Absolute contrast estimation for soft X-ray photon fluctuation spectroscopy using a variational droplet model.

X-ray photon fluctuation spectroscopy using a two-pulse mode at the Linac Coherent Light Source has great potential for the study of quantum fluctuations in materials as it allows for exploration of low-energy physics. However, the complexity of the data analysis and interpretation still prevent recovering real-time results during an experiment, and can even complicate post-analysis processes. This is particularly true for high-spatial resolution applications using CCDs with small pixels, which can decrease the photon mapping accuracy resulting from the large electron cloud generation at the detector. Droplet algorithms endeavor to restore accurate photon maps, but the results can be altered by their hyper-parameters. We present numerical modeling tools through extensive simulations that mimic previous x-ray photon fluctuation spectroscopy experiments. By modification of a fast droplet algorithm, our results demonstrate how to optimize the precise parameters that lift the intrinsic counting degeneracy impeding accuracy in extracting the speckle contrast. These results allow for an absolute determination of the summed contrast from multi-pulse x-ray speckle diffraction, the modus operandi by which the correlation time for spontaneous fluctuations can be measured.

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

Data systems for the Linac coherent light source.

The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available.

Presentation of available CTL epitopes that induction of cell-mediated immune response against HIV-1 Koran clade B strain using computational technology.

OBJECTIVE: Theoretical predicting cytotoxic T lymphocyte (CTL) epitopes are an important tool in vaccine design and CTL therapy for enhancing our understanding of the cellular immune system. We would like to identify available CTL epitopes against HIV-1 Korean clade B. CTL activity was assessed in freshly isolated peripheral blood mononuclear cells from Korean HIV patients in order to assess whether these CTL epitopes induce a cell-mediated immune response (CMI). METHODS: NetCTLpan1.1 software, which is the most popular prediction computer software package, and full atom-based simulation (FABS), which is a 3D modelling system for binding activity between epitopes and human leucocyte antigen (HLA) molecules, were used to predict the peptide-spanning Env region binding to HLA-A*24:02, HLA-A*02:01 and HLA-B*15:01, which are frequently found in the Korean population. Granzyme B and interferon-γ ELISPOT assays were used to determine whether identified CTL epitopes induce CMI. RESULTS: Three HIV-1 Korean clade B-specific Env CTL epitopes were identified: Gp41-RYL and Gp41-RQG are localized within gp41, and Gp120-LLQ within gp120. In in vitro assays using granzyme B ELISPOT, Gp120-LLQ and Gp41-RQG induced epitope-specific CTL responses in HLA-restricted cells. In ex vivo assay using IFN-γ ELISPOT, cell-mediated immune responses to Gp41-RYL were present in 50% of HLA-matched patients, and responses to Gp120-LLQ and Gp41-RQG were found in 33% of HLA-matched patients. CONCLUSION: In this study, we found that a prediction pipeline for CTL epitopes might be based on the most popular computer prediction software and FABS methods. Our results suggest that these CTL epitopes may provide useful tools and information for the development of a therapeutic vaccine against HIV-1 Korean clade B.

Post-infectious bronchiolitis obliterans in children: CT features that predict responsiveness to pulse methylprednisolone.

OBJECTIVE: Intravenous pulse methylprednisolone therapy (IPMT) is an important treatment option for post-infectious obliterative bronchiolitis (OB), although it must be used carefully and only in selected patients because of its drawbacks. This study evaluated whether CT and clinical features of children with post-infectious OB can predict their responsiveness to IPMT. METHODS: We searched the medical records for patients (less than 18 years of age) who were diagnosed with post-infectious OB between January 2000 and December 2011. 17 children who received IPMT were included in this study. All underwent chest CT before and after IPMT. The radiological features seen on pre-treatment CT were recorded. The air-trapping area percentages on pre- and post-treatment CT images were determined. The nine patients who exhibited decreased air trapping on post-treatment CT scans relative to pre-treatment scans were classed as responders. The patient ages and time from initial pneumonia to IPMT were recorded. RESULTS: All responders and only four non-responders had thickened bronchial walls before treatment (p = 0.029). The two groups did not differ significantly in terms of bronchiolitis, bronchiectasis or the extent of air trapping, although the responders had a significantly shorter median interval between initial pneumonia and IPMT (4 vs 50 months; p = 0.005) and were significantly younger (median, 2.0 vs 7.5 years; p = 0.048). CONCLUSION: Immediate IPMT may improve the degree of air trapping in children with post-infectious OB if they show a thickened bronchial wall on CT. ADVANCES IN KNOWLEDGE: Children with post-infectious OB may respond favourably to IPMT when pre-treatment CT indicates bronchial-wall thickening.

Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse.

Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.

Spatial propagation of protein polymerization.

We consider the spatial dependence of filamentous protein self-assembly. Through studying the cases where the spreading of aggregated material is dominated either by diffusion or by growth, we derive analytical results for the spatial evolution of filamentous protein aggregation, which we validate against Monte Carlo simulations. Moreover, we compare the predictions of our theory with experimental measurements of two systems for which we identify the propagation as either growth or diffusion controlled. Our results connect the macroscopic observables that characterize the spatial propagation of protein self-assembly with the underlying microscopic processes and provide physical limits on spatial propagation and prionlike behavior associated with protein aggregation.

Claudin-1 induces epithelial-mesenchymal transition through activation of the c-Abl-ERK signaling pathway in human liver cells.

Claudins (CLDNs) are a family of integral membrane proteins central to the formation of tight junctions, structures that are involved in paracellular transport and cellular growth and differentiation, and are critical for the maintenance of cellular polarity. Recent studies have provided evidence that CLDNs are aberrantly expressed in diverse types of human cancers, including hepatocellular carcinomas (HCCs). However, little is known about how CLDN expression is involved in cancer progression. In this study, we show that CLDN1 has a causal role in the epithelial-mesenchymal transition (EMT) in human liver cells, and that the c-Abl-Ras-Raf-1-ERK1/2 signaling axis is critical for the induction of malignant progression by CLDN1. Overexpression of CLDN1 induced expression of the EMT-regulating transcription factors Slug and Zeb1, and thereby led to repression of E-cadherin, ß-catenin expression, enhanced expression of N-cadherin and Vimentin, a loss of cell adhesion, and increased cell motility in normal liver cells and HCC cells. In line with these findings, inhibition of either c-Abl or ERK clearly attenuated CLDN1-induced EMT, as evidenced by a reversal of N-cadherin and E-cadherin expression patterns, and restored normal motility. Collectively, these results indicate that CLDN1 is necessary for the induction of EMT in human liver cells, and that activation of the c-Abl-Ras-Raf-1-ERK1/2 signaling pathway is required for CLDN1-induced acquisition of the malignant phenotype. The present observations suggest that CLDN1 could be exploited as a biomarker for liver cancer metastasis and might provide a pivotal point for therapeutic intervention in HCC.

c-Jun N-terminal kinase has a pivotal role in the maintenance of self-renewal and tumorigenicity in glioma stem-like cells.

Uncovering the mechanisms that govern the maintenance of stem-like cancer cells is critical for developing therapeutic strategies for targeting these cells. Constitutive activation of c-Jun N-terminal kinase (JNK) has been reported in gliomas and correlates with histological grade. Here, we found that JNK signaling is crucial for the maintenance of 'stemness' in glioma cells. Sphere-cultured glioma cells showed more phosphorylation of JNK compared with serum-containing monolayer cultures. Importantly, blockade of JNK signaling with SP600125 or small interfering RNAs targeting JNK1 or JNK2 significantly reduced the CD133(+)/Nestin(+) population and suppressed sphere formation, colony formation in soft agar, and expression of stem cell markers in sphere-cultured glioma cells. Intriguingly, sphere-cultured glioma cells exhibited enhanced expression of Notch-2, but not Notch-1, -3 or -4, and JNK inhibition almost completely abrogated this increase. Blocking the phosphoinoside 3-kinase (PI3K)/Akt pathway with LY294002 or si-Akt also suppressed the self-renewal of sphere-cultured glioma cells. PI3K, but not Akt, had a role as an upstream kinase in JNK1/2 activation. In addition, treatment with si-JNK greatly increased etoposide- and ionizing radiation (IR)-induced cell death in glioma spheres. Consistent with glioma cell lines, glioma stem-like cells isolated from primary patient glioma cells also had a higher activity of JNK and Notch-2 expression. Importantly, inhibition of JNK2 led to a decrease of Notch-2 expression and suppressed the CD133(+)/Nestin(+) cell population in patient-derived primary glioma cells. Finally, downregulation of JNK2 almost completely suppressed intracranial tumor formation by glioma cells in nude mice. Taken together, these data demonstrate that JNK signaling is crucial for the maintenance of self-renewal and tumorigenicity of glioma stem-like cells and drug/IR resistance, and can be considered a promising target for eliminating stem-like cancer cells in gliomas.

Comparison of saline wastewater treatment performance of SBR with repeated starvation under aerobic and non-aerobic conditions.

This study investigated the effects of repeated starvation and feeding on the performance of a sequencing batch reactor (SBR) used for treating saline wastewater. The effects of aerobic and non-aerobic conditions on the sludge during starvation were evaluated to recover the performance of the SBR in terms of floc size and pollutant removal after resuming wastewater feeding. The floc size, fractal dimension, sludge volume index (SVI), specific oxygen uptake rate (SOUR), and pollutant removal efficiency were monitored. Experiment results revealed that the floc size and fractal dimensions decreased during starvation under both aerobic and non-aerobic conditions and increased after re-feeding wastewater. However, the difference in floc physical characteristics and performance depended on the starvation condition and was pronounced as starvation and re-feeding were repeated. The floc size and fractal dimensions decreased from 152.7 to 72.2 and 1.98 to 1.79 at the end of the fourth starvation period, resulting in deterioration of the sludge settleability and effluent quality. On the other hand, the floc size and fractal dimensions decreased from 158.7 to 135.7 and 1.95 to 1.81 at the end of the fourth starvation period but remained relatively constant after sludge adaptation. Some correlations were observed between the parameters monitored in this study. The results showed that maintaining the sludge under non-aerobic conditions was an effective strategy for reducing the effects of repeated starvation.

The effects of outdoor air supply rate on work performance during 8-h work period.

UNLABELLED: The purpose of this study is to evaluate the effect of ventilation rate on work performance and perceived air quality through short-term laboratory experiments. The experiment was designed to simulate office work, and a laboratory space was modified using new finish materials to become a typical office space. High levels of volatile organic compounds (VOCs) were found in the exposure chamber, most probably originating from the new finishing materials that were present. Twenty-four subjects were divided into six groups that were randomly exposed to the three ventilation rates, 5, 10, and 20 l/s per person. The subjects performed work tasks three separate times for each ventilation rate over an 8-h exposure period. The work performance of the subjects logarithmically improved with increased ventilation rates, which was similar to the previous research findings. Statistical significance was found for addition task, text-typing task, and memorization task. Increased work performance in this experiment was slightly lower than the results of previous short-term laboratory experiments, yet remained higher than results of previous long-term field experiments. However, it was difficult to directly compare the results of this experiment with those of previous experiments, because of the higher concentration of VOC present in the office rooms and the learning effect associated with the repeated tasks. PRACTICAL IMPLICATIONS: The results of this experiment show that ventilation had positive impacts on perceived air quality and work performance for the subjects tested. Work performance logarithmically increased by approximately 2.5-5% as ventilation rates were increased from 5 to 20 l/s per person. The positive effect of ventilation rate on work performance was shown to be limited at the low ventilation rate. The positive effects on work performance were at lower ventilation rates. The learning effect in repeated work performance tasks could increase the uncertainty of the work performance analysis in 8-h exposure period.

Hdm2 negatively regulates telomerase activity by functioning as an E3 ligase of hTERT.

In this study, we identified posttranslational regulation of human telomerase reverse-transcriptase (hTERT) by the E3 ligase Hdm2. The telomerase activity generated by exogenous hTERT in U2OS cells was reduced on adriamycin treatment. The overexpressed levels of hTERT were also decreased under the same conditions. These processes were reversed by treatment with a proteasome inhibitor or depletion of Hdm2. Furthermore, intrinsic telomerase activity was increased in HCT116 cells with ablation of Hdm2. Immunoprecipitation analyses showed that hTERT and Hdm2 bound to each other in multiple domains. Ubiquitination analyses showed that Hdm2 could polyubiquitinate hTERT principally at the N-terminus, which was further degraded in a proteasome-dependent manner. An hTERT mutant with all five lysine residues at the N-terminus of hTERT that mutated to arginine became resistant to Hdm2-mediated ubiquitination and degradation. In U2OS cells, depletion of Hdm2 or addition of the Hdm2-resistant hTERT mutant strengthened the cellular protective effects against apoptosis. Similar results were obtained with the Hdm2-stable H1299 cell line. These observations indicate that Hdm2 is an E3 ligase of hTERT.

Lupus enteritis: clinical characteristics, risk factor for relapse and association with anti-endothelial cell antibody.

The study was undertaken to evaluate clinical and laboratory characteristics of patients with lupus enteritis and to investigate its association with anti-endothelial cell antibodies (AECAs). Systemic lupus erythematosus (SLE) patients who were admitted to Kangnam St. Mary's Hospital with complaints of acute abdominal pain from January 1990 to July 2006 were reviewed retrospectively. The clinical features, laboratory data and prognosis of these patients were analyzed. Among the 706 SLE patients admitted during the study period, 87 were found to admit for acute abdominal pain. Among them, 41 patients were identified with lupus enteritis. The SLE disease activity index score at admission and the mean prednisolone dose administered during the last three months prior to admission were significantly higher in patients with lupus enteritis than those with other causes (P < 0.001, P = 0.036). Serum anti-endothelial cell antibody (AECA-IgG) titer was also significantly higher in patients with lupus enteritis than those with other manifestations or healthy controls (P = 0.040, P < 0.001). Four out of 13 recurrent patients had pre-existing anti-phospholipid syndrome (APS), whereas only one out of 28 non-recurrent patients had pre-existing APS (P = 0.028). Most of the patients with lupus enteritis showed good response to high-dose intravenous steroids and there was no death directly associated with lupus enteritis.

High isolation rate of adenovirus serotype 7 from South Korean military recruits with mild acute respiratory disease.

Adenovirus is a major cause of acute respiratory disease (ARD) in military recruits. When South Korean military recruits with ARD were surveyed, adenovirus was identified in 122 (61.0%) of the 200 recruits studied. Moreover, all cases of ARD involving adenovirus were caused by serotype 7.

Up-regulation of IL-23p19 expression in rheumatoid arthritis synovial fibroblasts by IL-17 through PI3-kinase-, NF-kappaB- and p38 MAPK-dependent signalling pathways.

OBJECTIVE: To investigate the expression of interleukin (IL)-23p19 in human rheumatoid arthritis (RA) synovial fibroblasts and its up-regulation by IL-17 stimulation, and to define the signal pathways involved in the regulation of IL-23p19 expression in RA synovial fibroblasts. METHODS: Synovial fluid (SF) and serum levels of IL-23p19 in RA were determined by enzyme-linked immunosorbent assays. The levels of IL-23p19 mRNA and protein were measured after the RA synovial fibroblasts were treated with recombinant human IL-17 and various inhibitors of intracellular signal pathway molecules using reverse transcription (RT) polymerase chain reaction (PCR), real-time PCR and western blotting. RESULTS: Levels of IL-23p19 in the sera and SF were much higher in RA patients than in osteoarthritis patients or healthy controls. The expression of IL-23p19 mRNA and protein was enhanced in RA synovial fibroblasts by IL-17 stimulation. Such effects of IL-17 were completely blocked by inhibitors of phosphatidylinositol (PI)-kinase/Akt, nuclear factor (NF)-kappaB and p38 mitogen-activated protein kinase (MAPK). In accordance with the expression of IL-23p19, the phosphorylation of IkappaB, Akt and p38 MAPK in synovial fibroblasts also increased after IL-17 stimulation. CONCLUSION: IL-23p19 is over-expressed in RA synovial fibroblasts and IL-17 appears to up-regulate the expression of IL-23p19 in RA synovial fibroblasts via PI3-kinase/Akt, NF-kappaB- and p38-MAPK-mediated pathways. These results suggest that a disruption of interaction between IL-17 and IL-23p19 may provide a new therapeutic approach in the treatment of RA.

Correlation of sonographic severity with biochemical markers of synovium and cartilage in knee osteoarthritis patients.

OBJECTIVE: Ultrasonography can be used to detect soft tissue abnormalities within the joints that cannot be assessed using conventional X-rays. This study investigated the relationship between soft tissue and/or bony abnormalities on ultrasonography and the biochemical markers of the synovium and cartilage in the knee of osteoarthritis (OA) patients. METHODS: The knees from 51 OA patients who fulfilled the ACR criteria were enrolled in this study. Knee ultrasonography was performed in the affected knee joints using a 12 MHz linear probe to assess the presence of effusion, synovial proliferation, capsular distention, the length of osteophytes and the cartilage thickness. At the same time, the serum hyaluronic acid (HA) and the cartilage oligomeric protein (COMP) levels were measured by ELISA, and RIA was used to determine the serum osteocalcin levels. RESULTS: The patients with a longer medial osteophyte showed higher serum HA and COMP levels than those with a shorter one. The serum HA levels were significantly higher in those patients with a larger amount of effusion and/or synovial proliferation, which indicated inflammatory changes, than in those without. In addition, the severity of the capsular distention also correlated well with the serum HA and COMP levels. However, the length of the lateral osteophytes and the thickness of the femoral cartilage showed no correlation with the serum HA or COMP levels. In addition, the serum osteocalcin levels did not show any association with the above ultrasonographic parameters. CONCLUSION: This study demonstrated that the serum HA and COMP levels were elevated in the more severe OA patients by knee ultrasonography than in the less severe patients. This suggests that the detailed pathological changes in the soft tissue and/or bone of the OA joints on ultrasonography are directly reflected by the biochemical markers measured in the peripheral blood.

Effects of addition sequence and rapid mixing conditions on use of dual coagulants.

The performance of dual coagulants in clay suspension was investigated in this study using aluminium chloride and the cationic polymer as coagulants. According to the study results, the performance of dual coagulants was affected by dosage of aluminium chloride. Beneficial effect by use of dual coagulants were only noted when aluminium chloride was underdosed. The addition sequence of coagulants was important for the performance of dual coagulants. Simultaneous addition resulted in the best performance, while addition of the polymer first resulted in the worst performance. Addition of aluminium chloride first resulted in the similar performance as single use of aluminium chloride. Although sulphate ion improved the floc characteristics, similar results were obtained. The effectiveness of rapid mixing depended on dosage of aluminium chloride. Extending rapid mixing (6 min) was beneficial when aluminium chloride was underdosed so that coagulation occurred at the combination region. However, such benefit was not observed at the optimum condition, which belonged to the sweep coagulation region. Different floc formation caused the difference. Extended rapid mixing would be beneficial when collision between clay particles and Al(III) was necessary. However, such benefit would disappear at the optimum condition because rapid mixing could break up the floc already formed.