Evaluating Temporal Graphs Built from Texts via Transitive Reduction

Temporal information has been the focus of recent attention in information extraction, leading to some standardization effort, in particular for the task of relating events in a text. This task raises the problem of comparing two annotations of a given text, because relations between events in a story are intrinsically interdependent and cannot be evaluated separately. A proper evaluation measure is also crucial in the context of a machine learning approach to the problem. Finding a common comparison referent at the text level is not obvious, and we argue here in favor of a shift from event-based measures to measures on a unique textual object, a minimal underlying temporal graph, or more formally the transitive reduction of the graph of relations between event boundaries. We support it by an investigation of its properties on synthetic data and on a well-know temporal corpus.

Self-assembly of charged amphiphilic diblock copolymers with insoluble blocks of decreasing hydrophobicity: from kinetically frozen colloids to macrosurfactants

We have investigated the self-assembly properties in aqueous solution of amphiphilic diblock copolymers with insoluble blocks of different hydrophobicity and demonstrated that the condition to obtain dynamic micelles is to design samples with insoluble blocks of low enough hydrophobicity. We focus here on results with new water-soluble amphiphilic diblock copolymers poly(diethyleneglycol ethylether acrylate)-b-poly(acrylic acid), or PDEGA-b-PAA. The physical characteristics of PDEGA-b-PAA micelles at high ionization have been determined by small angle neutron scattering (SANS). We show that PDEGA-b-PAA samples form micelles at thermodynamic equilibrium. The critical micelle concentrations (CMCs) decrease strongly with ionic strength and temperature due to a solvent quality decrease for, respectively, the corona and the core. This behavior of reversible aggregation is remarkable as compared to the behavior of kinetically frozen aggregation that has been widely observed with samples of similar architecture and different hydrophobic blocks, for example, poly(styrene)-b-poly(acrylic acid), PS-b-PAA, and poly(butyl acrylate)-b-poly(acrylic acid), PBA-b-PAA. We have measured the interfacial tension between water and the homopolymers PDEGA and PBA at, respectively, 3 and 20 mN/m at room temperature, which permits one to estimate the energy cost to extract a unimer from a micelle. The results are consistent with a micelle association that is fast for PDEGA-b-PAA and kinetically frozen PBA-b-PAA. Hence, PDEGA-b-PAA samples form a new system of synthetic charged macrosurfactant with unique properties of fast dynamic association, tunable charge, and water solubility even at temperatures and NaCl concentrations as high as 65 °C and 1 M.

Abstract P1-03-07: Differential Effect of Specific p53 Mutations on Breast Cancer Growth and Response to Hsp90 Inhibition In Vivo

Background p53 mutation influences breast cancer cell growth and patient prognosis. However, different p53 mutations impart specific functions to the mutant protein, including dominant negative or gain of function effects. Mutant p53 molecules R273H and R175H are commonly found in primary breast cancers and are present in the MDA-MB-468 and SKBR3 cell lines, respectively. To compare the direct effects of these two mutations in vivo in an identical cellular background, H1299 (p53-null) cells were constructed to express R273H or R175H p53 mutants. Methods

Thirty female SCID mice were injected subcutaneously with 106 H1299 (p53-null), H1299/R273H or H1299/R175H cells in DMEM + Matrigel (50:50) suspension. Some mice were treated with an Hsp90 inhibitor, which is required for correct folding of many oncogenic proteins. Results

Xenografts bearing R175H showed a mean lag phase (time between cell injection and tumors at exponential growth) of 21 days and a doubling time of 5 days, whereas tumors bearing H1299 (p53-null) or R273H mutation had a lag phase of 31 days with a doubling time of 7 days. Immunohistochemical examination demonstrated a highly heterogeneous pattern of p53 protein expression in the more aggressive R175H expressing cells compared with R273H expressing cells. Hsp90 inhibitor treatment reduced the growth of H1299 and R273H cells, but not R175H cells. Conclusions

The specific p53 mutations directly influence the rate of tumor growth and the p53 protein staining pattern on immunohistochemistry. The differential effects of specific p53 mutations should be considered when interpreting clinical data involving p53 mutation such as in the EORTC 10994 trial, with implications for prognostic determination of individual breast cancer patients.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P1-03-07.

Adsorption kinetics of amphiphilic diblock copolymers: from kinetically frozen colloids to macrosurfactants

We investigated the spontaneous adsorption properties of charged amphiphilic diblock copolymers on hydrophobic surfaces and explained the transition of behavior from depleting frozen colloids (that do not adsorb at all) to fast adsorbing macrosurfactants when the hydrophobicity of the nonsoluble block is reduced. Three copolymer families have been used with the same hydrophilic block poly(acrylic acid), a weak acid whose ionization alpha can be varied by changing the pH. The hydrophobic blocks polystyrene, PS, poly(n-butyl acrylate), PBA, and poly(diethylene glycol ethyl ether acrylate), PDEGA, have interfacial tensions with water gammacore/solvent, respectively, of 32, 20, and 3 mN/m. We were mainly interested in the regime of high ionization alpha > 0.3, where PAA chains have no affinity for hydrophobic surfaces, and we verified experimentally that micelles do not adsorb directly. With the three copolymer families we show that the adsorption kinetics at an early stage is driven by the self-assembly properties in bulk solution: adsorption is hampered for PS-b-PAA (physically/kinetically frozen micelles in solution), controlled by unimer extraction for PBA-b-PAA (nonequilibrium micelles in solution with very low CMC < 10-4 wt %), and controlled by unimer diffusion and electrostatic repulsion for PDEGA-b-PAA (micelles at equilibrium in solution with high CMC is approximately 1-5 wt %). This explains the power law dependences of adsorption with concentration as C-1 for PBA-b-PAA and C-2 for PDEGA-b-PAA. It is finally the interfacial tension with water of the nonsoluble block and not its glass transition that is the main control of bulk solution self-assembly and consequently of the adsorption kinetics properties of amphiphilic diblocks. We also proved by preparative GPC that the fraction of non-self-assembling diblock chains, which exists in all highly hydrophobic amphiphilic diblock systems, plays a negligible role in the adsorption properties. Finally, we investigated the intrinsic thermodynamic affinity between amphiphilic diblocks and hydrophobic surfaces. We show quantitatively that this affinity depends dominantly on the interfacial energies between the hydrophobic block, the surface, and water: diblocks with strongly hydrophobic nonsoluble blocks (PS, PBA) have a low affinity for weakly hydrophobic surfaces, and oppositely, diblocks with weakly hydrophobic nonsoluble block (PDEGA) have a universal affinity for hydrophobic surfaces (like small-molecule surfactants but for different physical reasons). Finally, we showed via surface rheology that when adsorption occurs anchoring is strong and irreversible for very hydrophobic diblocks (PBA-b-PAA) and weaker and (partially) reversible for less hydrophobic diblocks (PDEGA-b-PAA).

Wetting transition on hydrophobic surfaces covered by polyelectrolyte brushes

We study the wetting by water of complex "hydrophobic-hydrophilic" surfaces made of a hydrophobic substrate covered by a hydrophilic polymer brush. Polystyrene (PS) substrates covered with polystyrene- block-poly(acrylic acid) PS- b-PAA diblock copolymer layers were fabricated by Langmuir-Schaefer depositions and analyzed by atomic force microscopy (AFM) and ellipsometry. On bare PS substrate, we measured advancing angles theta A = 93 +/- 1 degrees and receding angles theta R = 81 +/- 1 degrees . On PS covered with poorly anchored PS- b-PAA layers, we observed large contact angle hysteresis, theta A approximately 90 degrees and theta R approximately 0 degrees , that we attributed to nanometric scale dewetting of the PS- b-PAA layers. On well-anchored PS- b-PAA layers that form homogeneous PAA brushes, a wetting transition from partial to total wetting occurs versus the amount deposited: both theta A and theta R decrease close to zero. A model is proposed, based on the Young-Dupre equation, that takes into account the interfacial pressure of the brush Pi, which was determined experimentally, and the free energy of hydration of the polyelectrolyte monomers Delta G PAA (hyd), which is the only fitting parameter. With Delta G PAA (hyd) approximately -1300 J/mol, the model renders the wetting transition for all samples and explains why the wetting transition depends mainly on the average thickness of the brush and weakly on the length of PAA chains.

Interobserver variability in the measurement of fetal middle cerebral artery peak systolic velocity in a tertiary fetal medicine unit

OBJECTIVES

To investigate the interobserver variability of fetal middle cerebral artery (MCA) peak systolic velocity (PSV) Doppler measurements in a tertiary fetal medicine unit.

METHODS

This was a prospective cohort study of pregnant women between 22 and 34 weeks of gestation who underwent fetal MCA-PSV Doppler velocimetry by a paired combination of operators. A set protocol was followed; ease of scanning was recorded and three quality assurance parameters were analyzed. The interobserver variability was determined. In addition, individual operator characteristics were determined by analyzing the variation of each operator relative to all his/her paired colleagues, and their quality assurance parameters.

RESULTS

Two hundred and eighty-five women had completed paired fetal MCA-PSV Doppler measurements. Eighty-three (29%) of the ultrasound examinations requested were for suspected fetal anemia and 202 (71%) were for other obstetric indications. The interobserver variation was less than 10% in 78% of the paired MCA-PSV Doppler measurements whereas 99% had less than 15% variation. The intraclass correlation coefficient of each operator when compared with all his/her colleagues ranged from 0.82 to 0.95. The overall mean variability of the MCA-PSV recorded by a given operator, relative to all his/her paired colleagues, ranged from + 5.26% to - 6.47% in all but one operator whose value was + 13.5% (standard deviation factor, 1.13-1.22). Logistic regression analysis, using a 10% or greater variation in MCA-PSV as a binary outcome variable, showed a significant difference when inappropriate angle correction was detected (P < 0.001).

CONCLUSIONS

Clinically acceptable interobserver variability was obtained in fetal MCA-PSV Doppler measurements. Inappropriate angle correction was found to be a significant predictive factor for increased interobserver variability. Analysis of mean variation identified operators who were outliers enabling quality assurance within the unit.

[Chromomycosis in Guadeloupe]

BACKGROUND

Chromomycosis is a widespread subcutaneous fungal infection seen essentially in tropical and subtropical regions and transmitted via skin injury caused by the prickles of plants or infected wood splinters. It is prevalent throughout the West Indies including Guadeloupe, where its incidence is not well known.

PATIENTS AND METHODS

This retrospective and descriptive study concerns five histologically established cases of chromomycosis in Guadeloupe between 1995 and 2005. The five patients were diagnosed and treated at Pointe-à-Pitre University Teaching Hospital.

RESULTS

The study concerned four male patients and one female patient with an average age of 78 years; four were from the Basse-Terre district and one was from the Grande-Terre district. The most frequent clinical aspect was nodular or verrucous. The most common initial topography was the upper limbs. Fonsecaea pedrosoi was the only species identified. Diagnosis was confirmed by histopathology, which in all cases revealed sclerotic cells. Three patients underwent surgical treatment and two received medical treatment; only two patients were cured by 2005.

DISCUSSION

Our study confirms the presence of a source of chromomycosis in Guadeloupe, where Fonsecaea pedrosoi is clearly the best adapted species. It also highlights the difficulties of therapeutic care in tropical areas.

Chaperone-dependent stabilization and degradation of p53 mutants

p53 missense mutant proteins commonly show increased stability compared to wild-type p53, which is thought to depend largely on the inability of mutant p53 to induce the ubiquitin ligase MDM2. However, recent work using mouse models has shown that the accumulation of mutant p53 occurs only in tumour cells, indicating that stabilization requires additional factors. To clarify the stabilization of p53 mutants in tumours, we analysed factors that affect their folding and degradation. Although all missense mutants that we studied are more stable than wild-type p53, the levels correlate with individual structural characteristics, which may be reflected in different gain-of-function properties. In the absence of Hsp90 activity, the less stable unfolded p53 mutants preferentially associate in a complex with Hsp70 and CHIP (carboxy terminus of Hsp70-interacting protein), and we show that CHIP is responsible for ubiquitination and degradation of these mutants. The demonstration of a complex interplay between Hsp90, Hsp70 and CHIP that regulate the stability of different p53 mutant proteins improves our understanding of the pro-tumorigenic effects of increased Hsp90 activity during multi-stage carcinogenesis. Understanding the roles of Hsp90, Hsp70 and CHIP in cancers may also provide an important avenue through which to target p53 to enhance treatment of human cancers.

Chemical analysis and aqueous solution properties of charged amphiphilic block copolymers PBA-b-PAA synthesized by MADIX®

We have linked the structural and dynamic properties in aqueous solution of amphiphilic charged diblock copolymers poly(butyl acrylate)-b-poly(acrylic acid), PBA-b-PAA, synthesized by controlled radical polymerization, with the physico-chemical characteristics of the samples. Despite product imperfections, the samples self-assemble in melt and aqueous solutions as predicted by monodisperse microphase separation theory. However, the PBA core are abnormally large; the swelling of PBA cores is not due to AA (the Flory parameter chi(PBA/PAA), determined at 0.25, means strong segregation), but to h-PBA homopolymers (content determined by liquid chromatography at the point of exclusion and adsorption transition, LC-PEAT). Beside the dominant population of micelles detected by scattering experiments, capillary electrophoresis CE analysis permitted detection of two other populations, one of h-PAA, and the other of free PBA-b-PAA chains, that have very short PBA blocks and never self-assemble. Despite the presence of these free unimers, the self-assembly in solution was found out of equilibrium: the aggregation state is history dependant and no unimer exchange between micelles occurs over months (time-evolution SANS). The high PBA/water interfacial tension, measured at 20 mN/m, prohibits unimer exchange between micelles. PBA-b-PAA solution systems are neither at thermal equilibrium nor completely frozen systems: internal fractionation of individual aggregates can occur.

Molecular pathogenesis of Wilson and Menkes disease: correlation of mutations with molecular defects and disease phenotypes

The trace metal copper is essential for a variety of biological processes, but extremely toxic when present in excessive amounts. Therefore, concentrations of this metal in the body are kept under tight control. Central regulators of cellular copper metabolism are the copper-transporting P-type ATPases ATP7A and ATP7B. Mutations in ATP7A or ATP7B disrupt the homeostatic copper balance, resulting in copper deficiency (Menkes disease) or copper overload (Wilson disease), respectively. ATP7A and ATP7B exert their functions in copper transport through a variety of interdependent mechanisms and regulatory events, including their catalytic ATPase activity, copper-induced trafficking, post-translational modifications and protein-protein interactions. This paper reviews the extensive efforts that have been undertaken over the past few years to dissect and characterise these mechanisms, and how these are affected in Menkes and Wilson disease. As both disorders are characterised by an extensive clinical heterogeneity, we will discus how the underlying genetic defects correlate with the molecular functions of ATP7A and ATP7B and with the clinical expression of these disorders.

A phase I study of imatinib mesylate and paclitaxel in patients with advanced (stage IIIC/IV) or recurrent uterine papillary serous carcinoma (UPSC)

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Background: Uterine serous carcinoma (USC) is a rare, aggressive uterine tumor biologically distinct from typical endometrial cancers. Imatinib mesylate (IM)-associated kinases (kit, abl, PDGFR-B) are overexpressed and activated in most tumors from patients (pts) with USC. Single agent paclitaxel (TAX) has a good response rate but short duration of response in pts with USC. The purpose of this study was to determine the maximum tolerated dose (MTD) and dose limiting toxicity (DLT) of escalated doses of IM with a fixed dose of TAX. Methods: Pts with newly diagnosed (stage IIIC/IV) or recurrent USC were eligible (pts were required to have tumors that expressed at least one of the IM-targeted kinases by immunohistochemistry). Measurable disease was not required. TAX was administered at 175 mg/m2 every three weeks. One dose reduction to 135 mg/m2 was allowed. IM was given daily (400 mg, 500 mg or 600 mg). A 3+3 design was implemented. Pts with measurable disease were treated until progression or treatment associated toxicity. Pts with no measurable disease were treated for six cycles. Results: 11 pts were enrolled. The median age was 62 years (47–79). A total of 50 cycles were administered. Three pts were treated at the first dose level (400 mg), 6 pts treated at the second dose level (500 mg), and 2 pts were treated at the highest dose level (600 mg). Three DLTs were observed (1 at 500 mg level and 2 at 600 mg level) including: rash, neutropenia, and fatigue. IM 500 mg daily and TAX 175 mg/m2 every three weeks was the MTD. There were 3 serious adverse events not related to treatment (infection, dyspnea, pain). Neutropenia was the most common grade 3 or 4 toxicity but only one patient required TAX dose reduction. 8 pts were evaluated for efficacy (2 with measurable disease, 6 with no measurable disease). 1 (of 2) pts with measurable disease had a partial response and was treated for 13 cycles. Of the 6 pts with no measurable disease, 2 recurred (5 and 10 months). The median disease free interval for the pts without recurrent disease was 22 months (6–30). Conclusion: Combination therapy of IM and TAX is well tolerated with minimal side effects in pts with advanced or recurrent USC. Initiation of the phase II component of this study is warranted to better evaluate efficacy.

No significant financial relationships to disclose.

Antenatal phenobarbital for reducing neonatal jaundice after red cell isoimmunization

BACKGROUND

Neonates from isoimmunized pregnancies have increased morbidity from neonatal jaundice. The increased bilirubin from haemolysis often needs phototherapy, exchange transfusion or both after birth. Various trials in pregnant women who were not isoimmunized but had other risk factors for neonatal jaundice have shown a reduction in need for phototherapy and exchange transfusion by the use of antenatal phenobarbital. A recent retrospective case-controlled study showed reduction in the need for exchange transfusion for the neonates from isoimmunized pregnancies.

OBJECTIVES

To assess the effects of antenatal phenobarbital in red cell isoimmunized pregnancies in reducing the incidence of phototherapy and exchange transfusion for the neonate.

SEARCH STRATEGY

We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (June 2006).

SELECTION CRITERIA

Randomised and quasi-randomised controlled trials of pregnant women established to have red cell isoimmunization in the current pregnancy during their antenatal testing and given phenobarbital alone or in combination with other drugs before birth.

DATA COLLECTION AND ANALYSIS

All three review authors independently assessed study eligibility and quality.

MAIN RESULTS

No trials met the inclusion criteria for this review.

AUTHORS' CONCLUSIONS

The use of antenatal phenobarbital to reduce neonatal jaundice in red cell isoimmunized pregnant women has not been evaluated in randomised controlled trials.

Translocation of p21(Cip1/WAF1) from the nucleus to the cytoplasm correlates with pancreatic myofibroblast to fibroblast cell conversion

BACKGROUND AND AIMS

In the pancreas, myofibroblasts (MFBs) were shown to play an important role in the cellular response during inflammation and injury. However, there is only fragmentary information concerning the fate of these cells in pancreas regeneration and fibrosis development.

METHODS

Explant cultures of rat pancreatic tissue were used as a model to follow cellular dynamics and phenotype conversion of pancreatic MFBs in vitro. For detailed biochemical analyses a pancreatic fibroblast cell line (long culture fibroblast (LCF)) was generated from MFBs in a long term culture. Cerulein induced acute pancreatitis and dibutyltin dichloride induced pancreas fibrosis were used as experimental models for acute and chronic fibrogenic reactions, respectively.

RESULTS

In the explant culture, pancreatic MFBs which derived from fat storing fibroblastic cells underwent apoptosis or converted again to fibroblasts. The phenotype switch to fibroblasts was associated with translocation of p21(Cip1/WAF1) from the nucleus into the cytoplasm. Molecular analyses in LCFs revealed subsequent binding to and inhibition of the activities of Rho kinase 2 and apoptosis signal regulating kinase 1. In the experimentally established pancreas fibrosis, fibroblasts with cytoplasmic expression of p21(Cip1/WAF1) were distributed throughout fibrotic bands whereas in experimental acute pancreatitis MFBs with nuclear expression of p21(Cip1/WAF1) dominated.

CONCLUSIONS

The results indicate that pancreatic MFBs are transient and suggest that intracellular localisation of p21(Cip1/WAF1) can contribute to the phenotype conversion of these cells to fibroblasts in culture and experimental injury.

Discriminating functional and non-functional p53 in human tumours by p53 and MDM2 immunohistochemistry

Mutation and/or loss of the TP53 tumour suppressor gene is the single most common genetic abnormality in human cancer. The majority of TP53 mutations lead to stabilization of the protein, so that immunohistochemical staining for p53 can suggest mutation status in many cases. However, various false-positive and false-negative situations mean that simple immunostaining for p53 is not informative in a substantial number of tumours. In the present study, a series of 119 human cancers were immunostained using a highly sensitive technique that detects the low levels of wild-type protein expressed in normal cells, such that homozygous gene deletion or non-sense TP53 mutation can be identified by an absence of staining. TP53 gene status was also assessed using FASAY as a genetic/functional screen and in selected cases by direct sequencing. A quantitative scoring system was employed to assess p53 levels, and p53 post-translational modification was evaluated using antibodies that detect specific phosphorylation sites. Phosphorylated p53 correlated with total p53 levels and did not improve the prediction of TP53 mutation status. The transcriptional activity of TP53 was determined by staining for two downstream target genes, p21(WAF1) and MDM2, and statistical correlations between MDM2/p21(WAF1) and p53 were found in tumours with wild-type, but not mutant TP53. Measurement of staining for p53 and MDM2 accurately identifies the TP53 status of tumours. This simple and cost-effective method, applicable to automated staining and quantitation methods, improves the identification of TP53 status over standard methods for p53 immunostaining and provides information about tumour p53 phenotype that is complementary to genotyping data.

[Stem cells and regeneration of human myocardium]

A concept of impossibility of appearance of novel cardiomyocytes in the heart of adult men in exchange for those lost due to cardiovascular diseases had dominated medicine and biology for many long decades. However ability of human myocardium to regenerate was demonstrated during recent years in multiple studies. This dictated necessity to reconsider previously generally accepted concept. At present researchers and practicing physicians actively discuss possibility of the use of transplantation of bone marrow stem cells, proper cardiac stem cells, skeletal muscle myoblasts or precursors of endothelial cells in patients with myocardial infarction and heart failure in order to restore normal cardiac structure and function. Another potential method of restoration of the myocardium in patients with cardiovascular diseases is the use of cytokines which stimulate migration of stem cells into myocardium and their differentiation into cardiomyocytes.

Bacillus anthracis contamination and inhalational anthrax in a mail processing and distribution center

AIMS

Four inhalational anthrax cases occurred in a large mail processing and distribution center in Washington, DC, after envelopes containing Bacillus anthracis spores were processed. This report describes the results of sampling for B. anthracis spores during investigations conducted in October and December 2001.

METHODS AND RESULTS

Wet swabs, wet wipes, vacuum sock, and air-filter samples were collected throughout the facility to characterize the extent of building contamination. The results showed widespread contamination of B. anthracis spores, particularly associated with one delivery bar code sorter (DBCS) machine that had sorted the spore-containing envelopes and an area where the envelopes were handled by postal workers. Spore concentrations decreased as distance from the DBCS machine increased, but spores were widely dispersed into surrounding areas.

CONCLUSION

The spatial distribution of culture positive samples was closely related to the work areas of the inhalational anthrax cases and supported epidemiological evidence that the workers became ill from exposure to B. anthracis spores in areas where the contaminated envelopes had travelled.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this investigation were used to guide decontamination efforts and provided baseline spore concentrations for follow-up measurements after the building had been cleaned. Implementing methods to reduce aerosolization and dispersion of dust within the facility would reduce postal workers' potential exposures to bioterrorism agents.