julilili42/papers huggingface dataset:
Phase 2 study of PVAG (prednisone, vinblastine, doxorubicin, gemcitabine) in elderly patients with early unfavorable or advanced stage Hodgkin lymphoma
2011-09-15

Abstract Approximately 20% of all Hodgkin lymphoma (HL) patients are older than 60 years and have a poor prognosis, mainly because of increased treatment-related toxicity resulting in reduced overall dose intensity and more treatment-related mortality. To possibly improve the treatment of elderly HL patients, the German Hodgkin Study Group developed a new regimen, PVAG (prednisone, vinblastine, doxorubicin, and gemcitabine). In this multicenter phase 2 study, elderly HL patients in early unfavorable and advanced stages received 6 to 8 cycles of PVAG and additional radiotherapy if they were not in complete remission (CR) after chemotherapy. Endpoints included feasibility, acute toxicity, and response rate. Fifty-nine patients 60 to 75 years of age (median, 68 years) were eligible for analysis; 93% had advanced stage disease. WHO grade 3/4 toxicities were documented in 43 patients; 46 patients responded with CR/CR uncertain (78%). Within 37 months median observation time, 15 progressions or relapses and 17 deaths were observed, of which 8 were related to HL and 1 was the result of treatment-related toxicity. The 3-year estimates for overall survival and progression-free survival were 66% (95% CI, 50%-78%) and 58% (95% CI, 43%-71%), respectively. We conclude that PVAG is safe and feasible in elderly HL patients. This trial was registered at www.clinicaltrials.gov as #NCT00147875.
Novel ATP-driven Pathway of Glycolipid Export Involving TolC Protein
2011-09-15

Upon depletion of combined nitrogen, N(2)-fixing heterocysts are formed from vegetative cells in the case of the filamentous cyanobacterium Anabaena sp. strain PCC 7120. A heterocyst-specific layer composed of glycolipids (heterocyst envelope glycolipids (HGLs)) that functions as an O(2) diffusion barrier is deposited over the heterocyst outer membrane and is surrounded by an outermost heterocyst polysaccharide envelope. Mutations in any gene of the devBCA operon or tolC result in the absence of the HGL layer, preventing growth on N(2) used as the sole nitrogen source. However, those mutants do not have impaired HGL synthesis. In this study, we show that DevBCA and TolC form an ATP-driven efflux pump required for the export of HGLs across the Gram-negative cell wall. By performing protein-protein interaction studies (in vivo formaldehyde cross-linking, surface plasmon resonance, and isothermal titration calorimetry), we determined the kinetics and stoichiometric relations for the transport process. For sufficient glycolipid export, the membrane fusion protein DevB had to be in a hexameric form to connect the inner membrane factor DevC and the outer membrane factor TolC. A mutation that impaired the ability of DevB to form a hexameric arrangement abolished the ability of DevC to recognize its substrate. The physiological relevance of a hexameric DevB is shown in complementation studies. We provide insights into a novel pathway of glycolipid export across the Gram-negative cell wall.
Learning local linear Jacobians for flexible and adaptive robot arm control
2011-09-15

Successful planning and control of robots strongly depends on the quality of kinematic models, which define mappings between configuration space (e.g. joint angles) and task space (e.g. Cartesian coordinates of the end effector). Often these models are predefined, in which case, for example, unforeseen bodily changes may result in unpredictable behavior. We are interested in a learning approach that can adapt to such changes—be they due to motor or sensory failures, or also due to the flexible extension of the robot body by, for example, the usage of tools. We focus on learning locally linear forward velocity kinematics models by means of the neuro-evolution approach XCSF. The algorithm learns self-supervised, executing movements autonomously by means of goal-babbling. It preserves actuator redundancies, which can be exploited during movement execution to fulfill current task constraints. For detailed evaluation purposes, we study the performance of XCSF when learning to control an anthropomorphic seven degrees of freedom arm in simulation. We show that XCSF can learn large forward velocity kinematic mappings autonomously and rather independently of the task space representation provided. The resulting mapping is highly suitable to resolve redundancies on the fly during inverse, goal-directed control.
Vectors for improved Tet repressor-dependent gradual gene induction or silencing in Staphylococcus aureus
2011-09-16

A set of vectors for improved tetracycline-dependent gene regulation in Staphylococcus aureus is presented. Plasmid pRAB11 was generated from pRMC2 by adding a second tet operator within the TetR-regulated promoter P xyl/tet . Pronounced repression was observed in the absence of anhydrotetracycline (ATc) combined with high induction in the presence of the drug, as demonstrated for pRAB11 bearing staphylococcal nuclease nuc1 , lacZ or gfp . Also, in plasmid pCG261, the pRAB11 tetR –P xyl/tet regulatory architecture permitted tight repression and a stepwise increase in transcript amounts of the target gene rny (putative RNase) correlated with rising ATc concentrations. Additionally, pRAB11-derived vectors harbouring semi-rationally designed P xyl/tet -like fragments, mutated at up to six defined positions, were constructed. Sixteen mutant sequences with single to quadruple exchanges were analysed for transcriptional strength and ATc-dependent inducibility. A set of promoters with gradually decreased activities and improved repression is presented. Finally, the implementation of reverse TetR revtetR-r2 , which exhibits three amino acid exchanges and binds to tetO in the presence of ATc, yielded an efficiently co-repressible vector within the pRAB11 system. Intriguingly, revtetR was found to contain a fourth mutation only after propagation in S. aureus . We predict that the described vectors constitute valuable tools for staphylococcal genetics.
Var Gene Promoter Activation in Clonal Plasmodium falciparum Isolates Follows a Hierarchy and Suggests a Conserved Switching Program that Is Independent of Genetic Background
2011-09-16

Antigenic variation of Plasmodium falciparum is mediated by a mutually exclusive expression mechanism that limits expression to an individual member of the multicopy var gene family. This process determines the antigenic and adhesive phenotype of the infected red blood cell. Previously, we showed that var gene switching is influenced by chromosomal position. Here, we address whether var gene transcription follows a general conserved pattern in long-term laboratory parasites and in recently culture-adapted field parasites. Activation of the var gene family was monitored in biological replicates in each parasite isolate every 3-5 generations for up to 3 months. We used transgenic parasites carrying a drug-selectable marker at a defined var locus to characterize var gene activation after the exclusive expression of the transgene. Transgenic parasites exhibited a repeatable hierarchy of var gene activation and a fluctuating transcriptional activity of the transgenic var locus. Transcriptional profiling of wild-type laboratory and field parasites showed a universal bias toward transcription of UpsC var genes and a fluctuating transcriptional activity of the dominant var promoter. The data suggest the existence of an intrinsic var gene transcription program that is independent of genetic background.
Triggering of Erythrocyte Cell Membrane Scrambling by Ursolic Acid
2011-09-16

Ursolic acid (1), a triterpenoid with pleotropic effects including inhibition of tumor growth, is well known to trigger apoptosis of nucleated cells. The effect is at least partially due to altered gene expression and mitochondrial dysfunction. Erythrocytes lack nuclei and mitochondria but, similar to nucleated cells, may undergo suicidal cell death or eryptosis, which is characterized by cell shrinkage and phospholipid scrambling of the cell membrane. Triggers of eryptosis include increase of cytosolic Ca2+ activity ([Ca2+]i), ceramide formation and/or ATP depletion. The present study has investigated whether or not 1 induces eryptosis. [Ca2+]i was estimated from Fluo-3 fluorescence, cell volume from forward scatter, phospholipid scrambling from annexin V binding, hemolysis from hemoglobin release, and cytosolic ATP concentration ([ATP]i) utilizing a luciferase assay and ceramide-utilizing fluorescent antibodies in FACS analysis. As a result, exposure of erythrocytes for 48 h to 1 (≥5 μM) did not significantly modify [ATP]i, but significantly increased [Ca2+]i, stimulated ceramide formation, decreased forward scatter, triggered annexin V binding, and elicited hemolysis. At 5 μM, 1 stimulated phospholipid scrambling in 10% and hemolysis in 2% of treated erythrocytes. Annexin V binding was blunted in the nominal absence of Ca2+. In conclusion, the food component ursolic acid stimulates suicidal death of erythrocytes, i.e., cells devoid of nuclei and mitochondria.
Plasmodium falciparum-Infected Erythrocytes and IL-12/IL-18 Induce Diverse Transcriptomes in Human NK Cells: IFN-α/β Pathway versus TREM Signaling
2011-09-16

The protective immunity of natural killer (NK) cells against malarial infections is thought to be due to early production of type II interferon (IFN) and possibly direct NK cell cytotoxicity. To better understand this mechanism, a microarray analysis was conducted on NK cells from healthy donors PBMCs that were co-cultured with P. falciparum 3D7-infected erythrocytes. A very similar pattern of gene expression was observed among all donors for each treatment in three replicas. Parasites particularly modulated genes involved in IFN-α/β signaling as well as molecules involved in the activation of interferon regulatory factors, pathways known to play a role in the antimicrobial immune response. This pattern of transcription was entirely different from that shown by NK cells treated with IL-12 and IL-18, in which IFN-γ- and TREM-1-related genes were over-expressed. These results suggest that P. falciparum parasites and the cytokines IL-12 and IL-18 have diverse imprints on the transcriptome of human primary NK cells. IFN-α-related genes are the prominent molecules induced by parasites on NK cells and arise as candidate biomarkers that merit to be further investigated as potential new tools in malaria control.
NOS1 ex1f‐VNTR polymorphism affects prefrontal oxygenation during response inhibition tasks
2011-09-16

Abstract Impulsivity is a trait shared by many psychiatric disorders and therefore a suitable intermediate phenotype for their underlying biological mechanisms. One of the molecular determinants involved is the NOS1 ex1f‐VNTR, whose short variants are associated with a variety of impulsive behaviors. Fifty‐six healthy controls were stratified into homozygous long (LL) (30 probands) and short (SS) (26 probands) allele groups. Subjects completed a combined stop‐signal go/nogo task, while the oxygenation in the prefrontal cortex was measured with functional near‐infrared spectroscopy. Electromyography was recorded to control for differences in muscle activity in the two inhibition tasks. Two questionnaires on impulsive traits were completed. Differences between the two tasks are shown by distinct activation patterns within the prefrontal cortex. The nogo task resulted mainly in the activation of the dorsolateral prefrontal cortex (dlPFC), whereas successful and unsuccessful inhibition in the stop‐signal task elicited the predicted activity in the inferior frontal cortex (IFC). Although significant differences were found in neither the scores obtained on impulsivity‐related questionnaires nor the behavioral data, the LL group displayed increased dlPFC activity during nogo trials and the predicted activation in the IFC during successful inhibition in the stop‐signal task, while no significant activation was found in the SS group. Our data confirm an influence of NOS1 ex1f‐VNTR on impulsivity, as carriers of the short risk allele exhibited diminished activity of (pre‐)frontal brain regions during the inhibition in a stop‐signal task. Impairment of prefrontal control with consecutive failure of inhibitory processes might underlie association findings reported previously. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.
Schwinger-Dyson equations and disorder
2011-09-16

Using simple models in D=0+0 and D=0+1 dimensions we construct partition functions and compute two-point correlations. The exact result is compared with saddle-point approximation and solutions of Schwinger-Dyson equations. When integrals are dominated by more than one saddle-point we find Schwinger-Dyson equations do not reproduce the correct results unless the action is first transformed into dual variables.
PTEN deficiency in mast cells causes a mastocytosis-like proliferative disease that heightens allergic responses and vascular permeability
2011-09-17

Abstract Kit regulation of mast cell proliferation and differentiation has been intimately linked to the activation of phosphatidylinositol 3-OH kinase (PI3K). The activating D816V mutation of Kit, seen in the majority of mastocytosis patients, causes a robust activation of PI3K signals. However, whether increased PI3K signaling in mast cells is a key element for their in vivo hyperplasia remains unknown. Here we report that dysregulation of PI3K signaling in mice by deletion of the phosphatase and tensin homolog (Pten) gene (which regulates the levels of the PI3K product, phosphatidylinositol 3,4,5-trisphosphate) caused mast cell hyperplasia and increased numbers in various organs. Selective deletion of Pten in the mast cell compartment revealed that the hyperplasia was intrinsic to the mast cell. Enhanced STAT5 phosphorylation and increased expression of survival factors, such as Bcl-XL, were observed in PTEN-deficient mast cells, and these were further enhanced by stem cell factor stimulation. Mice carrying PTEN-deficient mast cells also showed increased hypersensitivity as well as increased vascular permeability. Thus, Pten deletion in the mast cell compartment results in a mast cell proliferative phenotype in mice, demonstrating that dysregulation of PI3K signals is vital to the observed mast cell hyperplasia.
Knickkopf protein protects and organizes chitin in the newly synthesized insect exoskeleton
2011-09-19

During each molting cycle of insect development, synthesis of new cuticle occurs concurrently with the partial degradation of the overlying old exoskeleton. Protection of the newly synthesized cuticle from molting fluid enzymes has long been attributed to the presence of an impermeable envelope layer that was thought to serve as a physical barrier, preventing molting fluid enzymes from accessing the new cuticle and thereby ensuring selective degradation of only the old one. In this study, using the red flour beetle, Tribolium castaneum , as a model insect species, we show that an entirely different and unexpected mechanism accounts for the selective action of chitinases and possibly other molting enzymes. The molting fluid enzyme chitinase, which degrades the matrix polysaccharide chitin, is not excluded from the newly synthesized cuticle as previously assumed. Instead, the new cuticle is protected from chitinase action by the T. castaneum Knickkopf (TcKnk) protein. TcKnk colocalizes with chitin in the new cuticle and organizes it into laminae. Down-regulation of TcKnk results in chitinase-dependent loss of chitin, severe molting defects, and lethality at all developmental stages. The conservation of Knickkopf across insect, crustacean, and nematode taxa suggests that its critical roles in the laminar ordering and protection of exoskeletal chitin may be common to all chitinous invertebrates.
Emotional valence and physical space: Limits of interaction.
2011-09-19

According to the body-specificity hypothesis, people associate positive things with the side of space that corresponds to their dominant hand and negative things with the side corresponding to their nondominant hand. Our aim was to find out whether this association holds also true for a response time study using linguistic stimuli, and whether such an association is activated automatically. Four experiments explored this association using positive and negative words. In Exp. 1, right-handers made a lexical judgment by pressing a left or right key. Attention was not explicitly drawn to the valence of the stimuli. No valence-by-side interaction emerged. In Exp. 2 and 3, right-handers and left-handers made a valence judgment by pressing a left or a right key. A valence-by-side interaction emerged: For positive words, responses were faster when participants responded with their dominant hand, whereas for negative words, responses were faster for the nondominant hand. Exp. 4 required a valence judgment without stating an explicit mapping of valence and side. No valence-by-side interaction emerged. The experiments provide evidence for an association between response side and valence, which, however, does not seem to be activated automatically but rather requires a task with an explicit response mapping to occur.
AdS-like spectrum of the asymptotically Gödel space-times
2011-09-19

A black hole immersed in a rotating Universe, described by the\\nGimon-Hashimoto solution, is tested on stability against scalar field\\nperturbations. Unlike the previous studies on perturbations of this solution,\\nwhich dealt only with the limit of slow Universe rotation j, we managed to\\nseparate variables in the perturbation equation for the general case of\\narbitrary rotation. This leads to qualitatively different dynamics of\\nperturbations, because the exact effective potential does not allow for\\nSchwarzschild-like asymptotic of the wave function in the form of purely\\noutgoing waves. The Dirichlet boundary conditions are allowed instead, which\\nresult in a totally different spectrum of asymptotically G\\\\"odel black holes:\\nthe spectrum of quasinormal frequencies is similar to the one of asymptotically\\nanti-de Sitter black holes. At large and intermediate overtones N, the spectrum\\nis equidistant in N. In the limit of small black holes, quasinormal modes\\n(QNMs) approach the normal modes of the empty G\\\\"odel space-time. There is no\\nevidence of instability in the found frequencies, which supports the idea that\\nthe existence of closed time-like curves (CTCs) and the onset of instability\\ncorrelate (if at all) not in a straightforward way.\\n
RF tissue-heating near metallic implants during magnetic resonance examinations: An approach in the ac limit
2011-09-19

The presented ac approach to RF heating near an implant, which mimics specific values for R, L, and C, allows for closed formulas to estimate the potential of RF energy transfer. A first reference point for worst-case determination in MR testing procedures can be obtained. Numerical approaches, necessary to determine spatially resolved heating maps, can be supported.
Christianson syndrome in a patient with an interstitial Xq26.3 deletion
2011-09-19

Abstract Interstitial deletions of chromosome band Xq26.3 are rare. We report on a 2‐year‐old boy in whom array comparative genomic hybridization analysis revealed an interstitial 314 kb deletion in Xq26.3 affecting SLC9A6 and FHL1. Mutations in SLC9A6 are associated with Christianson syndrome (OMIM 300243), a syndromic form of X‐linked mental retardation (XLMR) characterized by microcephaly, severe global developmental delay, ataxia and seizures. FHL1 mutations cause Emery–Dreifuss muscular dystrophy (OMIM 310300), X‐linked myopathy with postural muscle atrophy (XMPMA, OMIM 300696), scapuloperoneal myopathy (OMIM 300695), or reducing body myopathy (OMIM 300717, 300718). The clinical problems of the patient reported here comprised severe intellectual disability, absent speech, ataxia, epilepsy, and gastroesophageal reflux, and could mostly be attributed to SLC9A6 insufficiency. In contrast to the majority of reported Christianson syndrome patients who were microcephalic, this patient was normocephalic, but his head circumference had decelerated from the 50th centile at birth to the 25th centile at the age of \\scriptstyle 2 \\scriptstyle {12} years. Muscle problems due to the FHL1 deletion are not to be expected before late childhood, which is the earliest age of onset for FHL1 associated Emery–Dreifuss muscular dystrophy. This patient broadens the spectrum of SLC9A6 mutations and contributes to the clinical delineation of Christianson syndrome. This is also the first patient with a deletion affecting both SLC9A6 and the complete FHL1 gene. © 2011 Wiley Periodicals, Inc.
The Chitinase-Like Protein YKL-40 Modulates Cystic Fibrosis Lung Disease
2011-09-20

The chitinase-like protein YKL-40 was found to be increased in patients with severe asthma and chronic obstructive pulmonary disease (COPD), two disease conditions featuring neutrophilic infiltrates. Based on these studies and a previous report indicating that neutrophils secrete YKL-40, we hypothesized that YKL-40 plays a key role in cystic fibrosis (CF) lung disease, a prototypic neutrophilic disease. The aim of this study was (i) to analyze YKL-40 levels in human and murine CF lung disease and (ii) to investigate whether YKL-40 single-nucleotide polymorphisms (SNPs) modulate CF lung disease severity. YKL-40 protein levels were quantified in serum and sputum supernatants from CF patients and control individuals. Levels of the murine homologue BRP-39 were analyzed in airway fluids from CF-like Î2ENaC-Tg mice. YKL-40SNPs were analyzed in CF patients. YKL-40 levels were increased in sputum supernatants and in serum from CF patients compared to healthy control individuals. Within CF patients, YKL-40 levels were higher in sputum than in serum. BRP-39 levels were increased in airways fluids from Î2ENaC-Tg mice compared to wild-type littermates. In both CF patients and Î2ENaC-Tg mice, YKL-40/BRP-39 airway levels correlated with the severity of pulmonary obstruction. Two YKL-40 SNPs (rs871799 and rs880633) were found to modulate age-adjusted lung function in CF patients. YKL-40/BRP-39 levelsare increased in human and murine CF airway fluids, correlate with pulmonary function and modulate CF lung disease severity genetically. These findings suggest YKL-40 as a potential biomarker in CF lung disease.