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.

Cytomorphology of ovarian clear cell carcinomas in peritoneal effusions.

OBJECTIVE: To investigate and describe the cytomorphology of malignant effusions from ovarian clear cell carcinomas (OCCC). METHODS: Five cases of malignant peritoneal effusions from OCCC histologically confirmed were analysed and compared. RESULTS: Among the malignant peritoneal effusions exhibiting clear cell features, a characteristic feature of OCCC was the presence of large deposits of a hyaline matrix. This matrix may be typically arranged either in 'raspberry bodies' or 'globule-like' structures. Other rare neoplasms composed of clear cells must be considered in the differential diagnosis such as yolk sac tumour of the ovary, clear cell subtype of endometrial carcinoma and, less frequently, malignant peritoneal mesothelioma as well as metastatic renal cell carcinoma. CONCLUSIONS: Ovarian clear cell carcinomas have distinct morphological features that are helpful in making a cytological diagnosis of this entity. The role of cytological examination in ovarian neoplasms is of paramount importance, as stated by The International Federation of Gynecology and Obstetrics (FIGO) recommendations.

Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source.

Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, thus allowing simultaneous measurements at two separate instruments. In this report, the structure determination of a prototypical protein was performed using serial femtosecond crystallography simultaneously with a femtosecond time-resolved XANES studies of photoexcited spin transition dynamics in an iron spin-crossover system. The results of both experiments using the multiplexed beams are similar to those obtained separately, using a dedicated beam, with no significant differences in quality.

Functional regulation of the apurinic/apyrimidinic endonuclease 1 by nucleophosmin: impact on tumor biology.

Nucleophosmin 1 (NPM1) is a nucleolar protein involved in ribosome biogenesis, stress responses and maintaining genome stability. One-third of acute myeloid leukemias (AMLs) are associated with aberrant localization of NPM1 to the cytoplasm (NPM1c+). This mutation is critical during leukemogenesis and constitutes a good prognostic factor for chemotherapy. At present, there is no clear molecular basis for the role of NPM1 in DNA repair and the tumorigenic process. We found that the nuclear apurinic/apyrimidinic endonuclease 1 (APE1), a core enzyme in base excision DNA repair (BER) of DNA lesions, specifically interacts with NPM1 within nucleoli and the nucleoplasm. Cytoplasmic accumulation of APE1 is associated with cancers including, as we show, NPM1c+ AML. Here we show that NPM1 stimulates APE1 BER activity in cells. We provide evidence that expression of the NPM1c+ variant causes cytoplasmic accumulation of APE1 in: (i) a heterologous cell system (HeLa cells); (ii) the myeloid cell line OCI/AML3 stably expressing NPM1c+; and (iii) primary lymphoblasts of NPM1c+ AML patients. Consistent with impaired APE1 localization, OCI/AML3 cells and blasts of AML patients have impaired BER activity. Cytoplasmic APE1 in NPM1c+ myeloid cells is truncated due to proteolysis. Thus, the good prognostic response of NPM1c+ AML to chemotherapy may result from the cytoplasmic relocalization of APE1 and the consequent BER deficiency. NPM1 thus has an indirect but significant role in BER in vivo that may also be important for NPM1c+ tumorigenesis.

Measurement of muon antineutrino quasielastic scattering on a hydrocarbon target at Eν ~ 3.5 GeV.

We have isolated ν(µ) charged-current quasielastic (QE) interactions occurring in the segmented scintillator tracking region of the MINERvA detector running in the NuMI neutrino beam at Fermilab. We measure the flux-averaged differential cross section, dσ/dQ², and compare to several theoretical models of QE scattering. Good agreement is obtained with a model where the nucleon axial mass, M(A), is set to 0.99 GeV/c² but the nucleon vector form factors are modified to account for the observed enhancement, relative to the free nucleon case, of the cross section for the exchange of transversely polarized photons in electron-nucleus scattering. Our data at higher Q² favor this interpretation over an alternative in which the axial mass is increased.

Measurement of muon neutrino quasielastic scattering on a hydrocarbon target at Eν ~ 3.5 GeV.

We report a study of ν(µ) charged-current quasielastic events in the segmented scintillator inner tracker of the MINERvA experiment running in the NuMI neutrino beam at Fermilab. The events were selected by requiring a µ- and low calorimetric recoil energy separated from the interaction vertex. We measure the flux-averaged differential cross section, dσ/dQ², and study the low energy particle content of the final state. Deviations are found between the measured dσ/dQ² and the expectations of a model of independent nucleons in a relativistic Fermi gas. We also observe an excess of energy near the vertex consistent with multiple protons in the final state.

Profiling of drug-metabolizing enzymes/transporters in CD33+ acute myeloid leukemia patients treated with Gemtuzumab-Ozogamicin and Fludarabine, Cytarabine and Idarubicin.

Genetic heterogeneity in drug-metabolizing enzyme/transporter (DMET) genes affects specific drug-related cancer phenotypes. To investigate the relationships between genetic variation and response to treatment in acute myeloid leukemia (AML), we genotyped 1931 variants on DMET genes in 94 CD33-positive AML patients enrolled in a phase III multicenter clinical trial combining Gemtuzumab-Ozogamicin (GO) with Fludarabine-Cytarabine-Idarubicin (FLAI) regimen, with the DMET Plus platform. Two ADH1A variants showed statistically significant differences (odds ratio (OR)=5.68, P=0.0006; OR=5.35, P=0.0009) in allele frequencies between patients in complete/partial remission and patients without response, two substitutions on CYP2E1 (OR=0.13, P=0.001; OR=0.09, P=0.003) and one on SLCO1B1 (OR=4.68, P=0.002) were found to differently influence liver toxicity, and two nucleotide changes on SULTB1 and SLC22A12 genes correlated with response to GO (OR=0.24, P=0.0009; OR=2.75, P=0.0029). Genetic variants were thus found for the first time to be potentially associated with differential response and toxicity in AML patients treated with a combination of GO-FLAI regimen.

Neuroanatomical correlation between choroid plexus mass in thechoroidal fissure and the interventricular foramen area

Introduction: Our aim was to evaluate the correlation between choroid plexus mass (g) in the choroidalfissure and the ipsilateral interventricular foramen area, bilaterally. Material and methods: We analyzed sevencadaveric specimens with exposed brain, reaching the transcallosum access in all specimens, dissecting thecorpus callosum to reach the left and right choroidal fissure. After identifying the thalamostriate and septalveins, we localized the interventricular foramen scrapping all the choroid plexus in that region as well asits posterior extension allowing us to completely visualize the III ventricle. The area of the interventricularforamen was calculated with a pachimeter using the formula ðR2. The choroid plexus mass was measured withan appropriate scale. The choroid plexus mass and ipsilateral interventricular foramen correlation was evaluatedby the Pearson correlation. Results and conclusion: Neither difference between right and left choroid plexusmass was observed (Student t test – p = 0.374) nor with interventricular foramen area (p = 0.345) andwe decided to evaluate the 14 results together. There was correlation between choroid plexus mass and itsrespective IF (r = 0.6863; p < 0.01). A better knowledge of the choroidal fissure is very important to a moreprecise approach to the pathologic processes that affect the III ventricle. Different from the transforaminal,interforniceal, subchoroidal, and subforniceal, the choroidal fissure access is a natural approach. We speculatethat undetermined etiology hydrocephaly may have its origins in a deficit of ventricular drainage or in thechoroid plexus excess.

Kinetics of Th1/Th2 cytokines and lymphocyte subsets to predict chronic GVHD after allo-SCT: results of a prospective study.

The role of different cytokines and cells of immune system in the pathogenesis of chronic GVHD (cGVHD) is still controversial. Earlier studies, which were either retrospective or analysed one or a few factors, did not show unequivocal results. We prospectively evaluated cytokine levels and lymphocyte subsets in 30 patients who underwent Allo-SCT to investigate their possible correlation with cGVHD. Levels of IL-4, IL-6, IL-10, IFN-gamma, tumour necrosis factor-alpha (TNF-alpha) and its soluble receptors were assessed by ELISA in 30 patients at different times after SCT. Lymphocyte subsets were evaluated by flow cytometry in peripheral blood at the same times as cytokines. A multivariate analysis was performed using principal component analysis and multi-factor ANOVA (analysis of variance). Eighteen patients developed cGVHD at a median time of 6 months (range, 5-9) after SCT. In multivariate analysis, we observed a correlation between cGVHD and clusters of cytokines and lymphocyte subsets from the third to the sixth month after SCT. These clusters changed their composition over time, but they constantly included natural killer (NK) and CD152+ T cells as negative predictors of cGVHD. TNF-alpha prevailed among other cytokines before the onset of cGVHD. This prevalence could be related partly to the defect of immunoregulatory cells.

Inhibin A production after gonadotropin stimulus: a new method to detect ovarian tissue in ovotesticular disorder of sex development.

BACKGROUND/AIMS: While laboratory methods for the detection of testicular tissue are well standardized, currently there is no available test to demonstrate the presence of ovarian tissue. We evaluated the effectiveness of gonadal stimulation with luteinizing hormone (LH)/follicle-stimulating hormone (FSH) for the detection of ovarian tissue in patients with disorders of sex development (DSD). METHODS: Ten patients with congenital adrenal hyperplasia (CAH) as ovarian-positive controls, 10 with cryptorchidism (ovarian-negative controls), 13 patients with DSD of no defined etiology and 7 patients with ovotesticular DSD (true hermaphroditism, TH) were included in the study. They underwent a daily injection of both LH and FSH on 3 consecutive days. LH, FSH, estradiol, testosterone and inhibin A were measured before treatment, 24 h after the 1st dose and 24 h after the 3rd dose. RESULTS: Estradiol increased in all CAH and TH patients, with a median value of 155.1 and 92.6 pg/ml, respectively, after the 3rd injection. Inhibin A also increased in all CAH and TH patients, with a median value of 70.4 and 32.2 pg/ml, respectively, after the 3rd injection. There was no change in these hormones in the other groups. CONCLUSION: The LH/FSH stimulation test might be a useful method to detect the presence of ovarian tissue.

[Substitutive therapies in sepsis and acute renale failure]. / Trattamenti emergenti e/o alternativi nell'nsufficienza renale acuta associata a sepsi.

Substitutive treatment of sepsis associated acute renal failure is an emergent challenge in the intensive care unit due to the number of cases and to the high mortality rate. Standard hemofiltration is unable to improve survival, since a high mortality rate is sustained by the septic process. New therapeutic approaches currently available are based on the increased clearance of molecules ranging 10-30 kDa considered important in the physiopathology of sepsis and multiorgan failure. Clinical experiences in progress are: (1) adsorption resins able to bind bacterial products, cytokines, anaphylotoxins and several inflammation mediators; (2) the bioartificial kidney, that is the addition to hemofilter of human tubular cell culture grown in devices in order to mimic metabolic tubular function to a traditional hemofilter; (3) increased exchange volumes (high volume hemofiltration), up to 0-100 L/24 hr and; (4) increased membrane permeability associated with either discarded ultrafiltrate (high cut-off membranes) or plasma substitution plasmapheresis with regeneration by sorbents technology (C FA). Generally, by applying these new technologies to septic shock patients, the observed survival was higher than that predicted by the gravity score. While these results are encouraging, they are not conclusive and need further study.

Novel vasopressin type 2 (AVPR2) gene mutations in Brazilian nephrogenic diabetes insipidus patients.

Nephrogenic diabetes insipidus (NDI) is an inherited disorder characterized by renal resistance to the antidiuretic effect of arginine vasopressin (AVP), resulting in polyuria, polydipsia, and hypoosmolar urine. In the vast majority of cases, NDI is associated with germ-line mutations in the vasopressin receptor type 2 gene (AVPR2) and in about 8% of the cases with the water channel aquaporin-2 gene (AQP-2) mutations. To date, approximately 277 families with 185 germ-line mutations in the AVPR2 gene have been described worldwide. In the present study, the AVPR2 gene was genotyped in eight unrelated Brazilian kindred with NDI. In five of these NDI families, novel mutations were noted (S54R, I130L, S187R, 219delT, and R230P), whereas three seemingly unrelated probands were found to harbor previously described AVPR2 gene mutations (R106C, R137H, R337X). Additionally a novel polymorphism (V281V) was detected. In conclusion, although NDI is a rare disease, the findings of mutations scattered over the entire coding region of the AVPR2 gene are a valuable model to determine structure function relationship in G-protein-coupled receptor related diseases. Furthermore, our data indicate that in Brazil the spectrum of AVPR2 gene mutations is "family specific".

Choice of gender in 5alpha-reductase deficiency: a moving target.

Steroid 5alpha-reductase deficiency is a rare, male-limited autosomal recessive disorder caused by mutation in the SRD5A2 gene resulting in a deficiency of dihydrotestosterone (DHT) during fetal development. Here we report an affected 46,XY adolescent who was born with incompletely virilized genitalia and was raised in the female gender. At 12 years of age, the patient requested feminizing genital surgery. Surgery was withheld and psychiatric counseling was instituted. At 14 years of age, the patient's gender identity and role appeared to be in transition from a female to an increasingly male gender. This case demonstrates that in patients with disorders such as 5alpha-reductase deficiency, in which significant prenatal androgen exposures are combined with postnatal virilization, adult gender identity and gender role may be a dynamic process that is not complete until well after adolescence.

Incidence, outcome, and risk factors of late-onset noninfectious pulmonary complications after unrelated donor stem cell transplantation.

We evaluated the incidence, the risk factors, and the outcome of late-onset noninfectious pulmonary complications (LONIPCs) among 50 patients who underwent allogeneic stem cell transplantation from unrelated donors. Of the 39 patients surviving at least 3 months, 10 (26%) fulfilled the diagnostic criteria of LONIPCs and were further subclassified as having bronchiolitis obliterans (four patients), bronchiolitis obliterans with organizing pneumonia (four patients), and interstitial pneumonia (two patients). Two patients had a durable partial remission after treatment with prednisone and cyclosporine; the remaining eight patients did not respond to treatment and five of them died of respiratory failure. Advanced stage of disease at transplant and chronic extensive graft-versus-host disease (GVHD) were significantly associated with the development of LONIPCs. Pulmonary function test (PFT) results before transplantation were similar in all patients, but patients with LONIPCs had a significant decrease in PFT indexes at the third month after BMT compared with controls. Moreover, the rate of cyclosporine taper during the fourth and fifth months after BMT was significantly more rapid in patients with LONIPCs than in controls, suggesting that the risk of LONIPCs may be influenced by a faster reduction of GVHD prophylaxis.

Laboratorio / Laboratory

El objetivo principal de este primer módulo es de familiarizar a los profesionales de laboratorio con el problema de la infecció intrahospitalaria y proporcionarle los insturmentos necesarios para jugar el rol que le corresponde en el contexto hospitalario.

Prevención de infección / Prevention of infection

El segundo modulo se refiere a la identificación de los principales servicios del hospital en riesgo de producir infecciones intrahospitalarias instaurar la vigilancia epidemiológica correspondiente, impulsar para que le laboratorio se convierta en un actor y generador de conocimiento sobre la prevalencia de microorganismos patógenos, el laboratorio debe cumplirun rol importante en el apoyo al comite de control y prevención de infecciones con que cuente el hospital en el tema de identificación de actividades de riesgo, control de desinfectantes y seguimiento al personal de salud.