Generation and Characterization of Intense Ultralow-Emittance Electron Beams for Compact X-Ray Free-Electron Lasers.

The transverse emittance of the electron beam is a fundamental parameter in linac-based x-ray free-electron lasers (FELs). We present results of emittance measurements carried out at SwissFEL, a compact x-ray FEL facility at the Paul Scherrer Institute in Switzerland, including a description of the novel high-resolution measurement techniques and the optimization procedure. We obtained slice emittance values at the undulator entrance down to 200 nm for an electron beam with a charge of 200 pC and an rms duration of 30-40 fs. Furthermore, we achieved slice emittances as low as 100 nm for 10 pC beams with few fs duration. These values set new standards for electron linear accelerators. The quality, verification, and control of our electron beams allowed us to generate high-power FEL radiation for a wavelength as short as 0.1 nm using an electron beam with an energy of only 6 GeV. The emittance values demonstrated at SwissFEL would allow producing hard x-ray FEL pulses with even lower-energy beams, thus paving the way for even more compact and cost-effective FEL facilities.

Transverse gradient in Apple-type undulators.

Apple-type undulators are globally recognized as the most flexible devices for the production of variable polarized light in the soft X-ray regime, both at synchrotron and free-electron laser facilities. Recently, the implementation of transverse gradient undulators has been proposed to enhance the performance of new generation light sources. In this paper it is demonstrated that Apple undulators do not only generate linear and elliptical polarized light but also variable transverse gradient under certain conditions. A general theoretical framework is introduced to evaluate the K-value and its transverse gradient for an Apple undulator, and formulas for all regular operational modes and different Apple types (including the most recent Delta type and Apple X) are calculated and critically discussed.

Simulation of FEL pulse length calculation with THz streaking method.

Having accurate and comprehensive photon diagnostics for the X-ray pulses delivered by free-electron laser (FEL) facilities is of utmost importance. Along with various parameters of the photon beam (such as photon energy, beam intensity, etc.), the pulse length measurements are particularly useful both for the machine operators to measure the beam parameters and monitor the stability of the machine performance, and for the users carrying out pump-probe experiments at such facilities to better understand their measurement results. One of the most promising pulse length measurement techniques used for photon diagnostics is the THz streak camera which is capable of simultaneously measuring the lengths of the photon pulses and their arrival times with respect to the pump laser. This work presents simulations of a THz streak camera performance. The simulation procedure utilizes FEL pulses with two different photon energies in hard and soft X-ray regions, respectively. It recreates the energy spectra of the photoelectrons produced by the photon pulses and streaks them by a single-cycle THz pulse. Following the pulse-retrieval procedure of the THz streak camera, the lengths were calculated from the streaked spectra. To validate the pulse length calculation procedure, the precision and the accuracy of the method were estimated for streaking configuration corresponding to previously performed experiments. The obtained results show that for the discussed setup the method is capable of measuring FEL pulses with about a femtosecond accuracy and precision.

GHEP-ISFG collaborative exercise on mixture profiles of autosomal STRs (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03): results and evaluation.

One of the main objectives of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the area of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, three exercises have been organized (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03), with 32, 24 and 17 participant laboratories respectively. The exercise aims to give a general vision by addressing, through the proposal of mock cases, aspects related to the edition of mixture profiles and the statistical treatment. The main conclusions obtained from these exercises may be summarized as follows. Firstly, the data show an increased tendency of the laboratories toward validation of DNA mixture profiles analysis following international recommendations (ISO/IEC 17025:2005). Secondly, the majority of discrepancies are mainly encountered in stutters positions (53.4%, 96.0% and 74.9%, respectively for the three editions). On the other hand, the results submitted reveal the importance of performing duplicate analysis by using different kits in order to reduce errors as much as possible. Regarding the statistical aspect (GHEP-MIX02 and 03), all participants employed the likelihood ratio (LR) parameter to evaluate the statistical compatibility and the formulas employed were quite similar. When the hypotheses to evaluate the LR value were locked by the coordinators (GHEP-MIX02) the results revealed a minor number of discrepancies that were mainly due to clerical reasons. However, the GHEP-MIX03 exercise allowed the participants to freely come up with their own hypotheses to calculate the LR value. In this situation the laboratories reported several options to explain the mock cases proposed and therefore significant differences between the final LR values were obtained. Complete information concerning the background of the criminal case is a critical aspect in order to select the adequate hypotheses to calculate the LR value. Although this should be a task for the judicial court to decide, it is important for the expert to account for the different possibilities and scenarios, and also offer this expertise to the judge. In addition, continuing education in the analysis and interpretation of mixture DNA profiles may also be a priority for the vast majority of forensic laboratories.

Medical care for individual patients: concepts beyond evidence-based medicine.

Todays evidence-based medicine has brought the practicing physician a vast amount of statistical evidence from which various stakeholders in the healthcare system obtain their arguments for and against the use of new therapies. Physicians assume an obligation to prescribe these new treatment options for their patients, firstly because of their eagerness to provide the best medicine, and secondly because of their fear of litigations. On looking at the published data, however, we have observed that the arguments for saving lives with a new treatment are not always supported by the underlying data. Sometimes the data show that the effect of treatment, in real terms, is only a relatively small gain in life-time prolongation. It is concluded that EBM-based concepts such as NNT (number needed to treat), absolute risk and relative risk fall short in ensuring real benefit for the patient. We have, therefore, put forward a mathematic model which takes into account the benefit of a treatment for the individual patient in terms of expected gain in lifetime duration. This model is readily applicable to published results on the clinical effects of a medical therapy and gives the practicing physician a useful tool for deciding whether to administer a medical therapy or not. By looking at the duration of treatment and the individual gain in lifetime expected, we have derived an effectiveness coefficient which can be used to categorize medical treatments into highly effective (close to 100%) and not effective (< 5%), and at the same time arrive at a cost-benefit analysis of the treatment in question. These simple concepts will help physicians and individual patients to make informed decisions based only on those medical therapies which are proven and appropriate. The model we have developed provides a new perspective in therapy for the individual patient using medicines that constitute a rational therapy i.e. a therapy that makes "sense" (sense-orientated medicine = SOM).

Detection of chromosomal imbalances in papillary bladder tumors by comparative genomic hybridization.

OBJECTIVES: To identify those genetic alterations that are associated with bladder cancer invasion and progression. METHODS: A total of 30 specimens of transitional cell carcinoma of the bladder were analyzed by comparative genomic hybridization. The results were compared and summarized with previously reported studies. RESULTS: The most frequent chromosome changes detected in our series of tumors were losses in 9q, 9p, 8p, and 11p and gains in 8q, 1q, 20q, and 11q. Three regions of deletion on chromosome 9 were delineated, at 9p21-p22, 9q13-q22, and 9q31-q34. Gains in 1q and losses on 11p were significantly more frequent in pT1G2 tumors than in superficial (pTa) ones. In our study, the most striking differences were seen between pT1G3 and pT1G2 tumors. Gains on 10p and 6p and losses at 5q, 6q, and 18q were significantly more frequent in the former. CONCLUSIONS: A summary of our results and those available from published reports suggest that several groups of chromosomal imbalances may be associated with specific steps along bladder cancer progression. These genetic changes assume two different patterns: those that are shared, but are more intensive in one stage than in the other, and those such as a gain on 3p that are unique to invasive tumors.

The human astrocytoma cell line U373MG produces monocyte chemotactic protein (MCP)-1 upon stimulation with beta-amyloid protein.

Astrocytes associated with beta-amyloid (Abeta) accumulate in senile plaques of Alzheimer's disease (AD). To investigate the biological effects of Abeta/astrocyte interaction, we examined chemokine production by the human astrocytoma cell line U373MG stimulated with Abeta peptides. Northern blot analysis and specific immunoassays demonstrate that Abeta [1-42] and Abeta [25-35] induce mRNA expression and release of monocyte chemotactic protein (MCP)-1 but not of gamma-interferon inducible protein (IP)-10 by U373MG cells. The observation that Abeta induces astrocyte production of the potent microglia chemoattractant MCP-1 contributes to understanding mechanism of damage exerted by Abeta in AD senile plaques.

Synergistic effect of beta-amyloid protein and interferon gamma on nitric oxide production by C2C12 muscle cells.

Nitric oxide (NO) is an important mediator of diverse physiological and pathological responses. NO-induced oxidative stress has been proposed in the pathogenesis of muscle tissue damage in inclusion-body myositis (IBM), which is characterized by deposition of beta-amyloid protein (Abeta) in vacuolated muscle fibres. To determine whether Abeta can induce NO production in skeletal muscle, we stimulated C2C12 mouse skeletal muscle cells in vitro with Abeta[1-42] or Abeta[25-35] peptides in the presence or absence of interferon gamma (IFN-gamma). Neither Abeta peptides nor IFN-gamma were able to stimulate nitrite (NO(2)(-)) production by C2C12 cells when given alone. However, combination of IFN-gamma with either Abeta[1-42] or Abeta[25-35] resulted in significant NO(2)(-) release into cell-free supernatants. Northern blot analysis of RNA obtained from Abeta/IFN-gamma-stimulated C2C12 cells revealed increased mRNA accumulation of inducible nitric oxide synthase (iNOS). Moreover, approximately 4% of muscle cells incubated with Abeta peptides and IFN-gamma showed ultrastructural features of DNA fragmentation. These findings, taken together, indicate that the association of Abeta with IFN-gamma stimulates NO(2)(-) production via induction of iNOS gene expression in skeletal muscle cells, with occasional evidence for nuclear changes suggesting apoptotic morphology. These data further support a role for Abeta deposition in the pathogenesis of postulated oxidative damage in IBM.

Alpha-MSH peptides inhibit production of nitric oxide and tumor necrosis factor-alpha by microglial cells activated with beta-amyloid and interferon gamma.

Alpha-melanocyte stimulating hormone (alpha-MSH) is an ancient tridecapeptide with potent inhibitory activity in all major forms of inflammation. The anti-inflammatory message sequence of alpha-MSH resides in the COOH-terminal tripeptide alpha-MSH[11-13]. We tested the influence of alpha-MSH[1-13] and of alpha-MSH[11-13] in a cultured murine microglia cell line known to produce nitric oxide (NO(-)(2)) and tumor necrosis factor (TNFalpha) when stimulated with beta-amyloid protein (Abeta). Melanocortin peptides significantly inhibited release of both NO(-)(2) and TNFalpha into cell-free supernatants from microglia stimulated with Abeta[1-42] or Abeta[25-35] peptides and interferon gamma (IFNgamma). Northern blot analysis demonstrated that alpha-MSH[1-13] and alpha-MSH[11-13] inhibited accumulation of inducible nitric oxide synthase (iNOS) and TNFalpha mRNA was triggered by Abeta stimulation. Abeta/microglial interaction is believed to promote the progression of inflammatory and neurodegenerative changes in senile plaques in Alzheimer's disease. Our data indicate that alpha-MSH peptides might be used to modulate the local response of the brain to Abeta deposition in this neurodegenerative disease.

Proinflammatory profile of cytokine production by human monocytes and murine microglia stimulated with beta-amyloid[25-35].

Growing evidence indicates that amyloid (A beta) deposition and phagocyte activation participate in inflammatory reactions in the brain during the course of Alzheimer's disease. To further investigate the effects of A beta-phagocyte interaction, we examined the production of proinflammatory (IL-1beta, IL-6), chemotactic (MIP-1alpha, IP-10) and inhibitory (IL-1Ra, IL-10 and TGFbeta1) cytokines by cultured human monocytes and mouse microglial cells upon stimulation with A beta[25-35]. Northern blot analysis and specific immunoassays demonstrated that A beta[25-35] triggers mRNA expression and release of IL-1beta, IL-1Ra and MIP-1alpha but not of IL-6, IL-10, TGFbeta1 and IP-10 from human monocytes. Similar results were obtained by examining the production of IL-1beta, IL-6 and IL-10 from mouse microglial cells in the same experimental conditions. Taken together, these data indicate that A beta-phagocyte interaction can drive a different response towards cytokine production by monocytes and microglia, with a particular proinflammatory trend, and further support a role for A beta deposition as a triggering factor of inflammatory events in Alzheimer's disease.

Effects of amino acid substitutions in the hydrophobic core of alpha-lactalbumin on the stability of the molten globule state.

Five mutant alpha-lactalbumins, with one or two amino acid substitution(s) in the B helix, were engineered to examine the relation between the stability of the molten globule state and the hydrophobicity of these amino acids. The mutation sites (Thr29, Ala30 and Thr33) have been chosen on the basis of comparison of the amino acid sequences of goat, bovine and gunea pig alpha-lactalbumin, in which the guinea pig protein shows a remarkably more stable molten globule than the other proteins. The recombinant proteins were expressed Escherichia coli and then purified and refolded efficiently to produce the active proteins. The stability of the molten globule state of these engineered proteins has been investigated by urea-induced unfolding transition under an acidic condition (pH 2.0), where the molten globule state is stable in the absence of urea. The results show that the molten globule state is stabilized by the amino acid substitutions which raise the hydrophobicity of the residues, suggesting that the hydrophobic core in a globular protein plays an important role in the stability of the molten globule state. The change in stabilization free energy of the molten globule state caused by each amino acid substitution has been evaluated, and molecular mechanisms of stabilization of the molten globule state are discussed.

Induction of a Putative Ca-ATPase mRNA in NaCl-Adapted Cells.

A cDNA clone was isolated that encodes the partial sequence of a putative endoplasmic reticulum Ca(2+)-ATPase of tobacco. The 1.497-kb insert had an open reading frame of 1.149 kb. The deduced peptide had the greatest homology to the endoplasmic reticulum Ca(2+)-ATPases of Drosophila and Artemia, followed by the mammalian and avian enzymes (SERCA2 and 3). The cDNA insert hybridized to a single mRNA of 4.4 kb from tobacco cultured cells or plant tissues. The level of this transcript was induced about 2-fold by NaCl shock in 428 mm NaCl-deadapted tobacco cells that were maintained in medium without salt, but not in unadapted cells. The level of this transcript was 3- to 4-fold higher in 428 mm NaCl-adapted cells growing in salt than in unadapted cells growing without salt.

NaCl Regulation of Tonoplast ATPase 70-Kilodalton Subunit mRNA in Tobacco Cells.

A cDNA clone encoding the 70-kilodalton subunit of the tobacco (Nicotiana tabacum var Wisconsin 38) tonoplast ATPase has been isolated. The 1.656 kilobase insert contains only open reading frame that represents more than 80% of the carrot cDNA coding region. The deduced amino acid sequence has greater than 95% sequence identity with the homologous carrot sequence. A transcript of approximately 2.7 kilobase was detected on Northern blots of tobacco poly(A)(+) selected or total RNA using labeled probe produced from this clone. The gene was expressed throughout the growth cycle in unadapted and 428 millimolar NaCl adapted cells. Transcription of the 70-kilodalton subunit gene or mRNA stability was induced by short-term NaCl treatment in NaCl adapted cells or by abscisic acid treatment in both adapted and unadapted cells. Southern analysis indicated the presence of up to four genes encoding the 70-kilodalton subunit.