julilili42/papers huggingface dataset:
Neanderthals
2010-07-22

Neanderthals are a group of fossil humans that inhabited Western Eurasia from approximately 300 to 30,000 years ago (ka). They vanished from the fossil record a few millennia after the first modern humans appeared in Europe (ca. 40 ka BP). They are characterized by a unique combination of distinctive anatomical features, and are found with stone tools of the Mousterian stone tool industry. Current consensus views them as a distinct Eurasian human lineage isolated from the rest of the Old World and sharing a common ancestor with modern humans sometime in the early Middle Pleistocene. The extreme cold of the European Ice Ages is considered at least partly responsible for the evolution of some of the distinctive Neanderthal anatomy, although other factors (functional demands, effects of chance in small populations) were probably also important. The causes for the Neanderthal extinction are not well understood. Worsening climate and competition with modern humans are implicated. Neanderthals were our sister species, much more closely related to us than the chimpanzees, our closest living relatives are today.
First‐trimester combined screening for trisomy 21 at 7–14 weeks' gestation
2010-07-23

Abstract Objective To establish an algorithm for first‐trimester combined screening for trisomy 21 with biochemical testing from 7 to 14 weeks' gestation and ultrasound testing at 11–13 weeks. Methods This was a multicenter study of 886 pregnancies with trisomy 21 and 222 475 unaffected pregnancies with measurements of free β‐human chorionic gonadotropin (β‐hCG) and pregnancy‐associated plasma protein‐A (PAPP‐A) at 7–14 weeks' gestation. Multiple regression modeling of log‐transformed marker values was used to produce log multiples of the median (MoM) values for PAPP‐A and free β‐hCG. The models included terms for the center attended and the machine used for biochemical analysis, gestational age, maternal racial origin, maternal weight, smoking status and method of conception. Bivariate Gaussian distributions were fitted to log MoM PAPP‐A and log MoM free β‐hCG in trisomy 21 and in unaffected pregnancies. In each case the patient‐specific risk for trisomy 21 was estimated by multiplying the individual maternal age‐related risk with the likelihood ratio (LR) for fetal nuchal translucency (NT) according to the mixture model and the combined LR for maternal serum free β‐hCG and PAPP‐A. Estimates of detection rates for trisomy 21 and false‐positive rates were calculated for combined screening with measurements of NT at 12 weeks together with measurements of free β‐hCG and PAPP‐A from 8 to 13 weeks. Results In trisomy 21 pregnancies the mean log MoM free β‐hCG increased linearly with gestation between 7 and 14 weeks, whereas the relation between log MoM PAPP‐A and gestation was fitted by a quadratic equation such that the maximum separation between trisomy 21 and unaffected pregnancies occurs at 9–10 weeks. At a false‐positive rate of 3% the detection rate of combined screening at 12 weeks was 86% and this increased to 90% by biochemical testing at 9 weeks and ultrasound scanning at 12 weeks. The detection rate increased to 92% by measuring PAPP‐A at 9 weeks and free β‐hCG at the time of the scan at 12 weeks. Conclusion The performance of first‐trimester biochemical screening for trisomy 21 is best at 9–10 weeks rather than at 7–8 or 11–14 weeks. Copyright © 2010 ISUOG. Published by John Wiley &amp; Sons, Ltd.
Site-Specific Geometric and Electronic Relaxations at Organic-Metal Interfaces
2010-07-23

The correlation between the geometric and electronic structures of Zn-phthalocyanine (ZnPc) and F16ZnPc on Cu(111) were studied by x-ray standing wave and angle-resolved photoemission spectroscopy. We found evidence for a distortion of the planar molecules upon adsorption, with the central Zn atom in the molecule protruding towards the substrate. This modifies the energy levels of both the molecule and the substrate, which appear as interface states. The site-specific geometric and electronic relaxations are an important effect for organic-metal interface energetics.
MicroPrep: Chip‐based dielectrophoretic purification of mitochondria
2010-07-23

Abstract We have developed a microfluidic system – microPrep – for subcellular fractionation of cell homogenates based on dielectrophoretic sorting. Separation of mitochondria isolated from a human lymphoblastoid cell line was monitored by fluorescence microscopy and further characterized by western blot analysis. Robust high throughput and continuous long‐term operation for up to 60 h of the microPrep chip system with complex biological samples became feasible as a result of a comprehensive set of technical measures: (i) coating of the inner surfaces of the chip with BSA, (ii) application of mechanical actuators to induce periodic flow patterns, (iii) efficient cooling of the device to ensure integrity of organelle, (iv) a wide channel to provide for high fluidic throughput, and (v) integration of a serial arrangement of 10 dielectrophoretic deflector units to enable separation of samples with a high particle load without clogging. Hence, microPrep yields tens of micrograms of enriched and purified mitochondria within hours. Western blots of mitochondria fractions showed that contaminating endoplasmatic reticulum was reduced by a factor 6 when compared with samples prepared by state of the art centrifugation.
Can the burden of follow-up in low-grade noninvasive bladder cancer be reduced by photodynamic diagnosis, perioperative instillations, imaging, and urine markers?
2010-07-23

Emerging technologies in the field of tumor visualization in combination with urinary markers and effective instillation regimens can significantly reduce the risk of recurrence and progression in the long-term whilst providing less patient discomfort and simplifying the follow-up in patients of NIBC.
Inside Cover: Inhibition of Eimeria tenella CDK‐Related Kinase 2: From Target Identification to Lead Compounds (ChemMedChem 8/2010)
2010-07-23

The inside cover picture shows the validated drug target EtCRK2, a cyclin-dependent kinase of Eimeria tenella homologous to human CDK2 and chicken CDK3. A potential EtCRK2 inhibitor is docked into the active site of the protein. The inset shows the intermolecular H-bonding network. The inhibitor forms a H-bond to the selectivity switch residue Glu 88 (green stick representation). The positional analogue Lys 89 of human CDK2 and chicken CDK3 is superimposed in a red, translucent stick representation. For more details, see the Full Paper by P. M. Selzer et al. on p. 1259 ff.
Characterization of peptide deformylase homologues from Staphylococcus epidermidis
2010-07-24

The emergence of multi-drug-resistant strains of Staphylococcus epidermidis emphasizes the need to develop new antibiotics. The unique and essential role of the peptide deformylase (PDF) in catalysing the removal of the N-terminal formyl group from newly synthesized polypeptides in eubacteria makes it an attractive antibacterial drug target. In the present study, both deformylase homologues from S. epidermidis (SePDF-1 and SePDF-2) were cloned and expressed, and their enzymic activities were characterized. Co 2+ -substituted SePDF-1 exhibited much higher enzymic activity ( k cat / K m 6.3×10 4 M −1 s −1 ) than those of Ni 2+ - and Zn 2+ -substituted SePDF-1, and SePDF-1 showed much weaker binding ability towards Ni 2+ than towards Co 2+ and Zn 2+ , which is different from PDF in Staphylococcus aureus (SaPDF), although they share 80 % amino-acid sequence identity. The determined crystal structure of SePDF-1 was similar to that of (SaPDF), except for differences in the metal-binding sites. The other deformylase homologue, SePDF-2, was shown to have no peptide deformylase activity; the function of SePDF-2 needs to be further investigated.
Parametric quantified SAT solving
2010-07-25

We generalize successful algorithmic ideas for quantified satisfiability solving to the parametric case where there are parameters in the input problem. The output is then not necessarily a truth value but more generally a propositional formula in the parameters of the input. Since one can naturally embed propositional logic into first-order logic over Boolean algebras, our work amounts from a model-theoretic point of view to a quantifier elimination procedure for initial Boolean algebras. Our work is completely and efficiently implemented in the logic package Redlog contained in the open source computer algebra system Reduce. We describe this implementation and discuss computation examples pointing at possible applications of our work to configuration problems in the automotive industry.
On the Controls of Oxygen Fugacity in the Generation and Crystallization of Peralkaline Melts
2010-07-26

The formation of peralkaline melts is generally recognized to be related to enrichment of the mantle in sodium or potassium during a metasomatic event that predated magma generation. The wide range in mineral assemblages, mineral compositions, and fluid compositions in peralkaline melts are, to a large extent, a function of the sodium/potassium content of these mantle-metasomatizing fluids, which also governs redox conditions. We propose that sodic fluids will reduce the mantle assemblage by depleting ferric iron from garnet to form the aegirine component in pyroxene. In contrast, potassic fluids would oxidize the mantle assemblage by extracting Al2O3 from the garnet to make phlogopite. We suggest that during differentiation of peralkaline melts, once Fe–Ti oxides have been depleted from the assemblage, simple crystallization reactions of common solid phases such as aegirine or arfvedsonite control the oxygen fugacity by equilibria such as Hence, the more persodic a melt is, the more aegirine will be crystallized and the more reduced this melt will be. This is because without a mineral donor for ferric iron, the crystal chemical forcing of the coupled crystallization of Na with Fe3+ drives oxidation of the dominant Fe2+ in the melt and thereby reduction of the C–H–S–O-bearing fluid and/or melt phase. This is in convincing agreement with observations from a variety of silica-undersaturated peralkaline complexes such as Ilimaussaq in Greenland, Mt. St. Hilaire in Canada, Lovozero and Khibina in Russia, and Tamazeght in Morocco, and explains the occurrence of magmatic methane in the most sodic of these complexes. In silica-oversaturated peralkaline melts such as comendites and pantellerites, however, this equilibrium appears to be less influential and these melts are accordingly less reduced. In perpotassic melts, in contrast, no K–Fe3+ pyroxene is stable and K can only be incorporated into dominantly Fe2+-bearing phases such as biotite or K-amphibole, if no K-feldspar is stable. Here, redox conditions in the coexisting fluid and/or melt are either unaffected or even driven to more oxidized values by the crystallization reactions, which is in accordance with observations on the ultrapotassic rocks of the Roman Province (Italy) or the kalsilite-bearing Murun complex in Siberia. We conclude that peralkalinity in magmatic rocks is tightly connected to oxygen fugacity, that both the generation and the evolution and crystallization of peralkaline melts are governed by redox equilibria, and that these depend strongly on the Na/K ratio as well as on the (Na + K)/Al ratio of the melt. The specific features of peralkaline rocks, such as the difference between agpaitic and miaskitic rocks, the unusual enrichment of high field strength elements and the occurrence of magmatic hydrocarbons in some of them, can all be explained by the oxygen fugacity-controlling model reactions discussed in this study.
Genetic differentiation across the social transition in a socially polymorphic sweat bee, Halictus rubicundus
2010-07-26

Eusociality is widely considered a major evolutionary transition. The socially polymorphic sweat bee Halictus rubicundus, solitary in cooler regions of its Holarctic range and eusocial in warmer parts, is an excellent model organism to address this transition, and specifically the question of whether sociality is associated with a strong barrier to gene flow between phenotypically divergent populations. Mitochondrial DNA (COI) from specimens collected across the British Isles, where both solitary and social phenotypes are represented, displayed limited variation, but placed all specimens in the same European lineage; haplotype network analysis failed to differentiate solitary and social lineages. Microsatellite genetic variability was high and enabled us to quantify genetic differentiation among populations and social phenotypes across Great Britain and Ireland. Results from conceptually different analyses consistently showed greater genetic differentiation between geographically distant populations, independently of their social phenotype, suggesting that the two social forms are not reproductively isolated. A landscape genetic approach revealed significant isolation by distance (Mantel test r = 0.622, P < 0.001). The Irish Sea acts as physical barrier to gene flow (partial Mantel test r = 0.453, P < 0.01), indicating that geography, rather than expression of solitary or social behaviour (partial Mantel test r = -0.238, P = 0.053), had a significant effect on the genetic structure of H. rubicundus across the British Isles. Although we cannot reject the hypothesis of a genetic underpinning to differences in solitary and eusocial phenotypes, our data clearly demonstrate a lack of reproductive isolation between the two social forms.
Gastrointestinal graft‐versus‐host disease due to donor lymphocyte administration for rising autologous chimerism
2010-07-26

A 62-year-old man with acute myeloid leukemia (FAB M1) received a human leukocyte antigen-matched unrelated allogeneic stem cell transplantation after a reduced intensity conditioning regimen with fludarabin (3×; 30 mg/m2) and total body irradiation (2 Gy) which resulted in a complete remission of his leukemia. Analysis of chimerism constantly demonstrated autologous hematopoiesis after allogeneic transplantation. After termination of immunosuppression, the autologous chimerism was still increasing accompanied by generalized weakness and rising C-reactive protein. Therefore, treatment with pentostatin (2 mg/m2; 3.65 mg total) and a subsequent donor lymphocyte infusion (DLI) was initiated. However, while autologous chimerism was reduced, the patient developed erythema and massive diarrhea in the sense of an acute graft-versus-host disease (GVHD). Virologic and microbial stool investigations were unremarkable, duodenal and jejunal biopsies were compatible with GVHD grade II/III, and immunohistochemistry excluded cytomegalovirus infection. Under medication with mycophenolate mofetil (MMF) and escalation of immunosuppressive therapy with prednisolon (2 mg/kg) and the calcineurin inhibitor, tacrolimus symptoms resolved. Computed tomography (CT) illustrates the development and decay of the gastrointestinal GVHD (Image 1A–C). Coronal contrast-enhanced CT image before DLI (Image 1A) shows unremarkable enteric anatomy with nondilated bowel walls (Image 1A; arrow). After DLI with consecutive gastrointestinal GVHD (Image 1B), extensive wall thickening and mucosal enhancement of the small bowel (Image 1B; arrows) accompanied by mild engorgement of mesenteric vasa recta is observed. No mesenteric lymphadenopathy was appreciated, suggesting a noninfectious origin of enteric and mesenteric changes. Following intensified immunosuppression (Image 1C), coronal contrast-enhanced CT image shows partial resolution of GVHD-induced bowel wall thickening and hyperemia (Image 1C; arrow). Acute GVHD occurs when competent T lymphocytes are introduced into an immunocompromised recipient and usually presents within the first 100 days of allogeneic bone marrow transplantation [1]. The skin, gastrointestinal tract, and liver are the principal targets of GVHD. The histologic hallmark of acute GVHD in the gastrointestinal tract is epithelial cell apoptosis which makes differentiation from toxic effects due to conditioning regimens, proton pump inhibitors, MMF, or infectious agents like cytomegalovirus and cryptosporidium a challenge [2]. CT features of gastrointestinal GVHD include small bowel wall thickening, engorgement of the vasa recta adjacent to the affected bowel segments and mucosal enhancement. Serosal enhancement, ascites, and periportal edema are also found. High-grade (grade III/IV) GVHD, not present in this case, is associated with wall thickening involving the distal esophagus, ileum, or ascending colon [3].
Effects of MRI Contrast Agents on Human Embryonic Lung Fibroblasts
2010-07-27

No toxic effects on embryonic fetal lung fibroblasts were detectable after 4 and 24 hours of incubation in 6 MRI CM and 10x to 20x conc. in our setting. Antiproliferative effects, initially detected with Magnevist, Omniscan and Multihance, were rapidly compensated for.
Spatial behavior and linguistic representation: Collaborative interdisciplinary specialized workshop
2010-07-27

The Collaborative Interdisciplinary Specialized Workshop on Spatial Behavior and Linguistic Representation took place on April 23–24, 2010, at the Hanse-Wissenschaftskolleg, Institute for Advanced Study (HWK), in Delmenhorst, Germany. We report the scientific motivation for this workshop and report its outcomes together with the impact of a gathering of this kind for the scientific community.
Coherent Terahertz Emission of Intrinsic Josephson Junction Stacks in the Hot Spot Regime
2010-07-28

We report on THz emission measurements and low temperature scanning laser imaging of Bi2Sr2CaCu2O8 intrinsic Josephson junction stacks. Coherent emission is observed at large dc input power, where a hot spot and a standing wave, formed in the "cold" part of the stack, coexist. By changing bias current and bath temperature, the emission frequency can be varied by more than 40%; the variation matches the Josephson-frequency variation with voltage. The linewidth of radiation is much smaller than expected from a purely cavity-induced synchronization. Thus, an additional mechanism seems to play a role. Some scenarios, related to the presence of the hot spot, are discussed.
Formation of the resonant system HD 60532
2010-07-28

\\n Context. Among multi-planet planetary systems there are a large fraction of resonant systems. Studying the dynamics and formation of these systems can provide valuable informations on processes taking place in protoplanetary disks where the planets are thought have been formed. The recently discovered resonant system HD 60532 is the only confirmed case, in which the central star hosts a pair of giant planets in 3:1 mean motion resonance.\\n Aims. We intend to provide a physical scenario for the formation of HD 60532, which is consistent with the orbital solutions derived from the radial velocity measurements. Observations indicate that the system is in an antisymmetric configuration, while previous theroretical investigations indicate an asymmetric equilibrium state. The paper aims at answering this discrepancy as well.\\n Methods. We performed two-dimensional hydrodynamical simulations of thin disks with an embedded pair of massive planets. Additionally, migration and resonant capture are studied by gravitational N-body simulations that apply properly parametrized non-conservative forces.\\n Results. Our simulations suggest that the capture into the 3:1 mean motion resonance takes place only for higher planetary masses, thus favouring orbital solutions having relatively smaller inclination (i = ). The system formed by numerical simulations qualitatively show the same behaviour as HD 60532. We also find that the presence of an inner disk (between the inner planet and the star) plays a very important role in determining the final configurations of resonant planetary systems. Its damping effect on the inner planet's eccentricity is responsible for the observed antisymmetric state of HD 60532.\\n Conclusions. \\n
Dihydroartemisinin Induces Apoptosis by a Bak-Dependent Intrinsic Pathway
2010-07-28

Abstract The sesquiterpene lactone dihydroartemisinin (DHA), a semisynthetic derivative of the herbal antimalaria drug artemisinin, is cytotoxic to human tumor cells. Treatment of Jurkat T-lymphoma cells with DHA induced a breakdown of the mitochondrial transmembrane potential, release of cytochrome c, activation of caspases, and DNA fragmentation indicative of apoptosis induction. Although the absence of FADD or caspase-8 did not alter apoptosis rates in Jurkat cells, overexpression of dominant-negative caspase-9 or of antiapoptotic Bcl-xL or Bcl-2 largely decreased the cytotoxicity of DHA, demonstrating a role of the intrinsic death pathway. The proapoptotic Bcl-2 effector protein Bak and the Bcl-2 homology domain 3–only protein NOXA turned out to be important mediators of DHA-induced apoptosis in Jurkat cells. DHA treatment triggered the expression of NOXA and the activation of Bak. Furthermore, DHA-induced apoptosis was completely abrogated by loss of Bak and largely reduced in cells with siRNA-mediated downregulation of Bak or NOXA. Proapoptotic signaling of DHA also involved the formation of reactive oxygen species and membrane oxidation. Pretreatment with the lipophilic radical scavenger vitamin E or the hydrophilic radical scavengers glutathione and N-acetylcysteine reduced DHA-induced membrane oxidation and apoptosis, respectively. Oxidative changes also occurred in cells with disruption of the mitochondrial death pathway, suggesting a role of reactive oxygen species and oxidative membrane changes in death signaling upstream of the mitochondria. Interestingly, DHA increased the cytotoxic action of ionizing radiation and of the death receptor agonist tumor necrosis factor-related apoptosis-inducing ligand in Jurkat cells, suggesting a potential benefit of DHA in combined treatment strategies. Mol Cancer Ther; 9(9); 2497–510. ©2010 AACR.
Prevalence of THAP1 sequence variants in German patients with primary dystonia
2010-07-28

Abstract Primary dystonias are a clinically and genetically heterogeneous group of movement disorders, but only for two of them, i.e., dystonia 1 and dystonia 6, the disease causing gene has been identified. Dystonia 1 is characterized by an early onset and is caused by a mutation in the TOR1A gene. Only recently, mutations in THAP1 have been shown to be the cause of DYT6 dystonia. We analyzed 610 patients with various forms of dystonia for sequence variants in the THAP1 gene by means of high resolution melting to delineate the prevalence of sequence variants and phenotypic variability. We identified seven sequence variants in patients and one sequence variant in a control. The sequence variants were not detected in 537 healthy controls. Four patients present with generalized dystonia with speech involvement of early onset, another three patients suffered exclusively from cervical dystonia of adult onset. These findings suggest that THAP1 sequence variations seem to be associated with different ages of onset and distribution of symptoms. Consequently, the phenotypic spectrum might be broader than previously assumed. © 2010 Movement Disorder Society
Mineralogical and geochemical characterization of high-medieval lead–silver smelting slags from Wiesloch near Heidelberg (Germany)—an approach to process reconstruction
2010-07-29

Here, we present detailed electron microprobe analyses and age data of high-medieval lead–silver smelting slags. The mineral composition data provide a database of all silicate and oxide phases in the slag. Bulk chemistry as well as mineral composition is used to reconstruct liquidus, solidus, and viscosity of the slag melt. By calculating the mass balance of the smelting process, a mass ratio of the various compounds used in the smelting process is determined. Through this we were able to discriminate qualitatively between non-ferrous metal smelting slags and bloomery slags. We also report a new type and process of silver production in which argentiferous galmei (zinc carbonate) was used as a main silver ore together with galena. The results indicate a sophisticated high-medieval smelting technology, in which a slag with a low liquidus and a low viscosity was created.