julilili42/papers huggingface dataset:
Overexpression of Tumor-Associated Trypsin Inhibitor (SPINK1/TATI) in Hepatitis C-Associated Hepatocellular Carcinoma: Potential Implications for Viral Hepatocarcinogenesis
2014-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; The molecular pathomechanisms leading to hepatitis C virus (HCV)-induced hepatocarcinogenesis remain unclear. This study investigated the molecular pathways and key genes underlying HCV-positive hepatocellular carcinoma (HCC) using gene expression profiling. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Oligonucleotide arrays (Affymetrix HU133A) were used to determine and compare the tissue-specific gene expression profiles in 39 cases of HCV-positive or -negative HCC and non-malignant liver tissue. The expression values of the most overexpressed genes were validated by real-time polymerase chain reaction (RT-PCR). &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; 837 genes or expressed sequence tags (ESTs) were significantly differently expressed in HCV-positive HCC versus healthy tissue: 414 were upregulated and 423 were downregulated (p &lt; 0.05; &gt; 2-fold change in ≥ 70% of the samples). A specific gene expression profile for HCV-positive HCC was obtained using 2-dimensional cluster analysis and was confirmed using supervised neuronal network modeling. The most consistently overexpressed gene coded for serine protease inhibitor Kazal-type 1 (SPINK1)/tumor-associated trypsin inhibitor (TATI) (median fold change, 19.7; significantly overexpressed in 90% of the samples). SPINK1/TATI was coregulated with matrix metalloproteinases (MMPs) and their natural inhibitors (tissue inhibitors of metalloproteinases (TIMPs)). &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; Gene expression profiling identified specific dysregulated molecular pathways and &lt;i&gt;SPINK1/TATI&lt;/i&gt; as the most overexpressed gene in HCV-positive HCC. These data highlight the importance of SPINK1/TATI as a tumor marker for HCV-induced HCC and may lead to a better understanding of HCV-induced hepatocarcinogenesis.
Yeast phospholipid biosynthesis is linked to mRNA localization
2014-01-01

Localization of mRNAs and local translation are universal features in eukaryotes and contribute to cellular asymmetry and differentiation. In Saccharomyces cerevisiae, localization of mRNAs that encode membrane proteins requires the She protein machinery including the RNA-binding protein She2p as well as movement of the cortical endoplasmic reticulum (cER) to the yeast bud. In a screen for ER-specific proteins necessary for directional transport of WSC2 and EAR1 mRNAs, we have identified enzymes of the phospholipid metabolism. Loss of the phospholipid methyltransferase Cho2p, which showed the strongest impact on mRNA localization, disturbs mRNA localization as well as ER morphology and segregation due to an increase in cellular phosphatidylethanolamine (PE). Mislocalized mRNPs containing She2p co-localize with aggregated cER structures suggesting entrapment of mRNA and She2p by the elevated PE level, which is confirmed by elevated binding of She2p to PE-containing liposomes. These findings underscore the importance of ER membrane integrity in mRNA transport.
Si(SiMe3)2SiPh3 – a ligand for novel sub-valent tin cluster compounds
2014-01-01

[Si(SiMe<sub>3</sub>)<sub>2</sub>(SiPh<sub>3</sub>)]<sup>−</sup> can be used as a ligand in subvalent tin chemistry as shown by the synthesis of [Sn(Si(SiMe<sub>3</sub>)<sub>2</sub>SiPh<sub>3</sub>)<sub>2</sub>Cl]<sup>−</sup> and Cl<sub>4</sub>Sn<sub>4</sub>[Si(SiMe<sub>3</sub>)<sub>2</sub>SiPh<sub>3</sub>]<sub>4</sub>.
Antioxidant defense and stress protein induction following heat stress in the Mediterranean snailXeropicta derbentina[Pulmonata, Hygromiidae]
2014-01-01

Abstract The Mediterranean snail Xeropicta derbentina, being highly abundant in Southern France, has the need for efficient physiological adaptations to desiccation and over-heating posed by dry and hot environmental conditions. In consequence of heat, oxidative stress manifests in these organisms, which, in turn, leads to the formation of reactive oxygen species (ROS). In this study, we focused on adaptations on the biochemical level by investigation of antioxidant defenses and heat shock protein 70 (Hsp70) induction, both essential mechanisms of the heat stress response. We exposed snails to elevated temperature (25, 38, 40, 43, and 45°C) in the laboratory and measured the activity of the antioxidant enzymes catalase (CAT) and glutathione peroxidase (GPx), determined the Hsp70 level, and quantified lipid peroxidation. In general, we found a high constitutive level of CAT activity in all treatments, which may be interpreted as a permanent protection against ROS, i.e. hydrogen peroxide. CAT and GPx showed temperature-dependent activities: CAT activity was significantly increased in response to high temperatures (43 and 45°C), whereas GPx exhibited a significantly increased activity at 40°C, likely in response to high levels of lipid peroxides which already occurred in the 38°C treatment. Hsp70 showed a maximum induction at 40°C, followed by a decrease at higher temperatures. Our results reveal that X. derbentina possesses a set of efficient mechanisms to cope with damaging effects by heat. Furthermore, we could demonstrate that, beside the well documented Hsp70 stress response, the antioxidant defense plays a crucial role in these snails competence to survive extreme temperatures.
Disorganized behavior on Link's cube test is sensitive to right hemispheric frontal lobe damage in stroke patients
2014-01-01

One of Luria's favorite neuropsychological tasks for challenging frontal lobe functions was Link's cube test (LCT). The LCT is a cube construction task in which the subject must assemble 27 small cubes into one large cube in such a manner that only the painted surfaces of the small cubes are visible. We computed two new LCT composite scores, the constructive plan composite score, reflecting the capability to envisage a cubical-shaped volume, and the behavioral (dis-) organization composite score, reflecting the goal-directedness of cube construction. Voxel-based lesion-behavior mapping (VLBM) was used to test the relationship between performance on the LCT and brain injury in a sample of stroke patients with right hemisphere damage (N = 32), concentrated in the frontal lobe. We observed a relationship between the measure of behavioral (dis-) organization on the LCT and right frontal lesions. Further work in a larger sample, including left frontal lobe damage and with more power to detect effects of right posterior brain injury, is necessary to determine whether this observation is specific for right frontal lesions.
Early Pleistocene freshwater communities and rodents from the Pasinler Basin (Erzurum Province, north-eastern Turkey)
2014-01-01

The Pasinler-Horasan Basin is one of the major Cenozoic intramontane basins in eastern Anatolia. Geographically, the basin is situated close to the major regional drainage divide. The Pasinler-Horasan Basin itself is drained by
Turning Therapies: Placing Medical Diversity
2014-01-01

Click to increase image sizeClick to decrease image size ACKNOWLEDGMENTS We thank Henrike Donner and Michi Knecht who acted as discussants at the conference where this special issue was conceived. Additional informationNotes on contributorsKristine KrauseKRISTINE KRAUSE is Assistant Professor at the University of Amsterdam and Research Partner of the Max Planck Institute for the Study of Religious and Ethnic Diversity, Göttingen. Her research interests include political subjectivity and care, transnationalism and health, and medicine and religion, particularly global Pentecostalism.David ParkinDAVID PARKIN is Professor Emeritus of Social Anthropology at the University of Oxford, England, Honorary Professor at the School of Oriental and African Studies, London, and Senior Research Partner of the Max Planck Institute for the Study of Religious and Ethnic Diversity in Göttingen. He studies Islam and healing systems among Swahili-speaking Muslims and other Bantu-speaking non-Muslims in coastal eastern Africa, including Zanzibar. He has a general interest in cross-cultural semantics and language use.Gabi AlexGABI ALEX is Professor in the Department of Social and Cultural Anthropology, Eberhard Karls Universität Tübingen and Senior Research Partner of the Max Planck Institute for the Study of Religious and Ethnic Diversity in Göttingen. Her research interests include medical anthropology, ethnicity, healing and identity, and youth and childhood, on which she has conducted research in India and Germany.
Staurosporine-Induced Cell Death in &lt;em&gt;Trypanosoma brucei&lt;/em&gt; and the Role of Endonuclease G during Apoptosis
2014-01-01

Apoptosis in single-cell organisms like Trypanosoma or Leishmania was characterized in several studies in the last few years [1]-[4]. Cell death in these caspase lacking protozoa is still poorly understood and a conclusive apoptotic pathway has not been identified so far. In the work presented here, we studied the effects of prostaglandin D2 and staurosporine induced cell death in blood-forms of Trypanosoma brucei in a time dependent manner and focused on the role of a nuclease similar to endonuclease G of higher eukaryotes. We found that these parasites undergo apoptotic cell death as demonstrated by the appearance of several canonical hallmarks of apoptosis in higher eukaryotes, but that different stimuli induce remarkable differences in the way these cells die. We compared the effects of prostaglandin D2 and staurosporine in trypanosomes with and without endonuclease G overexpression by flow cytometric and electron microscopic methods with the result that endonuclease G overexpression led to a significant modification of intracellular organelles and accelerated apoptotic cell death in prostaglandin D2 or staurosporine treated cells. Our results demonstrate that different stimuli induce apoptosis even in these ancient organisms in different caspase-independent ways. Whereas central processes of apoptosis like ROS formation, loss of mitochondrial membrane potential, endonuclease G release, phosphatidylserine exposure and DNA fragmentation appeared in the same chronology during treatment with either one of both drugs, other effects like cell cycle arrest or change of cell shape occurred only in the case of prostaglandin D2 or staurosporine treatment. We conclude from these results that trypanosomes react to stimuli of apoptosis with the concerted action of cellular responses but cannot control the final outcome if additional stress, as in the case of staurosporine, is superimposed.
Performance Studies on Distributed Virtual Screening
2014-01-01

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs). We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation. Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid). As input we used benchmark datasets for protein kinases. Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly.
On hitting probabilities of beta coalescents and absorption times of coalescents that come down from innity
2014-01-01

Let X = (Xk)k=0;1;::: denote the jump chain of the block counting process of the -coalescent with = (2 ; ) being the beta distribution with parameter 2 (0;2). A solution for the hitting probability h(n;m) that the chain X ever visits the state m, conditional that it starts in the state X0 = n, is obtained via an analytic method based on generating functions. For 2 (1;2) the results are applied to characterize the distribution of the almost sure limit of the absorption times n of the coalescent restricted to a sample of size n. The latter result is generalized to arbitrary exchangeable coalescents (-coalescents) that come down
Radiocarbon Dating, Mineralogy, and Isotopic Composition of Hackberry Endocarps from the Neolithic Site of Aşikli Höyük, Central Turkey
2014-01-01

Carbonate is abundant in many Neolithic tells and is a potentially useful archive for dating and climate reconstruction. In this paper, we focus on the mineralogy, radiocarbon dating, and stable isotope systematics of carbonate in hackberry endocarps. Hackberry fruits and seeds are edible in fresh and stored forms, and they were consumed in large quantities in many Neolithic sites in the Near East, including the site of our study, Aşıkli Höyük in central Anatolia, an Aceramic Neolithic tell occupied from about 9.4 to &gt; 10.3 BP (7.4 to &gt; 8.3 BCE). Detailed 14 C age control provided by archaeological charcoal permits a test of the fidelity in 14 C dating of hackberry endocarps. Modern endocarps and leaves yield fraction modern 14 C values of 1.050–1.066, consistent with levels present in the atmosphere when sampled in 2009. On the other hand, archaeological endocarps yield consistently younger ages than associated charcoal by ca. 130 14 C years (ca. 220 calendar years) for samples about 10,000 years old. We speculate this is caused by the slight addition of calcite or recrystallization to calcite in the endocarp, as detected by scanning electron microscopy. Subtle addition or replacement of calcite by primary aragonite is not widely recognized in the 14 C community, even though similar effects are reported from other natural carbonates such as shell carbonate. This small (but consistent) level of contamination supports the usefulness of endocarps in dating where other materials like charcoal are lacking. Before dating, however, hackberries should be carefully screened for mineralogical preservation and context. We examined the carbon and oxygen isotopic systematics of the fossil endocarps to try to establish potential source areas for harvesting. Most of the hackberries are enriched in 18 O compared to local water sources, indicating that they were drawing on highly evaporated soil water, rather than the local (perched and regional) water table sampled in our study. Isotopic evidence therefore suggests that most but not all of the hackberries were harvested from nearby mesas well above the local streams and seeps fed by the water table.
Augmenting Plasticity Induction in Human Motor Cortex by Disinhibition Stimulation
2014-01-01

Cellular studies showed that disinhibition, evoked pharmacologically or by a suitably timed priming stimulus, can augment long-term plasticity (LTP) induction. We demonstrated previously that transcranial magnetic stimulation evokes a period of presumably GABA(B)ergic late cortical disinhibition (LCD) in human primary motor cortex (M1). Here, we hypothesized that, in keeping with cellular studies, LCD can augment LTP-like plasticity in humans. In Experiment 1, patterned repetitive TMS was applied to left M1, consisting of 6 trains (intertrain interval, 8 s) of 4 doublets (interpulse interval equal to individual peak I-wave facilitation, 1.3-1.5 ms) spaced by the individual peak LCD (interdoublet interval (IDI), 200-250 ms). This intervention (total of 48 pulses applied over ∼45 s) increased motor-evoked potential amplitude, a marker of corticospinal excitability, in a right hand muscle by 147% ± 4%. Control experiments showed that IDIs shorter or longer than LCD did not result in LTP-like plasticity. Experiment 2 indicated topographic specificity to the M1 hand region stimulated by TMS and duration of the LTP-like plasticity of 60 min. In conclusion, GABA(B)ergic LCD offers a powerful new approach for augmenting LTP-like plasticity induction in human cortex. We refer to this protocol as disinhibition stimulation (DIS).
Pyrene chromophores for the photoreversal of psoralen interstrand crosslinks
2014-01-01

Applying psoralen interstrand crosslinks for the photoactivation of nucleic acids is a new concept. To find chromophores that can efficiently stimulate crosslink repair we screened several pyrenes and appended them to peptide nucleic acids for their site-selective addressing. Even though pyrenes conjugated to uracil revealed desirable spectroscopic properties they were not effective in crosslink reversal. In contrast, bare pyrenes are well suitable for crosslink repair with 350 nm light showing an uncaging efficiency similar to classical photocaging groups.
Correlation analysis of histomorphometry and motor neurography in the median nerve rat model.
2014-01-01

These results contribute in a better interpretation of morphological predictors of nerve regeneration and verify the previously described electrophysiological assessment in the median nerve rat model as a valid method.
Spinal cord - skeletal muscle cocultures detect muscle-relaxant action of botulinum neurotoxin A
2014-01-01

The mouse LD50 assay is routinely used for potency testing of botulinum toxins. Unfortunately, this test is associated with severe pain and distress in animals and requires large quantities of mice. Here we used cocultures of spinal cord and muscle tissue as an alternative for probing botulinum toxins. Cocultures were prepared from mouse embryonic tissue (C57/BL6J) and cultured for 24-27 days. In these cultures spontaneous muscle activity was quantified in sham- and botulinum toxin-treated cultures for up to 3 days by video microscopy. At a concentration of 58 fmol/L or higher, incobotulinumtoxin A significantly reduced the frequency of muscle contractions within 24 hours after incubation. Hence, nerve-muscle-cultures are similar sensitive as the mouse LD50 assay. The limit of detection, as observed in our study, is close to the most sensitive cell-based bioassays, capable to detect concentrations of botulinum neurotoxin A between 30 and 50 fmol/L. However, spontaneous muscle activity of individual cultures displayed considerable fluctuations when evaluated on a day-to-day basis. Generally, the authors would like to emphasize, that in its present form, this in vitro assay might be too laborious for botulinum toxin potency testing. Thus, methodical improvements to decrease data variability are the next milestone to be passed towards developing this model into an assay that can be utilized for reducing animal experimentation.
Evaluating Emotions
2014-01-01

How are emotions related to values? This book argues against a perceptual theory of emotions, which sees emotions as perception-like states that help us gain evaluative knowledge, and argues for a car
Reporting of dental status from full-arch radiographs: Descriptive analysis and methodological aspects
2014-01-01

Data about dental findings from radiographs is, if at all possible, only comparable with serious limitations. A standardization of both, assessing and reporting entities of dental status from radiographs is missing and has to be established within a report guideline.
Age-dependent neuroprotection of retinal ganglion cells by tempol-C8 acyl ester in a rat NMDA toxicity model
2014-01-01

In contrast to tempol itself, tempol-C8 acyl ester was neuroprotective in pre-adolescent rats in the NMDA- induced RGC damage model. Therefore, neuroprotection by tempol acyl esters seems to be superior to that of tempol under certain conditions.
Beta Decay and the Cosmic Neutrino Background
2014-01-01

In 1964 Penzias and Wilson detected the Cosmic Microwave Background (CMB). Its spectrum follows Planck’s black body radiation formula and shows a remarkable constant temperature of T0γ ≈ 2:7 K independent of the direction. The present photon density is about 370 photons per cm3. The size of the hot spots, which deviates only in the fifth decimal of the temperature from the average value, tells us, that the universe is flat. About 380 000 years after the Big Bang at a temperature of T0γ = 3000 K already in the matter dominated era the electrons combine with the protons and the 4He and the photons move freely in the neutral universe. So the temperature and distribution of the photons give us information of the universe 380 000 years after the Big Bang. Information about earlier times can, in principle, be derived from the Cosmic Neutrino Background (CνB). The neutrinos decouple already 1 second after the Big Bang at a temperature of about 1010 K. Today their temperature is ∼ 1:95 K and the average density is 56 electron-neutrinos per cm3. Registration of these neutrinos is an extremely challenging experimental problem which can hardly be solved with the present technologies. On the other hand it represents a tempting opportunity to check one of the key element of the Big Bang cosmology and to probe the early stages of the universe evolution. The search for the CνB with the induced beta decay νe + 3H → 3He + e− is the topic of this contribution. The signal would show up by a peak in the electron spectrum with an energy of the neutrino mass above the Q value. We discuss the prospects of this approach and argue that it is able to set limits on the CνB density in our vicinity. We also discuss critically ways to increase with modifications of the present KATRIN spectrometer the source intensity by a factor 100, which would yield about 170 counts of relic neutrino captures per year. This would make the detection of the Cosmic Neutrino Background possible. Presently such an increase seems not to be possible. But one should be able to find an upper limit for the local density of the relic neutrinos (Cosmic Neutrino Background) in our galaxy.
Syntheses, structures and flexible coordination of sterically demanding di- and “tri”-lithiated methandiides
2014-01-01

Sequential lithiation of a sterically demanding bis(iminophosphoranyl)methane afforded di- and trianionic methandiide lithium complexes and their structures and coordination behaviour have been studied with solid state and solution methods.
Predicting Wrist Movement Trajectory from Ipsilesional ECoG in Chronic Stroke Patients
2014-01-01

Recently, there have been several approaches to utilize a Brain-Computer Interface (BCI) for chronic stroke patients. The prediction of movement trajectory based on recorded brain activity could thereby help to improve BCI-guided stroke rehabilitation or could be used for control of an assistive device, like an orthosis or a robotic arm. One problem in predicting movement trajectory in stroke patients are compensatory movements, which make it difficult to link specific brain activity to movement intention. In this paper we compare different methods for trajectory prediction and show how Canonical Correlation Analysis (CCA) can be used to predict movement trajectories. Based on the results, we argue that the resulting trajectory prediction is closer to the actual movement intention. We further show how the transformation matrices obtained by CCA can be interpreted and discuss how this interpretation might be useful to get information regarding compensatory movements in stroke and the underlying patterns of brain activity.
Stiffness of Left Ventricular Cardiac Fibroblasts Is Associated With Ventricular Dilation in Patients With Recent-Onset Nonischemic and Nonvalvular Cardiomyopathy
2014-01-01

Our data suggest that a decrease in single-cell stiffness of left ventricular fibroblasts could trigger left ventricular dilation in patients with ROCM. This implies a new potential mechanism for the ventricular dilation with this disease.