Nonlinear optics from an ab initio approach by means of the dynamical Berry phase: Application to second- and third-harmonic generation in semiconductors

We present an ab initio real-time-based computational approach to study nonlinear optical properties in condensed matter systems that is especially suitable for crystalline solids and periodic nanostructures. The equations of motion and the coupling of the electrons with the external electric field are derived from the Berry-phase formulation of the dynamical polarization [Souza et al., Phys. Rev. B 69, 085106 (2004)]. Many-body effects are introduced by adding single-particle operators to the independent-particle Hamiltonian. We add a Hartree operator to account for crystal local effects and a scissor operator to correct the independent particle band structure for quasiparticle effects. We also discuss the possibility of accurately treating excitonic effects by adding a screened Hartree-Fock self-energy operator. The approach is validated by calculating the second-harmonic generation of SiC and AlAs bulk semiconductors: an excellent agreement is obtained with existing ab initio calculations from response theory in frequency domain [Luppi et al., Phys. Rev. B 82, 235201 (2010)]. We finally show applications to the second-harmonic generation of CdTe and the third-harmonic generation of Si. 

SN 2012ec: mass of the progenitor from PESSTO follow-up of the photospheric phase

We present the results of a photometric and spectroscopic monitoring campaign of SN 2012ec, which exploded in the spiral galaxy NGC 1084, during the photospheric phase. The photometric light curve exhibits a plateau with luminosity L = 0.9 x 10(42) erg s(-1) and duration similar to 90 d, which is somewhat shorter than standard Type II-P supernovae (SNe). We estimate the nickel mass M(Ni-56) = 0.040 +/- 0.015 M-circle dot from the luminosity at the beginning of the radioactive tail of the light curve. The explosion parameters of SN 2012ec were estimated from the comparison of the bolometric light curve and the observed temperature and velocity evolution of the ejecta with predictions from hydrodynamical models. We derived an envelope mass of 12.6 M-circle dot, an initial progenitor radius of 1.6 x 10(13) cm and an explosion energy of 1.2 foe. These estimates agree with an independent study of the progenitor star identified in pre-explosion images, for which an initial mass of M = 14-22 M-circle dot was determined. We have applied the same analysis to two other Type II-P SNe (SNe 2012aw and 2012A), and carried out a comparison with the properties of SN 2012ec derived in this paper. We find a reasonable agreement between the masses of the progenitors obtained from pre-explosion images and masses derived from hydrodynamical models. We estimate the distance to SN 2012ec with the standardized candle method (SCM) and compare it with other estimates based on other primary and secondary indicators. SNe 2012A, 2012aw and 2012ec all follow the standard relations for the SCM for the use of Type II-P SNe as distance indicators.

The Type IIP Supernova 2012aw in M95: Hydrodynamical Modeling of the Photospheric Phase from Accurate Spectrophotometric Monitoring

We present an extensive optical and near-infrared photometric and spectroscopic campaign of the Type IIP supernova SN 2012aw. The data set densely covers the evolution of SN 2012aw shortly after the explosion through the end of the photospheric phase, with two additional photometric observations collected during the nebular phase, to fit the radioactive tail and estimate the ⁵⁶Ni mass. Also included in our analysis is the previously published Swift UV data, therefore providing a complete view of the ultraviolet-optical- infrared evolution of the photospheric phase. On the basis of our data set, we estimate all the relevant physical parameters of SN 2012aw with our radiation-hydrodynamics code: envelope mass M _env ∼ 20 M _⊙, progenitor radius R ∼ 3 × 10¹³ cm (∼430 R_⊙), explosion energy E ∼ 1.5 foe, and initial ⁵⁶Ni mass ∼0.06 M_⊙. These mass and radius values are reasonably well supported by independent evolutionary models of the progenitor, and may suggest a progenitor mass higher than the observational limit of 16.5 ± 1.5 M _⊙of the Type IIP events. 

Interactions between soil, toxicant, and a lux-marked bacterium during solid phase-contact toxicity testing

Bioluminescence-based, solid-contact toxicity assays allow test bacterium and toxicant to interact at the solid-solution interface. A lux- marked bacterium, Burkholderia sp. RASC, and 2,4-dichlorophenol (2,4-DCP) were used to characterize these interactions. In the basic bioassay, cells were added to soil slurries containing 2,4-DCP (0-120 μg ml^-1). After 15 min, soil was removed by centrifugation, and bioluminescence in the supernatant was determined. Investigation of 2,4-DCP adsorption to soil revealed that sorption was linear and not significantly (p > 0.1) affected by the presence of Burkholderia cells. The numbers of culturable Burkholderia cells in the assay supernatant were 48.2 to 64.8% of the inoculum and independent of the soil weight. The effect of soil on 2,4-DCP toxicity was investigated by comparing soil aqueous extract and contact assays. The percentage bioluminescence for the contact assay was consistently higher than the extract assay at all test concentrations, and counts of viable Burkholderia cells were enhanced by the presence of 2,4-DCP in the contact assay. Expressing results as specific bioluminescence decreased the variability in response and the discrepancy in results between the two protocols. We suggest that solid-contact assays need improvement to ensure defined contact between cells and solid phase, and that the reporting of specific activity should be emphasized.

EGF61 polymorphism predicts complete pathologic response to cetuximab-based chemoradiation independent of KRAS status in locally advanced rectal cancer patients

BACKGROUND: Cetuximab has shown significant clinical activity in metastatic colon cancer. However, cetuximab-containing neoadjuvant chemoradiation has not been shown to improve tumor response in locally advanced rectal cancer patients in recent phase I/II trials. We evaluated functional germline polymorphisms of genes involved in epidermal growth factor receptor pathway, angiogenesis, antibody-dependent cell-mediated cytotoxicity, DNA repair, and drug metabolism, for their potential role as molecular predictors for clinical outcome in locally advanced rectal cancer patients treated with preoperative cetuximab-based chemoradiation.

METHODS: 130 patients (74 men and 56 women) with locally advanced rectal cancer (4 with stage II, 109 with stage III, and 15 with stage IV, 2 unknown) who were enrolled in phase I/II clinical trials treated with cetuximab-based chemoradiation in European cancer centers were included. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor samples and genotyping was done by using PCR-RFLP assays. Fisher's exact test was used to examine associations between polymorphisms and complete pathologic response (pCR) that was determined by a modified Dworak classification system (grade III vs. grade IV: complete response).

RESULTS: Patients with the epidermal growth factor (EGF) 61 G/G genotype had pCR of 45% (5/11), compared with 21% (11/53) in patients heterozygous, and 2% (1/54) in patients homozygous for the A/A allele (P < 0.001). In addition, this association between EGF 61 G allele and pCR remained significant (P = 0.019) in the 59 patients with wild-type KRAS.

CONCLUSION: This study suggested EGF A+61G polymorphism to be a predictive marker for pCR, independent of KRAS mutation status, to cetuximab-based neoadjuvant chemoradiation of patients with locally advanced rectal cancer.

The use of erythropoiesis-stimulating agents with ruxolitinib in patients with myelofibrosis in COMFORT-II: an open-label, phase 3 study assessing efficacy and safety of ruxolitinib versus best available therapy in the treatment of myelofibrosis

BACKGROUND: Anemia is considered a negative prognostic risk factor for survival in patients with myelofibrosis. Most patients with myelofibrosis are anemic, and 35-54 % present with anemia at diagnosis. Ruxolitinib, a potent inhibitor of Janus kinase (JAK) 1 and JAK2, was associated with an overall survival benefit and improvements in splenomegaly and patient-reported outcomes in patients with myelofibrosis in the two phase 3 COMFORT studies. Consistent with the ruxolitinib mechanism of action, anemia was a frequently reported adverse event. In clinical practice, anemia is sometimes managed with erythropoiesis-stimulating agents (ESAs). This post hoc analysis evaluated the safety and efficacy of concomitant ruxolitinib and ESA administration in patients enrolled in COMFORT-II, an open-label, phase 3 study comparing the efficacy and safety of ruxolitinib with best available therapy for treatment of myelofibrosis. Patients were randomized (2:1) to receive ruxolitinib 15 or 20 mg twice daily or best available therapy. Spleen volume was assessed by magnetic resonance imaging or computed tomography scan.

RESULTS: Thirteen of 146 ruxolitinib-treated patients had concomitant ESA administration (+ESA). The median exposure to ruxolitinib was 114 weeks in the +ESA group and 111 weeks in the overall ruxolitinib arm; the median ruxolitinib dose intensity was 33 mg/day for each group. Six weeks before the first ESA administration, 10 of the 13 patients had grade 3/4 hemoglobin abnormalities. These had improved to grade 2 in 7 of the 13 patients by 6 weeks after the first ESA administration. The rate of packed red blood cell transfusions per month within 12 weeks before and after first ESA administration remained the same in 1 patient, decreased in 2 patients, and increased in 3 patients; 7 patients remained transfusion independent. Reductions in splenomegaly were observed in 69 % of evaluable patients (9/13) following first ESA administration.

CONCLUSIONS: Concomitant use of an ESA with ruxolitinib was well tolerated and did not affect the efficacy of ruxolitinib. Further investigations evaluating the effects of ESAs to alleviate anemia in ruxolitinib-treated patients are warranted (ClinicalTrials.gov identifier, NCT00934544; July 6, 2009).

Monte Carlo studies of phase transitions and adsorption : application to n-6 Lennard-Jones, C60 and zeolite systems

The solid-fluid transition properties of the n - 6 Lennard-Jones system are studied by means of extensive free energy calculations. Different values of the parameter n which regulates the steepness of the short-range repulsive interaction are investigated. Furthermore, the free energies of the n < 12 systems are calculated using the n = 12 system as a reference. The method relies on a generalization of the multiple histogram method that combines independent canonical ensemble simulations performed with different Hamiltonians and computes the free energy difference between them. The phase behavior of the fullerene C60 solid is studied by performing NPT simulations using atomistic models which treat each carbon in the molecule as a separate interaction site with additional bond charges. In particular, the transition from an orientationally frozen phase at low temperatures to one where the molecules are freely rotating at higher temperatures is studied as a function of applied pressure. The adsorption of molecular hydrogen in the zeolite NaA is investigated by means of grand-canonical Monte Carlo, in a wide range of temperatures and imposed gas pressures, and results are compared with available experimental data. A potential model is used that comprises three main interactions: van der Waals, Coulomb and induced polarization by the permanent electric field in the zeolite.

Joint compensation of IQ-imbalance and carrier phase sychronization errors in communication receivers

This work addresses the joint compensation of IQimbalances and carrier phase synchronization errors of zero- IF receivers. The compensation scheme based on blind-source separation which provides simple yet potent means to jointly compensate for these errors independent of modulation format and constellation size used. The low-complexity of the algorithm makes it a suitable option for real-time deployment as well as practical for integration into monolithic receiver designs.

Superior outcome of women with stage I/II cutaneous melanoma: pooled analysis of four European Organisation for Research and Treatment of Cancer phase III trials.

PURPOSE: Several studies observed a female advantage in the prognosis of cutaneous melanoma, for which behavioral factors or an underlying biologic mechanism might be responsible. Using complete and reliable follow-up data from four phase III trials of the European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, we explored the female advantage across multiple end points and in relation to other important prognostic indicators. PATIENTS AND METHODS: Patients diagnosed with localized melanoma were included in EORTC adjuvant treatment trials 18832, 18871, 18952, and 18961 and randomly assigned during the period of 1984 to 2005. Cox proportional hazard models were used to calculate hazard ratios (HRs) and 95% CIs for women compared with men, adjusted for age, Breslow thickness, body site, ulceration, performed lymph node dissection, and treatment. RESULTS: A total of 2,672 patients with stage I/II melanoma were included. Women had a highly consistent and independent advantage in overall survival (adjusted HR, 0.70; 95% CI, 0.59 to 0.83), disease-specific survival (adjusted HR, 0.74; 95% CI, 0.62 to 0.88), time to lymph node metastasis (adjusted HR, 0.70; 95% CI, 0.51 to 0.96), and time to distant metastasis (adjusted HR, 0.69; 95% CI, 0.59 to 0.81). Subgroup analysis showed that the female advantage was consistent across all prognostic subgroups (with the possible exception of head and neck melanomas) and in pre- and postmenopausal age groups. CONCLUSION: Women have a consistent and independent relative advantage in all aspects of the progression of localized melanoma of approximately 30%, most likely caused by an underlying biologic sex difference.

Caractérisation cytogénétique et moléculaire des translocations chromosomiques dans la phase blastique de la leucémie myéloïde chronique

La leucémie myéloïde chronique (LMC) est un modèle d’évolution tumorale dans les cancers humains. Le processus d’évolution de la LMC de la phase chronique (PC) à la phase blastique (PB) est caractérisé par un arrêt de différenciation et l’acquisition de la capacité d’autorenouvellement incontrôlé d’une cellule souche ou d’un progéniteur hématopoïétique. La LMC en PB est associée à la présence d’anomalies génétiques additionnelles à la fusion BCR-ABL1 qui résulte de la translocation chromosomique t(9;22). Contrairement aux patients en PC, les patients en PB de la LMC n’obtiennent pas une réponse moléculaire complète à long terme avec 1’Imatinib mesylate, un inhibiteur de la tyrosine kinase (ITK) BCR-ABL1. De plus, les ITKs de deuxième et troisième générations sont moins efficaces en PB de la LMC lorsque les cellules leucémiques ont acquis une résistance au traitement indépendante des mutations de BCR-ABL1. Les mécanismes moléculaires des voies de signalisation impliquées dans la progression de la LMC en PB ne sont pas entièrement élucidés. Le but de notre travail est de caractériser de nouvelles anomalies génétiques dans la PB de la LMC. Nous avons identifié en cytogénétique, quatre nouvelles translocations chromosomiques : t(1;21)(p36;q22), t(7;17)(p15;q22), t(8;17)(q11;q22) et t(2;12)(q31;p13) dans les cellules leucémiques de patients en PB de la LMC résistants au traitement. En utilisant des techniques d'hybridation in situ en fluorescence, de RT-PCR et de séquençage, nous avons délimité les régions à investiguer au niveau des points de cassure et identifié un réarrangement de plusieurs gènes codant pour des facteurs de transcription importants lors de l’hématopoïèse tels que RUNX1, ETV6, PRDM16 et HOXA. L’altération de ces gènes pourrait expliquer l’arrêt de différenciation et/ou l’acquisition de la capacité d’autorenouvellement caractéristiques de la LMC en PB. Nous avons identifié les fusions RUNX1-PRDM16, MSI2-HOXA, MSI2-SOX17 et ETV6-HOXD11, respectivement associées aux translocations chromosomiques t(1;21), t(7;17), t(8;17) et t(2;12). Ces fusions génèrent différents transcrits alternatifs qui maintiennent et altèrent le cadre ouvert de lecture. L’analyse des séquences des transcrits chimériques identifiés dans ce projet, incluant RUNX1-PRDM16, MSI2-HOXA9, MSI2-HOXA10, MSI2-HOXA11 et ETV6-HOXD11, nous a permis de prédire les domaines fonctionnels potentiellement présents au niveau des protéines chimériques prédites. Les transcrits de fusion qui respectent le cadre ouvert de lecture peuvent générer des domaines fonctionnels des deux partenaires. C’est le cas des deux transcrits identifiés pour la fusion RUNX1-PRDM16 où le domaine de liaison à l’ADN RHD (Runt homology domain) de RUNX1 est fusionné avec la quasi-totalité des domaines de PRDM16. Les transcrits de fusion qui ne respectent pas le cadre ouvert de lecture donnent des formes tronquées des transcrits RUNX1, MSI2 et ETV6. La juxtaposition des régions promotrices de ces derniers en 5’ de leurs partenaires entraîne l’activation de la forme courte oncogénique de PRDM16 dans la t(1;21) ou de différents gènes HOXA/D dans les t(7;17) et t(2;12), ainsi que l’expression aberrante d’un nouveau transcrit alternatif de SOX17 dans la t(8;17). Notre étude nous a permis d’identifier de nouveaux gènes de fusion et/ou une activation de gènes qui pourraient coopérer avec la fusion BCR-ABL1 dans la progression de la LMC et être impliqués dans la résistance au traitement de la LMC en phase avancée. La caractérisation des événements génétiques associés à la transformation blastique de la LMC est essentielle pour l’investigation des voies moléculaires impliquées dans cette phase de la maladie. Investiguer la résistance au traitement de ces patients pourrait aussi contribuer à identifier de nouvelles cibles thérapeutiques dans cette leucémie.

Le délai entre le traumatisme médullaire et la chirurgie a-t-il un impact sur la survenue de complications durant la phase aigüe d’hospitalisation

Le délai optimal entre une lésion médullaire traumatique (LMT) et la chirurgie demeure indéterminé. Cependant, la relation entre la prévention de complications et le délai chirurgical n’a jamais été spécifiquement étudiée. L’objectif principal de ce travail était de détecter si les taux de complications chez des LMT étaient associés avec le délai chirurgical. L’objectif secondaire était d’identifier si le délai chirurgical est un prédicteur indépendant de la survenue de complications. Un premier article présente l’analyse d’une cohorte rétrospective de 431 LMTs. Une chirurgie réalisée dans un délai inférieur à 24h (ou inférieur à 72h si un délai de 24h ne peut être respecté) prédisait une diminution du taux de l’ensemble des complications, du taux de pneumonies et du taux de plaies de pression. Les autres facteurs prédictifs de complications identifiés étaient : l’âge, la sévérité de l’atteinte neurologique de la lésion selon l’échelle ASIA, un traumatisme cervical plutôt que thoracique, la présence de comorbidités, la sévérité du traumatisme selon l’échelle ISS et la complexité de la chirurgie. Les connaissances actuelles suggèrent qu’une opération chirurgicale rapide n’a que peu d’effet sur la récupération neurologique chez les LMTs complètes (interruption complète des fonctions sensorimotrices). Pour cette raison, notre second article analyse l’impact du délai chirurgical sur la survenue des complications à partir d’une sous-population de 197 LMTs complètes de notre cohorte. Un délai chirurgical supérieur à 24h prédisait une augmentation des complications, notamment les pneumonies et les infections urinaires. Bien que des études prospectives randomisées sont nécessaires pour confirmer nos conclusions, nos études supportent un délai chirurgical rapide afin de diminuer le taux de complications non neurologiques chez les LMTs.

Déficience dans la réparation par excision de nucléotides en phase S induite par la séquestration du facteur de réplication RPA

Introduction Les lésions induites par les rayons UV peuvent causer des blocages dans la réplication de l'ADN. Ces dommages sont éliminés par le processus moléculaire très conservé de réparation par excision de nucléotides (NER). Nous avons précédemment démontré que la protéine ATR, une kinase majeure impliquée dans le stress réplicatif, est requise pour une NER efficace, et ce exclusivement durant la phase S. Des résultats subséquents ont suggéré que ce prérequis n’était pas lié à la réponse induite par ATR, mais plutôt d’une conséquence globale causée par la présence de stress réplicatif. En ce sens, nous mettons l’emphase qu’après irradiation UV, le complexe RPA joue un rôle crucial dans l'activation des mécanismes de NER ainsi que dans le redémarrage des fourches de réplication bloquées. Hypothèses: En général, les mutations qui confèrent une augmentation du stress réplicatif engendrent une séquestration excessive du facteur RPA aux fourches de réplication bloquées ce qui réduit son accessibilité pour le NER. Méthodes et résultats: Le modèle de la levure a été choisi pour vérifier cette hypothèse. Nous avons développé un essai de NER spécifique à chacune des phases du cycle cellulaire pour démontrer que les cellules déficientes en Mec1, l’homologue d’ATR, sont défectives dans la réparation par excision de nucléotides spécifiquement en phase S. De plus, plusieurs autres mutants de levure, caractérisés par un niveau de dommages spontanés élevé, ont aussi exhibé un défaut similaire. Ces mutants ont démontré une fréquence et une intensité de formation de foyers de RPA plus élevée. Finalement, une diminution partielle de RPA dans les levures a induit un défaut significatif dans le NER spécifiquement durant la phase S. Conclusion: Nos résultats supportent la notion que la séquestration de RPA aux fourches de réplication endommagées durant la phase S prévient son utilisation pour la réparation par excision de nucléotides ce qui inhibe fortement l'efficacité de réparation. Cette étude chez la levure facilite l’élucidation du phénomène analogue chez l’humain et, ultimement, comprend des implications majeures dans la compréhension du mécanisme de développement des cancers UV-dépendants.

Ultrasonic Study Of The Elastic Properties And Phase Transitions In Selected Mixed Sulphate Crystals

The thesis investigated the elastic properties and phase transitions in selected mixed sulphate crystals – Lithium Hydrazinium Sulphate [LiN2H2SO4], Lithium Ammonium Sulphate [LiNH4SO4] and Lithium Potassium Sulphate [LiKSO4] – using ultrasonic technique. The pulse echo overlap technique has been used for measuring ultrasonic velocity and its dependence on temperature along different directions with waves of longitudinal and transverse polarizations. Two major numerical techniques and the corresponding computer programs developed as part of present work are presented in this thesis. All the 9 elastic constants of LHS are determined accurately from ultrasonic measurements and applying misorientation correction refines the constants. Ultrasonic measurements are performed in LAS to determine the elastic constants and to study the low temperature phase transitions. Temperature variation studies of elastic constant of LAS are performed for 6 different modes of propagation for heating and cooling at low temperatures. All the 5 independent elastic constants of LPS is determined using ultrasonic measurements. It is concluded that LPS crystal does not undergo a phase transition near this temperature. A comparison of the three crystals studied shows that LPS has maximum number of phase transitions and LHS has the least number. It is interesting to note that LPS has the simplest formula unit among the three. There is considerable scope for the future work on these crystals and others belonging to the sulphate family.

Molecular computations for reactions and phase transitions: applications to protein stabilization, hydrates and catalysis

In this work we have made significant contributions in three different areas of interest: therapeutic protein stabilization, thermodynamics of natural gas clathrate-hydrates, and zeolite catalysis. In all three fields, using our various computational techniques, we have been able to elucidate phenomena that are difficult or impossible to explain experimentally. More specifically, in mixed solvent systems for proteins we developed a statistical-mechanical method to model the thermodynamic effects of additives in molecular-level detail. It was the first method demonstrated to have truly predictive (no adjustable parameters) capability for real protein systems. We also describe a novel mechanism that slows protein association reactions, called the “gap effect.” We developed a comprehensive picture of methioine oxidation by hydrogen peroxide that allows for accurate prediction of protein oxidation and provides a rationale for developing strategies to control oxidation. The method of solvent accessible area (SAA) was shown not to correlate well with oxidation rates. A new property, averaged two-shell water coordination number (2SWCN) was identified and shown to correlate well with oxidation rates. Reference parameters for the van der Waals Platteeuw model of clathrate-hydrates were found for structure I and structure II. These reference parameters are independent of the potential form (unlike the commonly used parameters) and have been validated by calculating phase behavior and structural transitions for mixed hydrate systems. These calculations are validated with experimental data for both structures and for systems that undergo transitions from one structure to another. This is the first method of calculating hydrate thermodynamics to demonstrate predictive capability for phase equilibria, structural changes, and occupancy in pure and mixed hydrate systems. We have computed a new mechanism for the methanol coupling reaction to form ethanol and water in the zeolite chabazite. The mechanism at 400°C proceeds via stable intermediates of water, methane, and protonated formaldehyde.

The phase relations of normal ears compared with the phase relations of otosclerotic ears before and after the fenestration operation

This paper discusses the fenestration operation and its effect on hearing.