julilili42/papers huggingface dataset:
Sr Nd Pb isotopic compositions of Early Cretaceous granitoids from the Dabie orogen: Constraints on the recycled lower continental crust
2012-10-27

In order to characterize the recycled lower continental crust (LCC) in the Dabie orogen, 17 Early Cretaceous low-Mg adakitic (LMA) and 9 normal (non-adakitic) granitoids have been investigated for Sr-Nd-Pb isotopes. Combined with literature data, LMA have low epsilon(Nd)(t) (-27.8 to -14.7) and Pb-206/Pb-204(i) (15.69-17.16) and low to moderately high Sr-87/Sr-86(i) (0.7066 to 0.7087) ratios. Normal granitoids yield isotope ratios similar to adakitic rocks, except a few with Sr-87/Sr-86 (i) up to 0.7105. Dabie LMA define a linear trend parallel to the North Hemisphere Reference Line (NHRL) in a Pb-208/Pb-204(i)- Pb-206/Pb-204(i) diagram. For a given Pb-206/Pb-204(i), the Pb-208/Pb-204(i) or Delta 8/4 (152-217) of Dabie LMA are close to the majority of UHP gneisses and the Neoproterozoic mafic rocks from the northern margin of the South China Block (SCB), but significantly higher than adakitic rocks from the North China Block (Delta 8/4<150). Considering the commonly present Neoproterozoic inherited zircons, we suggest that the LMA in the Dabie orogen are derived from a thickened LCC that could be dominantly composed of ancient SCB lower crust. The Sr-Nd-Pb isotopic composition of LMA are similar to those of Post-Collisional Mafic Igneous rocks (PCMI) from the Dabie orogen, but different to exhumed UHP rocks. The Sr-Nd-Pb isotopic system of the mantle source of the PCMI could be enriched in components dominantly from delaminated LCC of the Dabie orogen instead of deeply subducted continental crust, which is in contrast to O- and C-isotope data by [Zhao, Z.F., Zheng, Y.F., Wei, C.S., Wu, Y.B., Chen, F.K, and Jahn, B.M., 2005. Zircon U-Pb age, element and C-O isotope geochemistry of post-collisional mafic-ultramafic rocks from the Dabie orogen in east-central China. Lithos 83(1-2), 1-28; Dai, L.Q., Zhao, Z.F., Zheng, Y.F., Li, Q.L., Yang, Y.H., and Dai, M.N., 2011. Zircon Hf-O isotope evidence for crust-mantle interaction during continental deep subduction. Earth and Planetary Science Letters 308, 229-244]. Combining the Sr-Nd- Pb-Hf and O-C isotopic data, two types of commonly present magma components have been identified in the PCMI, reflecting crust-mantle interaction during the Triassic subduction and the Early Cretaceous orogen collapse, respectively. (C) 2012 Elsevier B.V. All rights reserved.
Biochemical Large-Scale Identification of MHC Class I Ligands
2012-10-29

The large-scale identification of MHC class I presented peptides is indispensable for gaining insight into the fundamental rules of immune recognition as well as it is an invaluable tool in identifying potential targets for the immunotherapy of disease. In this chapter we briefly review the existing strategies for the analysis of MHC ligandomes and provide an in-depth protocol for the immunoaffinity purification of MHC class I presented peptides from primary tissues or cells.
Characterization of a mazEF Toxin-Antitoxin Homologue from Staphylococcus equorum
2012-10-29

ABSTRACT Toxin-antitoxin (TA) systems encoded in prokaryotic genomes fall into five types, typically composed of two distinct small molecules, an endotoxic protein and a cis -encoded antitoxin of ribonucleic or proteinaceous nature. In silico analysis revealed seven putative type I and three putative type II TA systems in the genome of the nonpathogenic species strain Staphylococcus equorum SE3. Among these, a MazEF system orthologue termed MazEF seq was further characterized. 5′ rapid amplification of cDNA ends (RACE) revealed the expression and the transcriptional start site of mazE seq , indicating an immediately upstream promoter. Heterologous expression of the putative toxin-encoding mazF seq gene imposed growth cessation but not cell death on Escherichia coli . In vivo and in vitro , MazF seq was shown to cleave at UACAU motifs, which are remarkably abundant in a number of putative metabolic and regulatory S. equorum gene transcripts. Specific interaction between MazF seq and the putative cognate antitoxin MazE seq was demonstrated by bacterial two-hybrid analyses. These data strongly suggest that MazEF seq represents the first characterized TA system in a nonpathogenic Staphylococcus species and indicate that MazEF modules in staphylococci may also control processes beyond pathogenicity.
On the origin of sellaite (MgF2)-rich deposits in Mg-poor environments
2012-10-29

Sellaite (MgF2) forms from melts, fluids, and gases under variable temperature, pressure, fO2, and fluid salinity conditions. It is typically associated with, but much rarer, than fluorite (CaF2). The Clara mine near Oberwolfach (Schwarzwald, Germany) is an extensive hydrothermal vein-type deposit, where sellaite occurs in huge quantities (thousands of tons) in veins of mostly Jurassic/Cretaceous age. The sellaite mineralization, occurring in gneisses altered prior to and during sellaite mineralization, represents a stockwork-like network of veins and fissures, which is overlain and sealed by sediments, preventing the inflow of and fluid-mixing with sedimentary formation waters. The occurrence of sellaite is unique among the more than 1000 hydrothermal vein-type occurrences of the Schwarzwald ore district. The favored formation of sellaite compared to fluorite requires the initial Ca/Mg-ratio of the mineralizing fluid to be unusually low. These conditions are possible if fluids equilibrate with pre-altered rocks that lost some or much of their Ca during an earlier hydrothermal alteration event. Indeed, calculations demonstrate that rock-buffered fluids of pre-altered rocks (i.e., gneiss around the Clara mine altered during prior hydrothermal events) show significantly lower Ca/Mg-ratios than fluids equilibrated with unaltered gneisses, because Ca-phases (e.g., the anorthite component of plagioclase) are more prone to hydrothermal destruction. Due to the network-like structure of the sellaite-bearing portion of the Clara fluorite vein, the fluid is shielded from sedimentary formation water, resulting in fractionation processes of the repeatedly ascending mineralizing fluid. In addition, fluid cooling and formation of water-bearing phases like illite that consume fluids, favor sellaite, and later fluorite precipitation. The rarity of this combination of prerequisites explains the limited occurrence of sellaite in hydrothermal vein-type deposits.
The biosynthesis of caprazamycins and related liponucleoside antibiotics: new insights
2012-10-29

Abstract The first step in the membrane cycle of reactions during peptidoglycan biosynthesis is the transfer of phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide to undecaprenyl phosphate, catalyzed by the integral membrane protein MraY translocase. Different MraY inhibitors are known and can be subdivided into classes depending on their structural composition. Caprazamycins belong to the liponucleoside class of antibiotics isolated from Streptomyces sp. MK730-62F2. They possess activity in vitro against Gram-positive bacteria, in particular against the genus Mycobacterium including Mycobacterium intracellulare , Mycobacterium avium and Mycobacterium tuberculosis. Caprazamycins and the structurally related liposidomycins and A-90289 share a unique composition of moieties. Their complex structure is derived from 5′-(β- O -aminoribosyl)-glycyluridine and comprises a unique N,N′ -dimethyldiazepanone ring. Recently, the corresponding biosynthetic gene clusters of caprazamycins, liposidomycins and A-90289 have been discovered and will be compared in this review. New information is also emerging regarding the biosynthesis of liponucleoside antibiotics obtained by gene disruption experiments and biochemical investigations.
The nautilus analyzer
2012-10-29

When developing data transformations - a task omnipresent in applications like data integration, data migration, data cleaning, or scientific data processing -developers quickly face the need to verify the semantic correctness of the transformation. Declarative specifications of data transformations, e.g., SQL or ETL tools, increase developer productivity but usually provide limited or no means for inspection or debugging. In this situation, developers today have no choice but to manually analyze the transformation and, in case of an error, to (repeatedly) fix and test the transformation. The goal of the Nautilus project is to semi-automatically support this analysis-fix-test cycle. This demonstration focuses on one main component of Nautilus, namely the Nautilus Analyzer that helps developers in understanding and debugging their data transformations. The demonstration will show the capabilities of this component for data transformations specified in SQL on scenarios from different domains that are based on real-world data.
Neolithic cremation in south‐east Arabia: archaeological and anthropological observations at FAY‐NE10 in the Emirate of Sharjah (UAE)
2012-10-29

Small fragments of cremated human bone, clearly representing numerous individuals, were found in a stratified Neolithic context in a small cave at Jebel Faya in the Central Region of the Emirate of Sharjah, United Arab Emirates. With radiocarbon dates between 6500 and 5800 cal BC , they are among the earliest well‐documented cases of cremations in south‐west Asia. Taxonomic identification of the small burned bone fragments is based on morphological and histological analysis. The deposits are to date the oldest human remains found in south‐east Arabia and represent a phase during the Middle Neolithic for which no other types of burials have yet been documented.
Establishing MHC Class I Peptide Motifs
2012-10-29

Major histocompatibility complex (MHC) class I peptide motifs are used on a regular basis to identify and predict MHC class I ligands and CD8(+) T-cell epitopes. This approach is above all an invaluable tool for the identification of disease-associated epitopes. As a matter of fact, the vast majority of T-cell epitopes discovered during the past two decades was identified by means of epitope prediction. Here we describe the steps which are necessary to establish MHC class I peptide motifs and to compose a reliable scoring matrix for epitope prediction. As an example, a scoring matrix for the prediction of HLA-B*35-presented T-cell epitopes will be developed by examining the characteristics of 76 naturally presented HLA ligands.
A Pan‐European Study of theC9orf72Repeat Associated withFTLD: Geographic Prevalence, Genomic Instability, and Intermediate Repeats
2012-10-30

We assessed the geographical distribution of C9orf72 G(4) C(2) expansions in a pan-European frontotemporal lobar degeneration (FTLD) cohort (n = 1,205), ascertained by the European Early-Onset Dementia (EOD) consortium. Next, we performed a meta-analysis of our data and that of other European studies, together 2,668 patients from 15 Western European countries. The frequency of the C9orf72 expansions in Western Europe was 9.98% in overall FTLD, with 18.52% in familial, and 6.26% in sporadic FTLD patients. Outliers were Finland and Sweden with overall frequencies of respectively 29.33% and 20.73%, but also Spain with 25.49%. In contrast, prevalence in Germany was limited to 4.82%. In addition, we studied the role of intermediate repeats (7-24 repeat units), which are strongly correlated with the risk haplotype, on disease and C9orf72 expression. In vitro reporter gene expression studies demonstrated significantly decreased transcriptional activity of C9orf72 with increasing number of normal repeat units, indicating that intermediate repeats might act as predisposing alleles and in favor of the loss-of-function disease mechanism. Further, we observed a significantly increased frequency of short indels in the GC-rich low complexity sequence adjacent to the G(4) C(2) repeat in C9orf72 expansion carriers (P < 0.001) with the most common indel creating one long contiguous imperfect G(4) C(2) repeat, which is likely more prone to replication slippage and pathological expansion.
Enhanced Ca2+Entry, Ceramide Formation, and Apoptotic Death of Erythrocytes Triggered by Plumbagin
2012-10-30

Plumbagin (5-hydroxy-2-methyl-1,4-naphthoquinone, 1), a natural product from plants with potential anticancer potency, induces apoptosis. Mechanisms involved in 1-induced apoptosis include mitochondrial depolarization, inactivation of NF-κB, and altered expression of anti- and proapoptotic Bcl proteins. Similar to nucleated cells, erythrocytes may undergo suicidal death or eryptosis, which, like apoptosis, results in cell shrinkage and cell membrane scrambling with phosphatidylserine exposure at the cell surface. Triggers of eryptosis include increase of cytosolic Ca(2+) activity ([Ca(2+)]i) and ceramide formation. The present study explored whether 1 stimulates eryptosis. Cell volume was estimated from forward scatter, phosphatidylserine exposure from annexin-V-binding, hemolysis from hemoglobin release, [Ca(2+)]i from Fluo-3 fluorescence, and ceramide abundance utilizing antibodies. A 48 h exposure to 1 (2 μM) decreased forward scatter and increased annexin-V-binding significantly, events paralleled by increased [Ca(2+)]i and ceramide formation. Exposure to 1 was followed by a slight but significant increase of hemolysis. Removal of extracellular Ca(2+) slightly, but significantly blunted the effect of 1 (2 μM) on annexin-V-binding. The present observations demonstrate that 1 may trigger suicidal death of erythrocytes, cells devoid of mitochondria and nuclei.
Laboratory markers of disease severity in Plasmodium knowlesi infection: a case control study
2012-10-30

Abstract Background Plasmodium knowlesi malaria causes severe disease in up to 10% of cases in Malaysian Borneo and has a mortality rate of 1 - 2%. However, laboratory markers with the ability to identify patients at risk of developing complications have not yet been assessed as they have for other species of Plasmodium. Methods A case control study was undertaken in two hospitals in Sarikei and Sibu, Malaysian Borneo. One hundred and ten patients with uncomplicated (n = 93) and severe (n = 17) P. knowlesi malaria were studied. Standardized pigment-containing neutrophil (PCN) count, parasite density and platelet counts were determined and analysed by logistic regression and receiver operating characteristic (ROC) analysis. Results The PCN count was strongly associated with risk of disease severity. Patients with high parasite density (≥ 35,000/μl) or with thrombocytopaenia (≤ 45,000/μl) were also more likely to develop complications (odds ratio (OR) = 9.93 and OR = 5.27, respectively). The PCN count yielded the highest area under the ROC curve (AUC) estimate among all markers of severity (AUC = 0.8561, 95% confidence interval: 0.7328, 0.9794). However, the difference between all parameter AUC estimates was not statistically significant (Wald test, p = 0.73). Conclusion Counting PCN is labour-intensive and not superior in predicting severity over parasitaemia and platelet counts. Parasite and platelet counts are simpler tests with an acceptable degree of precision. Any adult patient diagnosed with P. knowlesi malaria and having a parasite count ≥35,000/μl or ≥1% or a platelet count ≤45,000/μl can be regarded at risk of developing complications and should be managed according to current WHO guidelines for the treatment of severe malaria.
Rhodium Complexes Bearing 1,10-Phenanthroline Analogue Bis-NHC Ligands Are Active Catalysts for Transfer Hydrogenation of Ketones
2012-10-30

Synthesis of a new example of the pyridazine annelated bis(N-heterocyclic carbene) ligand 3b (vegi) bearing benzyl substituents is reported, as well as the synthesis of its cationic Rh(cod) complex 5b. The mechanism of formation of the [Rh(cod)(vegi)]+ complexes was investigated, showing a stepwise deprotonation of the imidazolium moieties via the mono-carbene imidazolium Rh(cod)Cl species 4. The [Rh(cod)(vegi)]+ complexes 5a,b show catalytic activity in the transfer hydrogenation of even sterically hindered ketones.
Inhibition of Suicidal Erythrocyte Death by Probucol
2012-10-30

Probucol, an antioxidant and anti-inflammatory agent counteracting atherosclerosis and restenosis, is partially effective by influencing suicidal cell death or apoptosis. In analogy to apoptosis of nucleated cells, suicidal death of erythrocytes or eryptosis is characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine exposure at the erythrocyte surface. Eryptosis is stimulated by increase in cytosolic Ca(2+) activity, for example, after energy depletion or oxidative stress. The present study explored whether probucol influences eryptosis. Phosphatidylserine exposure was estimated from annexin-V-binding, cell volume from forward scatter (FSC), and cytosolic Ca(2+) concentration from fluo-3 fluorescence in flow cytometry. As a result, energy depletion (48-hour glucose removal) increased annexin-V-binding, decreased FSC, and increased fluo-3 fluorescence. Probucol (≤30 μM) did not significantly modify annexin-V-binding, FSC, or fluo-3 fluorescence in the presence of glucose but (at ≥5 μM) blunted the effect of glucose depletion on annexin-V-binding. Probucol (≥20 μM) only slightly blunted the effects of glucose depletion on FSC and fluo-3 fluorescence. Ca(2+) ionophore ionomycin (1 μM) and oxidative stress (30-minute exposure to 0.3 mM of tert-butylhydroperoxide) increased annexin-V-binding, effects again blunted by 30 μM of probucol. In conclusion, probucol blunts cell membrane scrambling after energy depletion and oxidative stress, effects primarily because of interference with the scrambling effects of increased cytosolic Ca(2+) concentration.
(Carb)2SnF4 (Carb = 2, 3‐Dihydro‐1, 3‐diisopropyl‐4, 5‐dimethylimidazol‐2‐yliden – ein Carbenkomplex des vierwertigen Zinns
2012-10-30

Abstract 2, 3‐Dihydro‐1, 3‐diisopropyl‐4, 5‐dimethylimidazol‐2‐ylidene ( 1 , Carb) reacts with tin tetrafluoride to give the complex (Carb) 2 SnF 4 ( 3 ). The ligand properties of 1 are discussed in terms of the crystal structure and NMR data of 3 .
Screen Space Spherical Harmonic Occlusion
2012-10-30

In this paper we present a new algorithm for real-time directional occlusion sampling. We combine the real-time capabilities of Screen Space Ambient Occlusion (SSAO) with the Spherical Harmonics (SH) representation of local directional occlusion. SH are well established and used in modern off-line rendering implementations such as PantaRay [PFHA10]. Through our combination we are able to transfer a method for realistic local directional occlusion effects from offline rendering to dynamic real-time applications. These local occlusion effects react to the environmental lighting situation and lead to dynamic and colored local occlusion shadows while only generating a small computational overhead compared to SSAO. Unlike other real-time directional occlusion algorithms such as Screen Space Direction Occlusion (SSDO) [RGS09] our occlusion sampling is separated from the actual lighting process and therefore can be easily integrated in existing SH lighting methods such as Irradiance Volumes [GSHG98]. We furthermore extend our algorithm to include first bounce indirect illumination effects.
CMV and Immunosenescence: from basics to clinics
2012-10-31

Alone among herpesviruses, persistent Cytomegalovirus (CMV) markedly alters the numbers and proportions of peripheral immune cells in infected-vs-uninfected people. Because the rate of CMV infection increases with age in most countries, it has been suggested that it drives or at least exacerbates "immunosenescence". This contention remains controversial and was the primary subject of the Third International Workshop on CMV & Immunosenescence which was held in Cordoba, Spain, 15-16th March, 2012. Discussions focused on several main themes including the effects of CMV on adaptive immunity and immunosenescence, characterization of CMV-specific T cells, impact of CMV infection and ageing on innate immunity, and finally, most important, the clinical implications of immunosenescence and CMV infection. Here we summarize the major findings of this workshop.
A Novel BACHD Transgenic Rat Exhibits Characteristic Neuropathological Features of Huntington Disease
2012-10-31

Huntington disease (HD) is an inherited progressive neurodegenerative disorder, characterized by motor, cognitive, and psychiatric deficits as well as neurodegeneration and brain atrophy beginning in the striatum and the cortex and extending to other subcortical brain regions. The genetic cause is an expansion of the CAG repeat stretch in the HTT gene encoding huntingtin protein (htt). Here, we generated an HD transgenic rat model using a human bacterial artificial chromosome (BAC), which contains the full-length HTT genomic sequence with 97 CAG/CAA repeats and all regulatory elements. BACHD transgenic rats display a robust, early onset and progressive HD-like phenotype including motor deficits and anxiety-related symptoms. In contrast to BAC and yeast artificial chromosome HD mouse models that express full-length mutant huntingtin, BACHD rats do not exhibit an increased body weight. Neuropathologically, the distribution of neuropil aggregates and nuclear accumulation of N-terminal mutant huntingtin in BACHD rats is similar to the observations in human HD brains. Aggregates occur more frequently in the cortex than in the striatum and neuropil aggregates appear earlier than mutant htt accumulation in the nucleus. Furthermore, we found an imbalance in the striatal striosome and matrix compartments in early stages of the disease. In addition, reduced dopamine receptor binding was detectable by in vivo imaging. Our data demonstrate that this transgenic BACHD rat line may be a valuable model for further understanding the disease mechanisms and for preclinical pharmacological studies.
Single-dose cyclophosphamide synergizes with immune responses to the renal cell cancer vaccine IMA901
2012-10-31

The development of efficient immunotherapies requires strong rationalization. We have recently implemented a large analysis of biomarkers in two studies involving the multi-peptide vaccine IMA901 and advanced renal cell cancer patients. Our findings demonstrate that the breadth of immune responses was associated with clinical benefits and that single-dose cyclophosphamide reduced the amount of regulatory T cells and was associated with prolonged survival after vaccination.
The Impact of Group Membership on Collaborative Learning with Wikis
2012-10-31

The social web stimulates learning through collaboration. However, information in the social web is often associated with information about its author. Based on previous evidence that ingroup information is preferred to outgroup information, the current research investigates whether group memberships of wiki authors affect learning. In an experimental study, we manipulated the group memberships (ingroup vs. outgroup) of wiki authors by using nicknames. The designated group memberships (being fans of a soccer team or not) were completely irrelevant for the domain of the wiki (the medical disorder fibromyalgia). Nevertheless, wiki information from the ingroup led to more integration of information into prior knowledge as well as more increase of factual knowledge than information from the outgroup. The results demonstrate that individuals apply social selection strategies when considering information from wikis, which may foster, but also hinder, learning and collaboration. Practical implications for collaborative learning in the social web are discussed.