Hard x-ray intensity autocorrelation using direct two-photon absorption

An intensity autocorrelation measurement is demonstrated to characterize a pulse duration of 9-keV x-ray free-electron laser (XFEL) pulses from a split-delay optical (SDO) system with four-bounce silicon 220 reflections in each branch. XFEL pulse replicas with variable time delays are generated by the SDO system itself. High intensity of >2×1016W/cm2 achieved in a self-seeding operation and careful data analysis allow the measurement with direct two-photon absorption. The autocorrelation trace gave a duration of 7.6±0.8fs in full width at half maximum for a Gaussian assumption. Furthermore, the trace shows good agreement with a simulation of the XFEL pulse shape propagating through the SDO system, irrespective of spectral chirps in the original XFEL pulses. Our results open the door toward direct temporal characterization of narrowband XFELs at the hard x-ray regime, such as self-seeded and future cavity-based XFELs, and indicate a solid way for temporal tailoring of ultrafast x-ray pulses with perfect crystals.Osaka T., Inoue I., Yamada J., et al. Hard x-ray intensity autocorrelation using direct two-photon absorption. Physical Review Research, 4, 1, L012035. https://doi.org/10.1103/PhysRevResearch.4.L012035

Analysis of Expressed Sequence Tags from the Fungus Aspergillus oryzae Cultured Under Different Conditions

We performed random sequencing of cDNAs from nine biologically or industrially important cultures of the industrially valuable fungus Aspergillus oryzae to obtain expressed sequence tags (ESTs). Consequently, 21 446 raw ESTs were accumulated and subsequently assembled to 7589 non-redundant consensus sequences (contigs). Among all contigs, 5491 (72.4%) were derived from only a particular culture. These included 4735 (62.4%) singletons, i.e. lone ESTs overlapping with no others. These data showed that consideration of culture grown under various conditions as cDNA sources enabled efficient collection of ESTs. BLAST searches against the public databases showed that 2953 (38.9%) of the EST contigs showed significant similarities to deposited sequences with known functions, 793 (10.5%) were similar to hypothetical proteins, and the remaining 3843 (50.6%) showed no significant similarity to sequences in the databases. Culture-specific contigs were extracted on the basis of the EST frequency normalized by the total number for each culture condition. In addition, contig sequences were compared with sequence sets in eukaryotic orthologous groups (KOGs), and classified into the KOG functional categories

Spectrum adapted expectation-conditional maximization algorithm for extending high–throughput peak separation method in XPS analysis

We introduced the spectrum-adapted expectation-conditional maximization (ECM) algorithm to improve the efficiency of the peak fitting of spectral data by various fitting models. The spectrum-adapted ECM algorithm can perform the peak fitting by using the Pseudo–Voigt mixture model and Doniach–Šunjić–Gauss mixture model which are generally used for the peak fitting in the X-ray photoelectron spectroscopy. Analyses of the synthetic and experimental spectral data showed that the proposed method quickly completed the calculation and estimated well-fitted curves to spectral data. This result suggests that the spectrum adapted ECM algorithm efficiently perform the peak fitting for large number of spectral data sets

High-throughput XPS spectrum modeling with autonomous background subtraction for 3d5/2 peak mapping of SnS

We propose a fitting model that automatically conducts the background subtraction during high-throughput peak fitting. The fitting model consists of the pseudo-Voigt mixture model and the ramp-sum background model, and each model represents the peak and background component, respectively. The optimization of the fitting model is performed by the spectrum adapted ECM algorithm that enables us to perform the peak fitting and background subtraction simultaneously through the high-throughput calculation. Application of the proposed model to the synthetic spectral data showed appropriate decomposition of the peak and background component. We also applied the proposed model to 3721 spectral data collected from the SnS sheet by X-ray photoelectron spectroscopy. The spectral data from the SnS sheet were successfully decomposed to the component of Sn $$3{d_{3/2}}$$ peak, Sn $$3{d_{5/2}}$$ peak and background, respectively. As the spectrum adapted ECM algorithm can efficiently analyze a large amount of spectral data, we can obtain the color map showing spatial distribution of Sn(II) and Sn(IV) using the parameter of Sn $$3{d_{5/2}}$$ peak. The proposed model supports us to obtain the insightful spatial distribution of peak component that has been difficult to obtain by conventional peak fitting

Urine Lactoferrin as a Potential Biomarker Reflecting the Degree of Malignancy in Urothelial Carcinoma of the Bladder

Urothelial carcinoma of the bladder (UCB) is potentially life-threatening; therefore, we aimed to discover a novel urine biomarker for diagnosis and prognostication of UCB. This is a retrospective case-control study. Exploration of a new biomarker using urine from 20 UCB patients in the present study revealed that urinary level of lactoferrin (LF), a multifunctional glycoprotein released from neutrophils, was higher in 11 of 15 with invasive/high-grade UCB than 5 with non-invasive one, and 2 healthy adults. We therefore focused on LF and assessed the value of urine LF normalized by urine creatinine concentration (LF/Cr) using an enzyme-linked immunosorbent assay. Diagnostic performance of urine LF/Cr was examined using urine from 92 patients with primary (newly diagnosed) untreated UCB and 166 controls without UCB, including 62 patients with pyuria, and 104 subjects without pyuria consisting of 84 patients and 20 healthy adults. However, the diagnostic accuracies were accompanied by the risk of bias. In 92 primary UCB patients, both pyuria and tumor-infiltrating neutrophils (TINs) were independent predictors for urine LF/Cr. In contrast, TINs or urine LF/Cr were independent predictors for invasive histology, whereas pyuria was not. In terms of prognostication, urine LF/Cr and nodal metastasis were independent predictors of disease-specific survival in 22 patients with muscle-invasive bladder cancer, characterized by a high mortality rate, in the Cox proportional hazards model. In conclusion, urine LF/Cr linked to TINs was a predictor of both invasive histology and prognosis in UCB. Urine LF/Cr is a potential biomarker reflecting the degree of malignancy in UCB

Altered balance of epidermis-related chemokines in epidermolysis bullosa

Background: Epidennolysis bullosa (EB) is a congenital, refractory skin disease and there are no fundamental treatments. Recently, allogenic cell therapies are beginning to be applied as potential treatments, that are based on the concept that the allogenic cells can migrate into the skin and reconstitute the skin components. Although the mechanisms of cell migration into skin are not fully understood, chemokines are regarded as key factors in recruiting bone marrow-derived cells. Objectives: Our study aims to elucidate the expression of chemokines in the EB patients. Methods: We determined the expression of wound-healing related chemokines in the sera, keratinocytes, and skin tissues of EB patients and compared them to those of healthy volunteers by enzyme-linked immunosorbent assays, quantitative reverse transcription PCR, and immunofluorescence staining. Results: The serum levels of CXCL12 and HMGB1 were found to be significantly elevated in the EB patients. Conversely, the serum levels of CCL21 were found to be lower in the EB patients than in healthy controls. In addition, the serum levels of CXCL12 tended to increase and the serum levels of CCL27 tended to decrease with an increase in the affected body surface areas. To detect the origin of the circulating chemokines, we performed immunofluorescence staining. CCL21, CCL27, HMGB1 and CXCL12 were stained more broadly in the EB patient tissues than those in the control tissues. Conclusions: These results suggest that fluctuations in chemokine levels may contribute in a coordinated way to the wound-healing process and lend clues toward efficient cell therapies for EB

Surface finishing method using plasma chemical vaporization machining for narrow channel walls of x-ray crystal monochromators

Channel-cut Si crystals are useful optical devices for providing monochromatic X-ray beams with extreme angular stability. Owing to difficulties in the high-precision surface finishing of narrow-channel inner walls of the crystals, typical channel-cut crystals have considerable residual subsurface crystal damage and/or roughness on their channel-wall reflection surfaces that decrease intensity and distort the wavefronts of the reflected X-rays. This paper proposes a highprecision surface finishing method for the narrowchannel inner walls based on plasma chemical vaporization machining, which is a local etching technique using atmospheric-pressure plasma. Cylinderand nozzle-shaped electrodes were designed for channel widths of more than 5 and 3 mm, respectively. We optimized process conditions for each electrode using commercial Si wafers, and obtained a removal depth of 10 μm with a surface flatness and roughness of less than 1 μm and 1 nmRMS, respectively, which should allow the damaged layers to be fully removed while maintaining the wavefront of coherent X-rays.Takashi Hirano, Yuki Morioka, Shotaro Matsumura, Yasuhisa Sano, Taito Osaka, Satoshi Matsuyama, Makina Yabashi, and Kazuto Yamauchi, “Surface Finishing Method Using Plasma Chemical Vaporization Machining for Narrow Channel Walls of X-Ray Crystal Monochromators,” Int. J. Automation Technol., Vol.13, No.2, pp. 246-253, 2019

High-throughput XPS spectrum modeling with autonomous background subtraction for 3<i>d</i>_5/2 peak mapping of SnS

We propose a fitting model that automatically conducts the background subtraction during high-throughput peak fitting. The fitting model consists of the pseudo-Voigt mixture model and the ramp-sum background model, and each model represents the peak and background component, respectively. The optimization of the fitting model is performed by the spectrum adapted ECM algorithm that enables us to perform the peak fitting and background subtraction simultaneously through the high-throughput calculation. Application of the proposed model to the synthetic spectral data showed appropriate decomposition of the peak and background component. We also applied the proposed model to 3721 spectral data collected from the SnS sheet by X-ray photoelectron spectroscopy. The spectral data from the SnS sheet were successfully decomposed to the component of Sn 3d3/2 peak, Sn 3d5/2 peak and background, respectively. As the spectrum adapted ECM algorithm can efficiently analyze a large amount of spectral data, we can obtain the color map showing spatial distribution of Sn(II) and Sn(IV) using the parameter of Sn 3d5/2 peak. The proposed model supports us to obtain the insightful spatial distribution of peak component that has been difficult to obtain by conventional peak fitting.</p