julilili42/papers huggingface dataset:
A long-term intensive behavioral treatment study in patients with persistent vegetative state or minimally conscious state
2011-01-01

This study indicates the possibility of achieving behavioural improvements with regard to the responsiveness of patients with long-lasting persistent vegetative state and minimally conscious state by use of long-term treatment.
Regulation of the Glutamate Transporters by JAK2
2011-01-01

The Janus-activated kinase-2 JAK2 is involved in the signaling of leptin and erythropoietin receptors and mediates neuroprotective effects of the hormones. In theory, JAK2 could be effective through modulation of the glutamate transporters, carriers accounting for the clearance of glutamate released during neurotransmission. The present study thus elucidated the effect of JAK2 on the glutamate transporters EAAT1, EAAT2, EAAT3 and EAAT4. To this end, cRNA encoding the carriers was injected into Xenopus oocytes with or without cRNA encoding JAK2 and glutamate transport was estimated from glutamate induced current (I(glu)). I(glu) was observed in Xenopus oocytes expressing EAAT1 or EAAT2 or EAAT3 or EAAT4, but not in water injected oocytes. Coexpression of JAK2 resulted in an increase of I(glu) by 83% (EAAT1), 67% (EAAT2), 42% (EAAT3) and 126% (EAAT4). As shown for EAAT4 expressing Xenopus oocytes, the effect of JAK2 was mimicked by gain of function mutation (V617F)JAK2 but not by the inactive mutant (K882E)JAK2. Incubation with JAK2 inhibitor AG490 (40 μM) resulted in a gradual decrease of I(glu) by 53%, 79% and 92% within 3, 6 and 24 hours. Confocal microscopy and chemiluminescence analysis revealed that JAK2 coexpression increased EAAT4 protein abundance in the cell membrane. Disruption of transcription did not appreciably modify the up-regulation of I(glu) in EAAT4 expressing oocytes. The decay of I(glu) following inhibition of carrier insertion with brefeldin A was similar in oocytes expressing EAAT4 + JAK2 and oocytes expressing EAAT4 alone, indicating that JAK2 did not appreciably affect carrier retrieval from the membrane. In conclusion, JAK2 is a novel powerful regulator of glutamate transporters and thus participates in the protection against excitotoxicity.
Functional Characterization of Three Aquaglyceroporins from <i>Trypanosoma brucei</i> in Osmoregulation and Glycerol Transport
2011-01-01

Previous studies using bloodstream form Trypanosoma brucei have shown that glycerol transport in this parasite occurs via specific membrane proteins, namely a glycerol transporter and glycerol channels [1]. Later, we cloned, expressed and characterized the transport properties of all three aquaglyceroporins (AQP1-3) [2], which were found permeable for water, glycerol and other small uncharged solutes like dihydroxyacetone [3]. Here, we report on the cellular localization of TbAQP1 and TbAQP3 in bloodstream form trypanosomes. Indirect immunofluorescence analysis showed that TbAQP1 is exclusively localized in the flagellar membrane, whereas TbAQP3 was found in the plasma membrane.In addition, we analyzed the functions of all 3 AQPs, using an inducible inheritable double-stranded RNA interference methodology. All AQP knockdown cell lines were still able to survive hypo-osmotic stress conditions, except AQP2 knockdown parasites. Depleted TbAQP2 negatively impacted cell growth and the regulatory volume recovery, whereas AQP1 und 3 knockdown trypanosomes displayed phenotypes consistent with their localization in external membranes. A simultaneous knockdown of all 3 AQPs showed that the cells were able to substitute the missing glycerol uptake capability through a putative glycerol transporter.
Structural and functional protein network analyses predict novel signaling functions for rhodopsin
2011-01-01

Orchestration of signaling, photoreceptor structural integrity, and maintenance needed for mammalian vision remain enigmatic. By integrating three proteomic data sets, literature mining, computational analyses, and structural information, we have generated a multiscale signal transduction network linked to the visual G protein-coupled receptor (GPCR) rhodopsin, the major protein component of rod outer segments. This network was complemented by domain decomposition of protein-protein interactions and then qualified for mutually exclusive or mutually compatible interactions and ternary complex formation using structural data. The resulting information not only offers a comprehensive view of signal transduction induced by this GPCR but also suggests novel signaling routes to cytoskeleton dynamics and vesicular trafficking, predicting an important level of regulation through small GTPases. Further, it demonstrates a specific disease susceptibility of the core visual pathway due to the uniqueness of its components present mainly in the eye. As a comprehensive multiscale network, it can serve as a basis to elucidate the physiological principles of photoreceptor function, identify potential disease-associated genes and proteins, and guide the development of therapies that target specific branches of the signaling pathway.
Analysis of Polymorphisms in the Lactotransferrin Gene Promoter and Dental Caries
2011-01-01

Regarding host aspects, there has been strong evidence for a genetic component in the etiology of caries. The salivary protein lactotransferrin (LTF) exhibits antibacterial activity, but there is no study investigating the association of polymorphisms in the promoter region of LTF gene with caries. The objective of this study was firstly to search the promoter region of the human LTF gene for variations and, if existent, to investigate the association of the identified polymorphisms with dental caries in 12-year-old students. From 687 unrelated, 12-year-old, both sex students, 50 individuals were selected and divided into two groups of extreme phenotypes according to caries experience: 25 students without (DMFT = 0) and 25 with caries experience (DMFT ≥ 4). The selection of individuals with extreme phenotypes augments the chances to find gene variations which could be associated with such phenotypes. LTF gene-putative promoter region (+39 to −1143) of the selected 50 individuals was analyzed by high-resolution melting technique. Fifteen students, 8 without (DMFT = 0) and 7 with caries experience (mean DMFT = 6.28), presented deviations of the pattern curve suggestive of gene variations and were sequenced. However, no polymorphisms were identified in the putative promoter region of the LTF gene.
Competition between grain growth and grain-size reduction in polar ice
2011-01-01

Abstract Static (or ‘normal’) grain growth, i.e. grain boundary migration driven solely by grain boundary energy, is considered to be an important process in polar ice. Many ice-core studies report a continual increase in average grain size with depth in the upper hundreds of metres of ice sheets, while at deeper levels grain size appears to reach a steady state as a consequence of a balance between grain growth and grain-size reduction by dynamic recrystallization. The growth factor k in the normal grain growth law is important for any process where grain growth plays a role, and it is normally assumed to be a temperature-dependent material property. Here we show, using numerical simulations with the program Elle, that the factor k also incorporates the effect of the microstructure on grain growth. For example, a change in grain-size distribution from normal to log-normal in a thin section is found to correspond to an increase in k by a factor of 3.5.
Introduction to Aquatic Redox Chemistry
2011-01-01

Oxidation-reduction (redox) reactions are among the most important and interesting chemical reactions that occur in aquatic environmental systems, including soils, sediments, aquifers, rivers, lakes, and water treatment systems. Redox reactions are central to major element cycling, to many sorption processes, to trace element mobility and toxicity, to most remediation schemes, and to life itself. Over the past 20 years, a great deal of research has been done in pursuit of process-level understanding aquatic redox chemistry, but the field is only beginning to converge around a unified body of knowledge. This chapter provides a very broad overview of the state of this convergence, including clarification of key terminology, some relatively novel examples of core thermodynamic concepts (involving redox ladders and Eh-pH diagrams), and some historical perspective on the persistent challenges of how to characterize redox intensity and capacity of real, complex, environmental materials. Finally, the chapter attempts to encourage further convergence among the many facets of aquatic redox chemistry by briefly reviewing major themes in this volume and several past volumes that overlap partially with this scope.
Impact of Bicarbonate, Ammonium Chloride, and Acetazolamide on Hepatic and Renal SLC26A4 Expression
2011-01-01

SLC26A4 encodes pendrin, a transporter exchanging anions such as chloride, bicarbonate, and iodide. Loss of function mutations of SLC26A4 cause Pendred syndrome characterized by hearing loss and enlarged vestibular aqueducts as well as variable hypothyroidism and goiter. In the kidney, pendrin is expressed in the distal nephron and accomplishes HCO(3)(-) secretion and Cl(-) reabsorption. Renal pendrin expression is regulated by acid-base balance. The liver contributes to acid-base regulation by producing or consuming glutamine, which is utilized by the kidney for generation and excretion of NH(4)(+), paralleled by HCO(3)(-) formation. Little is known about the regulation of pendrin in liver. The present study thus examined the expression of Slc26a4 in liver and kidney of mice drinking tap water without or with NaHCO(3) (150 mM), NH(4)Cl (280 mM) or acetazolamide (3.6 mM) for seven days. As compared to Gapdh transcript levels, Slc26a4 transcript levels were moderately lower in liver than in renal tissue. Slc26a4 transcript levels were not significantly affected by NaHCO(3) in liver, but significantly increased by NaHCO(3) in kidney. Pendrin protein expression was significantly enhanced in kidney and reduced in liver by NaHCO(3). Slc26a4 transcript levels were significantly increased by NH(4)Cl and acetazolamide in liver, and significantly decreased by NH(4)Cl and by acetazolamide in kidney. NH(4)Cl and acetazolamide reduced pendrin protein expression significantly in kidney, but did not significantly modify pendrin protein expression in liver. The observations point to expression of pendrin in the liver and to opposite effects of acidosis on pendrin transcription in liver and kidney.
The functor of toric varieties associated with Weyl chambers and Losev-Manin moduli spaces
2011-01-01

A root system of rank defines an -dimensional smooth projective toric variety associated with its fan of Weyl chambers. We give a simple description of the functor of in terms of the root system and apply this result in the case of root systems of type to give a new proof of the fact that the toric variety is the fine moduli space of stable -pointed chains of projective lines investigated by Losev and Manin.
Influence of Dexamethasone on Na<sup>+</sup>/H<sup>+</sup> Exchanger Activity in Dendritic Cells
2011-01-01

Glucocorticoids regulate the function of dendritic cells (DCs), antigen-presenting cells linking innate and adaptive immunity. Glucocorticoids influence the function of other cell types by modulating the activity of the Na(+)/H(+)exchanger (NHE), a carrier involved in the regulation of cytosolic pH and cell volume. The present study explored whether dexamethasone influences Na(+)/H(+) exchanger activity in DCs. The DCs were isolated from mouse bone marrow, cell volume was estimated from forward scatter in FACS analysis, cytosolic pH (pH(i)) utilizing BCECF fluorescence and Na(+)/H(+) exchanger activity from the Na(+) dependent realkalinization after an ammonium pulse. Treatment with the glucocorticoid dexamethasone (100 nM; 1, 4, 16 and 24h) significantly decreased pH(i) (≥4 h) and gradually increased Na(+)/H(+) exchanger activity (=16 h). The stimulation of Na(+)/H(+) exchanger activity by dexamethasone was virtually abrogated by glucocorticoid receptor blocker mefiprestone (1 μM) and NHE3 inhibitor dimethyl amiloride (5 μM), but not prevented by NHE1 inhibitor cariporide (10 μM). Dexamethasone treatment significantly increased SGK1 mRNA levels. Stimulation of Na(+)/H(+) exchanger activity by dexamethasone was blunted in DCs lacking SGK1. Dexamethasone treatment did not significantly alter ROS formation but significantly decreased the forward scatter. Exposure of DCs to lipopolysacharide (LPS, 1 μg/ml) led to a transient increase followed by a decline of Na(+)/H(+) exchanger activity and to enhanced forward scatter as well as ROS formation, all effects significantly blunted in the presence of dexamethasone (100 nM). In conclusion, glucocorticoid treatment decreased pH(i) and cell volume, effects paralleled by upregulation of Na(+)/H(+) exchanger activity in DCs. Moreover, glucocorticoids blunted the stimulation of Na(+)/H(+) exchanger activity, cell swelling and ROS formation following LPS treatment.
Association of Clusterin Gene Polymorphisms with Late-Onset Alzheimer’s Disease
2011-01-01

&lt;i&gt;Background/Aims:&lt;/i&gt; Some studies have implicated the role of apolipoprotein J [clusterin (CLU), apoJ] in the pathogenesis of Alzheimer’s disease (AD). In this study, we investigated the polymorphisms rs11136000 and rs9331888 within CLU in late-onset sporadic AD (LOAD) patients and nondemented subjects. &lt;i&gt;Methods:&lt;/i&gt; LOAD patients and control subjects were analyzed. Genotyping of rs11136000 and rs9331888 was performed using standard PCR following different restriction endonuclease digestion. &lt;i&gt;Results:&lt;/i&gt; Although there were no significant differences in genotype frequencies of these two polymorphisms, the haplotype CG was associated with a statistically significantly increased LOAD risk. &lt;i&gt;Conclusion:&lt;/i&gt; The rs11136000 and rs9331888 polymorphisms of the CLU gene are associated with LOAD.
A longitudinal study of dominance and aggression in greylag geese (Anser anser)
2011-01-01

A variety of factors are known to affect dominance and aggression in social vertebrates. In the present study, we used a long-term data set on greylag geese (Anser anser) to investigate the complex relationships between individual life histories, the social environment, and dominance-related behaviors. We applied a multifactorial approach to assess the relative importance of factors in different life-history stages. Previous studies in geese documented effects of sex and social status and achieved differing results for the effects of family size, age, and body weight on dominance and aggression. Extrinsic factors like season or flock structure were generally not considered. Our analyses showed that a considerable number of factors related to individual life histories, season, and the social environment affected dominance and aggression in greylag geese, but not all significant effects were necessarily strong effects. Pronounced effects on aggression rates were caused by the flock's sex ratio, parental effects, individual social status, and sex. Whether individuals interacted with the same opponents repeatedly was influenced most by parental effects and the sex ratio, whereas the strongest determinants of dominance rank were parental effects and social status. Hence, dominance behaviors may not only be influenced by intrinsic factors but also by season and an individual's social environment. Furthermore, our study indicates that optimal choices for achieving or maintaining a high dominance rank may vary considerably between life-history stages. This highlights the value of long-term studies and multifactorial approaches for understanding the complexities of dominance relationships in social vertebrates
Optical imaging of excited-state tautomerization in single molecules
2011-01-01

Tautomerism process of single fluorescent molecules was studied by means of confocal microscopy in combination with azimuthally or radially polarized laser beams. During a tautomerism process the transition dipole moment (TDM) of a molecule changes its orientation which can be visualized by the fluorescence excitation image of the molecule. We present experimental and theoretical studies of two porphyrazine-type molecules and one type of porphyrin molecule: a symmetrically substituted metal-free phthalocyanine and porphyrin, and nonsymmetrically substituted porphyrazine. In the case of phthalocyanine the fluorescence excitation patterns show that the angle between the transition dipole moments of the two tautomeric forms is near 90°, in agreement with quantum chemical calculations. For porphyrazine we find that the orientation change of the TDM is less than 60° or larger than 120°, as theoretically predicted. Most of the porphyrin molecules show no photoinduced tautomerization, while for 7% of the total number of investigated molecules we observed excitation patterns of two different trans forms of the same single molecule. We demonstrate for the first time that a molecule, undergoing a tautomerism process stays in one tautomeric trans conformation during a time comparable with the acquisition time of one excitation pattern. This allowed us to visualize the existence of each of the two trans forms of one single porphyrin molecule, as well as the sudden switching between these tautomers.
Kinematic evolution of the eastern Tethyan Himalaya: constraints from magnetic fabric and structural properties of the Triassic flysch in SE Tibet
2011-01-01

Abstract Anisotropy of magnetic susceptibility (AMS) combined with structural analysis are used in this work with the aim to characterize the tectonic evolution of the Triassic flysch within the eastern Tethyan Himalaya Thrust Belt in SE Tibet. The attitude of the magnetic foliation and lineation are concordant with the planar and linear structures of tectonic origin defined by the preferred orientation of the iron-bearing silicates. Two different tectonic domains can be defined: (a) the southern domain is controlled by the Eohimalayan tectonic foliation (S1) recorded in the magnetic foliation which trends east–west and dips to the north; (b) the northern domain is dominated by the Neohimalayan magnetic foliation with WNW–ESE strike and dips to the south opposite to the vergence of the main structures. A slightly prolate magnetic ellipsoid has been found in between the two domains recording the intersection of S1 and the subtle development of the S2 tectonic foliation. Hinterland propagation of the deformation lead to the Great Counter backthrust generation, pointed out by the SSW steeply plunging magnetic lineation. Furthermore different orientations of magnetic foliation may indicate an Early Miocene c. 20° clockwise vertical-axis rotation.
Regulatory T Cells and Parasites
2011-01-01

Human host encounters a wide array of parasites; however, the crucial aspect is the failure of the host immune system to clear these parasites despite antigen recognition. In the recent past, a new immunological concept has emerged, which provides a framework to better understand several aspects of host susceptibility to parasitic infection. It is widely believed that parasites are able to modulate the magnitude of effector responses by inducing regulatory T cell (Tregs) population and several studies have investigated whether this cell population plays a role in balancing protective immunity and pathogenesis during parasite infection. This review discusses the several mechanism of Treg‐mediated immunosuppression in the human host and focuses on the functional role of Tregs and regulatory gene polymorphisms in infectious diseases.
Integrating parallel analysis modules to evaluate the meaning of answers to reading comprehension questions
2011-01-01

Contextualised, meaning-based interaction in the foreign language is widely recognised as crucial for second language acquisition. Correspondingly, current exercises in foreign language teaching generally require students to manipulate both form and meaning. For intelligent language tutoring systems to support such activities, they thus must be able to evaluate the appropriateness of the meaning of a learner response for a given exercise. We discuss such a content-assessment approach, focusing on reading comprehension exercises. We pursue the idea that a range of simultaneously available representations at different levels of complexity and linguistic abstraction provide a good empirical basis for content assessment. We show how an annotation-based NLP architecture implementing this idea can be realised and that it successfully performs on a corpus of authentic learner answers to reading comprehension questions. To support comparison and sustainable development on content assessment, we also define a general exchange format for such exercise data.
Decreased α-Synuclein Serum Levels in Patients with Lewy Body Dementia Compared to Alzheimer’s Disease Patients and Control Subjects
2011-01-01

&lt;i&gt;Background/Aims:&lt;/i&gt; Detection and differentiation of neurodegenerative dementias, such as dementia with Lewy bodies (DLB) and Alzheimer’s disease (AD), with blood-based biomarkers would facilitate diagnosis and treatment. &lt;i&gt;Methods:&lt;/i&gt; By use of a commercially available ELISA kit, we measured α-synuclein levels in the serum of 40 DLB patients and controls, and of 80 AD patients. &lt;i&gt;Results:&lt;/i&gt; We found significantly reduced α-synuclein serum levels in DLB compared to both AD (p = 0.006) and control subjects (p = 0.001), reaching an area under the curve of &gt;0.70. &lt;i&gt;Conclusion:&lt;/i&gt; Although these results do not justify a definition of serum α-synuclein as a potential single biomarker, results may contribute to a multimarker strategy in DLB diagnosis.
Proteomics analysis identifies PARK7 as an important player for renal cell resistance and survival under oxidative stress
2011-01-01

Renal fibrosis is a process that is characterized by declining excretory renal function. The molecular mechanisms of fibrosis are not fully understood. Oxidative stress pathways were reported to be involved in renal tissue deterioration and fibrosis progression. In order to identify new molecular targets associated with oxidative stress and renal fibrosis, differential proteomics analysis was performed with established renal cell lines (TK173 and HK-2). The cells were treated with oxidative stress triggering factor H(2)O(2) and the proteome alterations were investigated. Two dimensional protein maps were generated and differentially expressed proteins were processed and identified using mass spectrometry analysis combined with data base search. Interestingly the increase of ROS in the renal cell lines upon H(2)O(2) treatment was accompanied by alteration of a large number of proteins, which could be classified in three categories: the first category grouped the proteins that have been described to be involved in fibrogenesis (e.g. ACTA2, VIN, VIM, DES, KRT, COL1A1, COL4A1), the second category, which was more interesting involved proteins of the oxidative stress pathway (PRDX1, PRDX2, PRDX6, SOD, PARK7, HYOU1), which were highly up-regulated under oxidative stress, and the third category represented proteins, which are involved in different other metabolic pathways. Among the oxidative stress proteins the up-regulation of PARK7 was accompanied by a shift in the pI as a result of oxidation. Knockdown of PARK7 using siRNA led to significant reduction in renal cell viability under oxidative stress. Under H(2)O(2) treatment the PARK7 knockdown cells showed up to 80% decrease in cell viability and an increase in apoptosis compared to the controls. These results highlight for the first time the important role of PARK7 in oxidative stress resistance in renal cells.