Using Dynamic Analysis for API Migration

When changing the API of a framework, we need to migrate its clients. This is best done automatically. In this paper, we focus on API migration where the mechanism for inversion of control changes. We propose to use dynamic analysis for such API migration since structural refactorings alone are often not sufficient. We consider JExample as a case-study. JExample extends JUnit with first-class dependencies and fixture injection. We investigate how dynamically collected information about test coverage and about instances under test can be used to detect dependency injection candidates.

Transmembrane tumor necrosis factor is a potent inducer of colitis even in the absence of its secreted form

Tumor necrosis factor (TNF) is cleaved proteolytically from a 26-kilodalton transmembrane precursor protein into secreted 17-kilodalton monomers. Transmembrane (tm) and secreted trimeric TNF are biologically active and may mediate distinct activities. We assessed the consequences of a complete inhibition of TNF processing on the course of colitis in recombination activating gene (RAG)2 -/- mice on transfer of CD4 CD45RB hi T cells.

The importance of growth hormone in the regulation of erythropoiesis, red cell mass, and plasma volume in adults with growth hormone deficiency

Total body water (TBW) is reduced in adult GH deficiency (GHD) largely due to a reduction of extracellular water. It is unknown whether total blood volume (TBV) contributes to the reduced extracellular water in GHD. GH and insulin-like growth factor I (IGF-I) have been demonstrated to stimulate erythropoiesis in vitro, in animal models, and in growing children. Whether GH has a regulatory effect on red cell mass (RCM) in adults is not known. We analyzed body composition by bioelectrical impedance and used standard radionuclide dilution methods to measure RCM and plasma volume (PV) along with measuring full blood count, ferritin, vitamin B12, red cell folate, IGF-I, IGF-binding protein-3, and erythropoietin in 13 adult patients with GHD as part of a 3-month, double blind, placebo-controlled trial of GH (0.036 U/kg.day). TBW and lean body mass significantly increased by 2.5 +/- 0.53 kg (mean +/- SEM; P < 0.004) and 3.4 +/- 0.73 kg (P < 0.004), respectively, and fat mass significantly decreased by 2.4 +/- 0.32 kg (P < 0.001) in the GH-treated group. The baseline RCM of all patients with GHD was lower than the predicted normal values (1635 +/- 108 vs. 1850 +/- 104 mL; P < 0.002). GH significantly increased RCM, PV, and TBV by 183 +/- 43 (P < 0.006), 350 +/- 117 (P < 0.03), and 515 +/- 109 (P < 0.004) mL, respectively. The red cell count increased by 0.36 +/- 0.116 x 10(12)/L (P < 0.03) with a decrease in ferritin levels by 39.1 +/- 4.84 micrograms/L (P < 0.001) after GH treatment. Serum IGF-I and IGF-binding protein-3 concentrations increased by 3.0 +/- 0.43 (P < 0.001) and 1.3 +/- 0.15 (P < 0.001) SD, respectively, but the erythropoietin concentration was unchanged after GH treatment. No significant changes in body composition or blood volume were recorded in the placebo group. Significant positive correlations could be established between changes in TBW and TBV, lean body mass and TBV (r = 0.78; P < 0.04 and r = 0.77; P < 0.04, respectively), and a significant negative correlation existed between changes in fat mass and changes in TBV in the GH-treated group (r = -0.95; P < 0.02). We conclude that 1) erythropoiesis is impaired in GHD; 2) GH stimulates erythropoiesis in adult GHD; and 3) GH increases PV and TBV, which may contribute to the increased exercise performance seen in these patients.

Altered response control and anterior cingulate function in attention-deficit/hyperactivity disorder boys

To investigate mechanisms and structures underlying prefrontal response control and inhibition in boys suffering from attention-deficit/hyperactivity disorder (ADHD).

Prospective risk stratification of sudden cardiac death in Marfan's syndrome.

BACKGROUND Marfan syndrome (MFS) is a variable, autosomal-dominant disorder of the connective tissue. In MFS serious ventricular arrhythmias and sudden cardiac death (SCD) can occur. The aim of this prospective study was to reveal underlying risk factors and to prospectively investigate the association between MFS and SCD in a long-term follow-up. METHODS 77 patients with MFS were included. At baseline serum N-terminal pro-brain natriuretic peptide (NT-proBNP), transthoracic echocardiogram, 12-lead resting ECG, signal-averaged ECG (SAECG) and a 24-h Holter ECG with time- and frequency domain analyses were performed. The primary composite endpoint was defined as SCD, ventricular tachycardia (VT), ventricular fibrillation (VF) or arrhythmogenic syncope. RESULTS The median follow-up (FU) time was 868 days. Among all risk stratification parameters, NT-proBNP remained the exclusive predictor (hazard ratio [HR]: 2.34, 95% confidence interval [CI]: 1.1 to 4.62, p=0.01) for the composite endpoint. With an optimal cut-off point at 214.3 pg/ml NT-proBNP predicted the composite primary endpoint accurately (AUC 0.936, p=0.00046, sensitivity 100%, specificity 79.0%). During FU, seven patients of Group 2 (NT-proBNP ≥ 214.3 pg/ml) reached the composite endpoint and 2 of these patients died due to SCD. In five patients, sustained VT was documented. All patients with a NT-proBNP<214.3 pg/ml (Group 1) experienced no events. Group 2 patients had a significantly higher risk of experiencing the composite endpoint (logrank-test, p<0.001). CONCLUSIONS In contrast to non-invasive electrocardiographic parameter, NT-proBNP independently predicts adverse arrhythmogenic events in patients with MFS.

Placental ABCA1 and ABCG1 expression in gestational disease: pre-eclampsia affects ABCA1 levels in syncytiotrophoblasts

INTRODUCTION Transplacental feto-maternal lipid exchange through the ATP-binding cassette transporters ABCA1 and ABCG1 is important for normal fetal development. However, only scarce and conflicting data exist on the involvement of these transporters in gestational disease. METHODS Placenta samples (n = 72) derived from common gestational diseases, including pre-eclampsia (PE), HELLP, intrauterine growth restriction (IUGR), intrahepatic cholestasis of pregnancy and gestational diabetes, were assessed for their ABCA1 and ABCG1 expression levels and compared to age-matched control placentas with qRT-PCR and immunohistochemistry. ABCA1 expression was additionally investigated with immunoblot in placental membrane vesicles. Furthermore, placental cholesterol and phospholipid contents were assessed. RESULTS ABCA1 mRNA levels differed significantly between preterm and term control placentas (p = 0.0013). They were down-regulated in isolated PE and PE with IUGR (p = 0.0006 and p = 0.0012, respectively), but unchanged in isolated IUGR, isolated HELLP and other gestational diseases compared to gestational age-matched controls. Correspondingly, in PE, ABCA1 protein expression was significantly reduced in the apical membrane of the villous syncytiotrophoblast (p = 0.011) and in villous fetal endothelial cells (p = 0.036). Furthermore, in PE there was a significant increase in the placental content of total and individual classes of phospholipids which were partially correlated with diminished ABCA1 expression. Conversely, ABCG1 mRNA and protein levels were stable in the investigated conditions. CONCLUSIONS In gestational disease, there is a specific down-regulation of placental ABCA1 expression at sites of feto-maternal lipid exchange in PE. At a functional level, the increase in placental lipid concentrations provides indirect evidence of an impaired transport capacity of ABCA1 in this disease.

High resolution quantitative computed tomography-based assessment of trabecular microstructure and strength estimates by finite-element analysis of the spine, but not DXA, reflects vertebral fracture status in men with glucocorticoid-induced osteoporosis

High-resolution quantitative computed tomography (HRQCT)-based analysis of spinal bone density and microstructure, finite element analysis (FEA), and DXA were used to investigate the vertebral bone status of men with glucocorticoid-induced osteoporosis (GIO). DXA of L1–L3 and total hip, QCT of L1–L3, and HRQCT of T12 were available for 73 men (54.6±14.0years) with GIO. Prevalent vertebral fracture status was evaluated on radiographs using a semi-quantitative (SQ) score (normal=0 to severe fracture=3), and the spinal deformity index (SDI) score (sum of SQ scores of T4 to L4 vertebrae). Thirty-one (42.4%) subjects had prevalent vertebral fractures. Cortical BMD (Ct.BMD) and thickness (Ct.Th), trabecular BMD (Tb.BMD), apparent trabecular bone volume fraction (app.BV/TV), and apparent trabecular separation (app.Tb.Sp) were analyzed by HRQCT. Stiffness and strength of T12 were computed by HRQCT-based nonlinear FEA for axial compression, anterior bending and axial torsion. In logistic regressions adjusted for age, glucocorticoid dose and osteoporosis treatment, Tb.BMD was most closely associated with vertebral fracture status (standardized odds ratio [sOR]: Tb.BMD T12: 4.05 [95% CI: 1.8–9.0], Tb.BMD L1–L3: 3.95 [1.8–8.9]). Strength divided by cross-sectional area for axial compression showed the most significant association with spine fracture status among FEA variables (2.56 [1.29–5.07]). SDI was best predicted by a microstructural model using Ct.Th and app.Tb.Sp (r2=0.57, p<0.001). Spinal or hip DXA measurements did not show significant associations with fracture status or severity. In this cross-sectional study of males with GIO, QCT, HRQCT-based measurements and FEA variables were superior to DXA in discriminating between patients of differing prevalent vertebral fracture status. A microstructural model combining aspects of cortical and trabecular bone reflected fracture severity most accurately.

High-temperature induced dehydration, phase transition and exsolution in amicite: A single-crystal X-ray study

Temperature dependent single-crystal X-ray data were collected on amicite K4Na4(Al8Si8O32)·11H2O from Kola Peninsula (Russia) in steps of 25 °C from room temperature to 175 °C and of 50 °C up to 425 °C. At room temperature amicite has space group I2 with a = 10.2112(1), b = 10.4154(1), c = 9.8802(1) Å, β = 88.458(1)°, V = 1050.416(18) Å3. Its crystal structure is based on a Si–Al ordered tetrahedral framework of the GIS type with two systems of eight-membered channels running along the a and c axes. Extraframework K and Na cations are ordered at two fully occupied sites. Above 75 °C amicite was found to partly dehydrate into two separate but coherently intergrown phases, both of space group I2/a, one K-rich ∼K8(Al8Si8O32) ·4H2O (at 75 °C: a = 10.038(2), b = 9.6805(19), c = 9.843(2) Å, β = 89.93(3)°, V = 956.5(3) Å3) and the other Na-rich ∼Na8(Al8Si8O32)·2H2O (at 75 °C: a = 9.759(2), b = 8.9078(18), c = 9.5270(19) Å, β = 89.98(3)°, V = 828.2(3) Å3). Upon further heating above 75 °C the Na- and K-phases lost remaining H2O with only minor influence on the framework structure and became anhydrous at 175 °C and 375 °C, respectively. The two anhydrous phases persisted up to 425 °C. Backscattered electron images of a heated crystal displayed lamellar intergrowth of the K- and Na-rich phases. Exposed to ambient humid conditions K- and Na-rich phases rehydrated and conjoined to the original one phase I2 structure.

Influence of manure scrapers on dairy cows in cubicle housing systems

Manure scrapers are widely used in dairy cow loose-housing systems. In order to evaluate the effects of the scrapers on the cows, we assessed their impact on the animals' cardiac activity, feeding behaviour, and the behavioural reactions of cows confronted with different types of scrapers. In part I of the study, we measured cardiac activity (mean R–R interval and RMSSD, a parameter of heart-rate variability) whilst observing the behaviour of 29 focal cows on three farms during situations with and without active manure scrapers. Lower RMSSD values were observed during scraping events while cows were either lying, standing or walking in the alleyway, standing completely in the lying cubicle, or standing half in the lying cubicle (P=0.03), but only tended to differ while directly confronted with the scraper (P=0.06). This indicates that dairy cows experienced at least some mild stress during manure-scraping events. In part II, the feeding behaviour of 12 cows on each of two farms was recorded by means of a jaw-movement sensor and compared between situations with the manure-scraping event following forage provision either within or outside the main daily feeding period (i.e. within 1 or after 2 h from forage provisioning, respectively). The duration of night-time feeding (P=0.049) and the number of feeding bouts (P=0.036) were higher when a manure-scraping event took place within the main daily feeding period, indicating that the cows' feeding behaviour had been disturbed. In part III, we observed the cows' behaviour on 15 farms during eight manure scraping events per farm, where each of five farms had one of three different scraper types. We assessed the cows' immediate reactions when confronted with the scraper. In addition, we recorded the number of animals present in the alleyways before and after the manure-scraping events. The more cows that were present in the alleyways before the scraping event, the lower the proportion of cows showing direct behavioural reactions both with (P=0.017) and without (P=0.028) scraper contact, and the higher the number of cows that left the alleyways (P<0.001). Scraper type did not influence the proportion of cows showing behavioural reactions. In conclusion, our results show that dairy cows perceive the manure-scraping event negatively in some situations, that feeding behaviour may be disturbed when scrapers are active during the main feeding period, and that cows avoid the scraper during crowded situations.

High myeloperoxidase positive cell infiltration in colorectal cancer is an independent favorable prognostic factor

BACKGROUND Colorectal cancer (CRC) infiltration by adaptive immune system cells correlates with favorable prognosis. The role of the innate immune system is still debated. Here we addressed the prognostic impact of CRC infiltration by neutrophil granulocytes (NG). METHODS A TMA including healthy mucosa and clinically annotated CRC specimens (n = 1491) was stained with MPO and CD15 specific antibodies. MPO+ and CD15+ positive immune cells were counted by three independent observers. Phenotypic profiles of CRC infiltrating MPO+ and CD15+ cells were validated by flow cytometry on cell suspensions derived from enzymatically digested surgical specimens. Survival analysis was performed by splitting randomized data in training and validation subsets. RESULTS MPO+ and CD15+ cell infiltration were significantly correlated (p<0.0001; r = 0.76). However, only high density of MPO+ cell infiltration was associated with significantly improved survival in training (P = 0.038) and validation (P = 0.002) sets. In multivariate analysis including T and N stage, vascular invasion, tumor border configuration and microsatellite instability status, MPO+ cell infiltration proved an independent prognostic marker overall (P = 0.004; HR = 0.65; CI:±0.15) and in both training (P = 0.048) and validation (P = 0.036) sets. Flow-cytometry analysis of CRC cell suspensions derived from clinical specimens showed that while MPO+ cells were largely CD15+/CD66b+, sizeable percentages of CD15+ and CD66b+ cells were MPO-. CONCLUSIONS High density MPO+ cell infiltration is a novel independent favorable prognostic factor in CRC.