PrDOS is a server that predicts the disordered regions of a protein from its amino acid sequence (http://prdos.hgc.jp). The server accepts a single protein amino acid sequence, in either plain text ...or FASTA format. The prediction system is composed of two predictors: a predictor based on local amino acid sequence information and one based on template proteins. The server combines the results of the two predictors and returns a two-state prediction (order/disorder) and a disorder probability for each residue. The prediction results are sent by e-mail, and the server also provides a web-interface to check the results.
The efficacy of programmed death-1 blockade in epidermal growth factor receptor gene (EGFR) mutation-positive non-small-cell lung cancer (NSCLC) patients with different mechanisms of acquired ...resistance to EGFR tyrosine kinase inhibitors (TKIs) is unknown. We retrospectively evaluated nivolumab efficacy and immune-related factors in such patients according to their status for the T790M resistance mutation of EGFR.
We identified 25 patients with EGFR mutation-positive NSCLC who were treated with nivolumab after disease progression during EGFR-TKI treatment (cohort A). Programmed death-ligand 1 (PD-L1) expression and tumor-infiltrating lymphocyte (TIL) density in tumor specimens obtained after acquisition of EGFR-TKI resistance were determined by immunohistochemistry. Whole-exome sequencing of tumor DNA was carried out to identify gene alterations. The relation of T790M status to PD-L1 expression or TIL density was also examined in an independent cohort of 60 patients (cohort B).
In cohort A, median progression-free survival (PFS) was 2.1 and 1.3months for T790M-negative and T790M-positive patients, respectively (P=0.099; hazard ratio of 0.48 with a 95% confidence interval of 0.20–1.24). Median PFS was 2.1 and 1.3months for patients with a PD-L1 expression level of≥1% or<1%, respectively (P=0.084; hazard ratio of 0.37, 95% confidence interval of 0.10–1.21). PFS tended to increase as the PD-L1 expression level increased with cutoff values of≥10% and≥50%. The proportion of tumors with a PD-L1 level of≥10% or≥50% was higher among T790M-negative patients than among T790M-positive patients of both cohorts A and B. Nivolumab responders had a significantly higher CD8+ TIL density and nonsynonymous mutation burden.
T790M-negative patients with EGFR mutation-positive NSCLC are more likely to benefit from nivolumab after EGFR-TKI treatment, possibly as a result of a higher PD-L1 expression level, than are T790M-positive patients.
We investigate rates of pathologic complete response (pCR) and tumor expression of ER, PgR, HER2 discordance after neoadjuvant chemotherapy using Japanese breast cancer registry data.
Records of more ...than 300 000 breast cancer cases treated at 800 hospitals from 2004 to 2013 were retrieved from the breast cancer registry. After data cleanup, we included 21 755 patients who received neoadjuvant chemotherapy and had no distant metastases. pCR was defined as no invasive tumor in the breast detected during surgery after neoadjuvant chemotherapy. HER2 overexpression was determined immunohistochemically and/or using fluorescence in situ hybridization.
pCR was achieved in 5.7% of luminal tumors (n = 8730), 24.6% of HER2-positive tumors (n = 4403), and 18.9% of triple-negative tumors (n = 3660). Among HER2-positive tumors, pCR was achieved in 31.6% of ER-negative tumors (n = 2252), 17.0% of ER-positive ones (n = 2132), 31.4% of patients who received trastuzumab as neoadjuvant chemotherapy (n = 2437), and 16.2% of patients who did not receive trastuzumab (n = 1966). Of the 2811 patients who were HER2-positive before treatment, 601 (21.4%) had HER2-negative tumors after neoadjuvant chemotherapy, whereas 340 (3.4%) of the 9947 patients with HER2-negative tumors before treatment had HER2-positive tumors afterward. Of the 10 973 patients with ER-positive tumors before treatment, 499 (4.6%) had ER-negative tumors after neoadjuvant chemotherapy, whereas 519 (9.3%) of the 5607 patients who were ER-negative before treatment had ER-positive tumors afterward.
We confirmed that loss of HER2-positive status can occur after neoadjuvant treatment in patients with primary HER2-positive breast cancer. We also confirmed that in practice, differences in pCR rates between breast cancer subtypes are the same as in clinical trials. Our data strongly support the need for retest ER, PgR, HER2 of surgical sample after neoadjuvant therapy in order to accurately determine appropriate use of targeted therapy.
Background
Drug‐induced hypersensitivity syndrome/drug rash with eosinophilia and systemic symptoms (DIHS/DRESS) and Stevens–Johnson syndrome (SJS)/toxic epidermal necrolysis (TEN) represent ...contrasting poles of severe drug eruptions, and sequential reactivations of several herpesviruses have exclusively been demonstrated in the former. No previous studies, however, were extended beyond the acute stage. We sought to investigate whether herpesvirus reactivations could also be observed in SJS/TEN and beyond the acute stage of both diseases.
Methods
Patients with SJS (n = 16), SJS/TEN overlap (n = 2), TEN (n = 10), and DIHS/DRESS (n = 34) were enrolled. We performed a retrospective analysis of Epstein–Barr virus (EBV), human herpesvirus 6 (HHV‐6), and cytomegalovirus (CMV) DNA loads sequentially determined by real‐time polymerase chain reaction during a 2‐year period after onset.
Results
Persistently increased EBV loads were detected in SJS during the acute stage and long after resolution, but not in others. In contrast, high HHV‐6 loads were exclusively detected in DIHS/DRESS during the acute stage. The dynamics of herpesvirus reactivation varied in DIHS/DRESS according to the use of systemic corticosteroids: While EBV loads were higher in patients not receiving systemic corticosteroids, CMV and HHV‐6 loads were higher in those receiving them.
Conclusions
Distinct patterns of herpesvirus reactivation according to the pathological phenotype and to the use of systemic corticosteroids were observed during the acute stage and follow‐up period, which may contribute, at least in part, to the difference in the clinical manifestations and long‐term outcomes. Systemic corticosteroids during the acute stage may improve the outcomes in DIHS/DRESS.
Generation and transmission of voltage signals in a kinetic inductance detector made of a superconducting nanowire stripline is investigated on the basis of superconducting electromagnetism. We show ...that electric signals traveling along the stripline in this detector can be regarded as a Swihart mode. An equation which can describe the generation and transmission of voltage pulses in this detector is derived. A pair of voltage pulses with opposite polarities are created when a spatiotemporal variation in the density of the superconducting condensate occurs in a small region of this superconducting nanowire. The voltage pulses propagate along the stripline in the directions opposite to each other with the Swihart velocity. The characteristic of the radiation detector named current-biased kinetic inductance detector (CB-KID) is well described by our model.
M. Shioya, S. Obayashi, H. Tabunoki, K. Arima, Y. Saito, T. Ishida and J. Satoh (2010) Neuropathology and Applied Neurobiology36, 320–330 Aberrant microRNA expression in the brains of ...neurodegenerative diseases: miR‐29a decreased in Alzheimer disease brains targets neurone navigator 3
Aims: MicroRNAs (miRNAs) are small non‐coding RNAs that regulate translational repression of target mRNAs. Accumulating evidence indicates that various miRNAs, expressed in a spatially and temporally controlled that manner in the brain plays a key role in neuronal development. However, at present, the pathological implication of aberrant miRNA expression in neurodegenerative events remains largely unknown. To identify miRNAs closely associated with neurodegeneration, we performed miRNA expression profiling of brain tissues of various neurodegenerative diseases. Methods: We initially studied the frontal cortex derived from three amyotrophic lateral sclerosis patients by using a microarray of 723 human miRNAs. This was followed by enlargement of study population with quantitative RT‐PCR analysis (n = 21). Results: By microarray analysis, we identified up‐regulation of miR‐29a, miR‐29b and miR‐338‐3p in amyotrophic lateral sclerosis brains, but due to a great interindividual variation, we could not validate these results by quantitative RT‐PCR. However, we found significant down‐regulation of miR‐29a in Alzheimer disease (AD) brains. The database search on TargetScan, PicTar and miRBase Target identified neurone navigator 3 (NAV3), a regulator of axon guidance, as a principal target of miR‐29a, and actually NAV3 mRNA levels were elevated in AD brains. MiR‐29a‐mediated down‐regulation of NAV3 was verified by the luciferase reporter assay. By immunohistochemistry, NAV3 expression was most evidently enhanced in degenerating pyramidal neurones in the cerebral cortex of AD. Conclusions: These observations suggest the hypothesis that underexpression of miR‐29a affects neurodegenerative processes by enhancing neuronal NAV3 expression in AD brains.
Synchronous occurrence of intraductal papillary mucinous neoplasm (IPMN) and ductal carcinoma of the pancreas has been reported. Branch duct IPMNs with lower likelihood of malignancy are not ...submitted to resection but are followed-up, so ductal carcinoma may develop during the follow-up. The development of ductal carcinoma of the pancreas during follow-up of branch duct IPMNs was investigated.
60 patients with branch duct IPMN who had an intraductal tumour of <10 mm on imaging examinations and a negative result for malignancy on cytological examination of the pancreatic juice were investigated. They were followed-up mainly by ultrasonography (US), and additionally by endoscopic ultrasonography (EUS), CT, magnetic resonance cholangiopancreatography (MRCP) or endoscopic retrograde cholangiopancreatography (ERCP) with cytological examination of the pancreatic juice for an average period of 87 months.
Ductal carcinoma of the pancreas distinct from IPMN developed in 5 of 60 (8%) branch duct IPMNs during follow-up. The 5-year rate of development of ductal carcinoma was 6.9% (95% CI 0.4% to 13.4%), the incidence of ductal carcinoma was 1.1% (95% CI 0.1% to 2.2%) per year and the standardised incidence ratio of development of ductal carcinoma was 26 (95% CI 3 to 48). Patients >70 years old developed ductal carcinoma significantly more frequently than those under 69. Four of five ductal carcinomas identified during follow-up were resectable. Cancer developed in IPMN in 2 of 60 (3%) branch duct IPMNs during follow-up.
During follow-up of branch duct IPMNs, ductal carcinoma of the pancreas not infrequently developed distinct from IPMN. In the follow-up of IPMN, special attention should be paid to the development of ductal carcinoma of the pancreas.
The free energy landscape (FEL) depends on temperature by its definition and the FEL is reorganized with time delay when the temperature is modulated. We investigate how the relaxation of the FEL ...manifests itself in physical properties. Exploiting a simple two-level model for the dielectric relaxation, we first show that the relaxation of the FEL produces time dependence of the relaxation time of the dielectric response. Then we discuss the relaxation of dielectric susceptibility when the temperature is suddenly increased/decreased and show that the susceptibility relaxes to the equilibrium value with the same relaxation time as the FEL in the long time limit. In order to show the general feature of the temperature modulation spectroscopy, we consider the dynamics of an order parameter of the Landau model which has a delayed response to the temperature modulation with relaxation time. When the temperature is modulated sinusoidally, we show that there appear second order responses at the sum and the difference of the frequencies of the external field and the temperature modulation and that the relaxation time of the FEL can be deduced from these two responses.
•Aging observed in super-cooled liquids are explained by the free energy landscape theory.•The relaxation time of the free energy landscape is shown to be obtained from the nonlinear dielectric response.•The temperature modulation spectroscopy is shown to be applied to any systems described by the Landau free energy.
Transmission of voltage pulses generated by local heating in a kinetic inductance detector made of a superconducting stripline is theoretically investigated on the basis of the TDGL equation. The ...effect of thermal diffusion is also incorporated into the electrodynamics of this system. We derive an equation that can describe the generation and transmission of voltage pulses in this detector. A pair of voltage pulses with opposite polarities are created when a spatiotemporal variation in the superconducting order parameter occurs in a small region of this superconducting stripline. We clarify the characteristic feature in the shape of the voltage pulse.
To develop lanthanoid-based magnetic materials and relevant devices, reliable prescriptions for molecular/crystal design have long been desired. Ln3+-ion dependence on the molecular magnetism was ...investigated in the isomorphous series Ln(hfac)3(2pyNO) (Ln = Tb, Dy, Ho, Er), where 2pyNO stands for tert-butyl 2-pyridyl nitroxide as a paramagnetic ligand, and hfac for 1,1,1,5,5,5-hexafluoropentane-2,4-dionate. The slow magnetization reversal was evaluated as an indication of single-molecule magnets (SMMs) by out-of-phase ac magnetic susceptibility χ". Whereas the Tb3+ (4f8) and Ho3+ (4f10) derivatives exhibited frequency-dependent χ", practically null χ" was recorded for the Dy3+(4f9) and Er3+ (4f11) derivatives. As for another series with Ln/radical = 1/2, Ln(hfac)3(TEMPO)2 complexes were prepared (Ln = Tb, Dy, Ho, Er, Tm; TEMPO = 2,2,6,6-tetramethylpiperidin-1-oxyl). The Dy3+ and Er3+ derivatives showed appreciable χ", but the Tb3+, Ho3+, and Tm3+ derivatives did not. Thus, the S = 1/2 paramagnetic ligands play a role of a spin-parity switch to regulate whether the compound behaves as an SMM. In the strongly exchange-coupled regime owing to the direct radical coordination bond, the whole molecular electron counting may provide a useful criterion to predict Kramers molecules and accordingly to explore potential SMM candidates.
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