified so far.
IL-28B Genotype is not associated with early HCV-RNA negativity in patients with symptomatic acute HCV infection
2013-01-11

Patients with acute hepatitis C are able to cure the infection spontaneously in 10–50% of cases. Factors being associated with spontaneously clearance are female sex, viral load, early HCV RNA declines kinetics and symptoms of hepatitis at presentation. The IL-28B genotype has also been associated with clearance of HCV infection but controversial data have been published in patients with symptomatic versus asymptomatic acute hepatitis C.
Multiplex in vivo RNAi screening instructs combination therapies to increase the therapeutic efficacy of the multikinase inhibitor sorafenib
2013-01-11

Hepatocellular carcinoma is the third common cause of cancer death with increasing incidence. Standard treatments are limited due to frequent tumor recurrence and a poor responsiveness to conventional chemotherapy. The approval of sorafenib, a small multikinase inhibitor as the first active systemic treatment against HCC, increases survival of HCC patients by less than 3 months. Thus, there is a need to understand the molecular mechanisms of sorafenib sensitivity and resistance in order to identify new combination therapies with higher therapeutic efficacy.
Human in vitro model of steatosis hepatis and the influence of anti-lipidemic drugs on energy metabolism in steatotic hepatocytes
2013-01-11

Non-alcoholic fatty liver disease (NAFLD) caused by an excessive caloric intake is already the most common chronic liver disease in western countries. Therefore fatty livers have become pivotal in surgical interventions and organ transplantation. Postoperatively, this results in decreased liver regeneration as well as reduced detoxification capacity and may lead to all degrees of hepatic failure. Therefore, there is need for fast clearance of liver fat from a surgical point of view. Epidemiologic studies suggest that Genistein (GEN) has a beneficial influence on lipid metabolism. Our aim was to establish a human in vitro steatosis model in order to investigate the effects of GEN on hepatic energy metabolism.
Down regulation of Sonic Hedgehog Signaling attenuates carcinogenesis in vitro and increased tumor necrosis in a Xenograft mouse model of cholangiocellular carcinoma
2013-01-11

Background: The Hedgehog signaling pathway controls cell proliferation and differentiation during embryonic development. Altered activation of Hedgehog has been found and described in different human tumor types. Cholangiocellular carcinoma (CCC) is the second most common primary malignant tumor in the liver. The vast majority of patients with CCC are not good candidates for curative surgery and conventional chemotherapeutic drugs are limited. In this study, we investigated the effects of Hedgehog inhibition by Cyclopamine and 5E1 in cultured human CCC cell lines and in vivo using a Xenograft mouse model.
In vivo RNAi screening identified MKK4 as a new therapeutic target for the improvement of liver regeneration
2013-01-11

We established a unique system for performing direct in vivo RNAi screens to genetically dissect cellular signaling networks that regulate proliferation control of hepatocytes during liver damage and regeneration. By combining the well characterized FAH-/- mouse model with a transposon based vector system, we generated chimeric mouse livers. In these mouse livers each hepatocyte expresses FAH, a marker gene and a microRNA based shRNA. To such mouse livers any form of liver damaging protocol can be applied and the regenerative process can be studied. We conducted a first in vivo RNAi screen, using a focused shRNAmir library consisting of 631 constructs targeting 362 genes. Mouse livers were stably repopulated with the shRNAmir library and after repopulation mice were subjected to chronic CCl4 treatment to induce chronic liver damage. The representation of each shRNAmir in the pool, the chimeric mouse liver and after chronic liver damage was determined by deep sequencing analysis. ShRNAs targeting MKK4 showed strong enrichment during liver damage and regeneration. MKK4 belongs to the Map kinase family and is part of two stress kinase signaling pathways, the JNK as well as the p38 pathway. Functional in vivo validation experiments showed that stable knock down of MKK4 by different shRNAs can significantly increase the repopulation efficiency of mouse hepatocytes and also increases the regenerative capacity of chronically damaged mouse livers. In addition we could show that MKK4 suppression also confers an increased robustness of hepatocytes in a model of acute liver failure, resulting in better survival of these animals. Beyond this, primary hepatocytes with stable MKK4 knockdown showed prolonged survival in cell culture and these cells could even be passaged and used to repopulate FAH-/- mouse livers. Protein array and western blot analyses of MKK4 shRNAs versus control-shRNA expressing livers revealed a complex activation pattern of JNK- and p38-signaling downstream factors. Interestingly, the observed pattern does not merely represent an increased JNK over p38 signaling but our data rather suggest that complex cross signaling events between both pathways are involved. Also hepatocytes with stable MKK4 knock down already show higher levels of CyclinD1, suggesting a priming of the cells to leave the G0 state and entering the G1 state of the cell cycle. We developed a new screening platform for pinpointing new regulators of hepatocyte proliferation and liver regeneration. A first in vivo RNAi screen identified MKK4 as an interesting new therapeutic target structure for improving the regenerative capacity under acute and chronic liver damaging conditions.
Search for very-high-energyγ-ray emission from Galactic globular clusters with H.E.S.S.
2013-01-12

Context. Globular clusters (GCs) are established emitters of high-energy (HE, 100 MeV &lt; E &lt; 100 GeV) γ-ray radiation which could originate from the cumulative emission of the numerous millisecond pulsars (msPSRs) in the clusters’ cores or from inverse Compton (IC) scattering of relativistic leptons accelerated in the GC environment. These stellar clusters could also constitute a new class of sources in the very-high-energy (VHE, E &gt; 100 GeV) γ-ray regime, judging from the recent detection of a signal from the direction of Terzan 5 with the H.E.S.S. telescope array.Aims. To search for VHE γ-ray sources associated with other GCs, and to put constraints on leptonic emission models, we systematically analyzed the observations towards 15 GCs taken with the H.E.S.S. array of imaging atmospheric Cherenkov telescopes.Methods. We searched for point-like and extended VHE γ-ray emission from each GC in our sample and also performed a stacking analysis combining the data from all GCs to investigate the hypothesis of a population of faint emitters. Assuming IC emission as the origin of the VHE γ-ray signal from the direction of Terzan 5, we calculated the expected γ-ray flux from each of the 15 GCs, based on their number of millisecond pulsars, their optical brightness and the energy density of background photon fields.Results. We did not detect significant VHE γ-ray emission from any of the 15 GCs in either of the two analyses. Given the uncertainties related to the parameter determinations, the obtained flux upper limits allow to rule out the simple IC/msPSR scaling model for NGC 6388 and NGC 7078. The upper limits derived from the stacking analyses are factors between 2 and 50 below the flux predicted by the simple leptonic scaling model, depending on the assumed source extent and the dominant target photon fields. Therefore, Terzan 5 still remains exceptional among all GCs, as the VHE γ-ray emission either arises from extra-ordinarily efficient leptonic processes, or from a recent catastrophic event, or is even unrelated to the GC itself.
Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies
2013-01-14

Antibodies can protect from Plasmodium falciparum (Pf) infection and clinical malaria disease. However, in the absence of constant reexposure, serum immunoglobulin (Ig) levels rapidly decline and full protection from clinical symptoms is lost, suggesting that B cell memory is functionally impaired. We show at the single cell level that natural Pf infection induces the development of classical memory B cells (CM) and atypical memory B cells (AtM) that produce broadly neutralizing antibodies against blood stage Pf parasites. CM and AtM contribute to anti-Pf serum IgG production, but only AtM show signs of active antibody secretion. AtM and CM were also different in their IgG gene repertoire, suggesting that they develop from different precursors. The findings provide direct evidence that natural Pf infection leads to the development of protective memory B cell antibody responses and suggest that constant immune activation rather than impaired memory function leads to the accumulation of AtM in malaria. Understanding the memory B cell response to natural Pf infection may be key to the development of a malaria vaccine that induces long-lived protection.
The Chick Embryo as an Experimental System for Melanoma Cell Invasion
2013-01-14

The chick embryo model is a feasible, cost-effective in vivo system to study invasion by cancer cells in an embryonic environment. It may be useful to study invasive behavior induced by embryonic oncogenes and for targeted manipulation of melanoma or breast cancer cells aiming at ablation of invasive properties.
Using transfer entropy to measure information flows between financial markets
2013-01-14

We use transfer entropy to quantify information flows between financial markets and propose a suitable bootstrap procedure for statistical inference. Transfer entropy is a model-free measure designed as the Kullback-Leibler distance of transition probabilities. Our approach allows to determine, measure and test for information transfer without being restricted to linear dynamics. In our empirical application, we examine the importance of the credit default swap market relative to the corporate bond market for the pricing of credit risk. We also analyze the dynamic relation between market risk and credit risk proxied by the VIX and the iTraxx Europe, respectively. We conduct the analyses for pre-crisis, crisis and post-crisis periods.
SchussenAktivplus: reduction of micropollutants and of potentially pathogenic bacteria for further water quality improvement of the river Schussen, a tributary of Lake Constance, Germany
2013-01-14

The project focuses on the efficiency of combined technologies to reduce the release of micropollutants and bacteria into surface waters via sewage treatment plants of different size and via stormwater overflow basins of different types. As a model river in a highly populated catchment area, the river Schussen and, as a control, the river Argen, two tributaries of Lake Constance, Southern Germany, are under investigation in this project. The efficiency of the different cleaning technologies is monitored by a wide range of exposure and effect analyses including chemical and microbiological techniques as well as effect studies ranging from molecules to communities.
Beyond the Competition-Colonization Trade-Off: Linking Multiple Trait Response to Disturbance Characteristics
2013-01-14

Disturbances' role in shaping communities is well documented but highly disputed. We suggest replacing the overused two-trait trade-off approach with a functional group scheme, constructed from combinations of four key traits that represent four classes of species' responses to disturbances. Using model results and field observations from sites affected by two highly different disturbances, we demonstrated that popular dichotomous trade-offs are not sufficient to explain community dynamics, even if some emerge under certain conditions. Without disturbances, competition was only sufficient to predict species survival but not relative success, which required some escape mechanism (e.g., long-term dormancy). With highly predictable and large-scale disturbances, successful species showed a combination of high individual tolerance to disturbance and, more surprisingly, high competitive ability. When disturbances were less predictable, high individual tolerance and long-term seed dormancy were favored, due to higher environmental uncertainty. Our study demonstrates that theories relying on a small number of predefined trade-offs among traits (e.g., competition-colonization trade-off) may lead to unrealistic results. We suggest that the understanding of disturbance-community relationships can be significantly improved by employing sets of relevant trait assemblies instead of the currently common approach in which trade-offs are assumed in advance.
Little Things With Big Effects
2013-01-14

Error diagnosis in ICALL typically analyzes learner input in an attempt to abstract and identify indicators of the learner's (mis)conceptions of linguistic properties. For written input, this process usually starts with the identification of tokens that will serve as the atomic building blocks of the analysis. In this paper, we discuss the consequences of mismatches between the learner's perception of a given token and the system's interpretation of its linguistic properties. Based on our analysis of the interaction of beginning learners of Portuguese with the ICALL system TAGARELA, we discuss why tokenization and the interpretation of accented characters deserve particular attention in a system used by language learners. On the computational side, we argue that the mismatches arising in such cases can be addressed in a general way by building ICALL systems on an annotation-based natural language processing architecture which monotonically enriches the representation of learner input.
Targeting Cancer Stem Cells with Defined Compounds and Drugs
2013-01-14

: Cancer stem cells (CSCs) are a subpopulation of tumor cells that possess self-renewal and tumor initiation capacity and the ability to give rise to the heterogenous lineages of cancer cells that comprise the tumor. CSCs possess numerous intrinsic mechanisms of resistance to chemotherapeutic drugs, novel tumor-targeted drugs and radiation therapy, allowing them to survive current cancer therapies and to initiate tumor recurrence and metastasis. Recently, different pathways that confer resistance and survival of CSCs, but also compounds and drugs that selectively target some of these pathways in CSCs have been identified. Such compounds and drugs include antibiotics like salinomycin, phytochemicals such as parthenolide, cyclopamine, EGCG, resveratrol, curcumin, sulforaphane and oxymatrine, the small molecule inhibitors vismodegib and repertaxin, monoclonal antibodies and antibody constructs raised against cell surface proteins expressed by CSCs, and, surprisingly, some classical drugs such as metformin, tranilast and thioridazine. These agents exhibit significant anti-CSC activity, alone or in combination with cytostatic drugs or tumor-targeted drugs, as recently shown in vitro and in human xenograft mice. Since current cancer therapies fail to eliminate CSCs, leading to cancer recurrence and progression, selective targeting of CSCs with compounds and drugs introduced herein may represent a novel therapeutic strategy to eradicate cancer.