Handling software upgradeability problems with MILP solvers

Upgradeability problems are a critical issue in modern operating systems. The problem consists in finding the "best" solution according to some criteria, to install, remove or upgrade packages in a given installation. This is a difficult problem: the complexity of the upgradeability problem is NP complete and modern OS contain a huge number of packages (often more than 20 000 packages in a Linux distribution). Moreover, several optimisation criteria have to be considered, e.g., stability, memory efficiency, network efficiency. In this paper we investigate the capabilities of MILP solvers to handle this problem. We show that MILP solvers are very efficient when the resolution is based on a linear combination of the criteria. Experiments done on real benchmarks show that the best MILP solvers outperform CP solvers and that they are significantly better than Pseudo Boolean solvers.Comment: In Proceedings LoCoCo 2010, arXiv:1007.083

Non-contact infrared temperature measurements in dry permafrost boreholes

While planning the COAST Expedition to the Siberian Laptev Sea in 2005, the question of how to make a short equilibrium temperature measurement in a dry borehole arose. As a result, an infrared borehole tool was developed and used in three dry boreholes (up to 60.2 m deep) in the coastal transition zone from terrestrial to sub-sea permafrost near Mamontovy Klyk in the western Laptev Sea. A depth versus temperature profile was acquired with equilibration times of 50 × 10−3 s at each depth interval. Comparison with a common resistor string revealed an offset due to limitations of accuracy of the infrared technique and the influence of the probe's massive steel housing. Therefore it was necessary to calibrate the infrared sensor with a high precision temperature logger in each borehole. The results of the temperature measurements show a highly dynamic transition zone with temperature gradients up to −0.092°C/m and heat flow of −218 mW/m. A period of submergence of only 600 years the drilled sub-sea permafrost is approaching the overlying seawater temperature at −1.61°C with a temperature gradient of 0.021°C/m and heat flow of 49 mW/m. Further offshore, 11 km from the coastline, a temperature gradient of 0.006°C/m and heat flow of 14 mW/m occur. Thus the sub-sea permafrost in the Mamontovy Klyk region has reached a critical temperature for the presence of interstitial ice. The aim of this article is to give a brief feasibility study of infrared downhole temperature measurements and to present experiences and results of its successful application

Influence of factor 5 rs6025 and factor 2 rs1799963 mutation on inhibitor development in patients with hemophilia A - an Israeli-German multicenter database study

AbstractObjectiveThe present cohort study was performed to investigate the impact of the factor 5 rs6025 [F5] and the factor 2 rs1799963 [F2] mutations on high-titer inhibitor development [HRI] in patients with severe/moderate-severe hemophilia A [HA].Patients and Methods216 patients with F8<2% born between 1980 and 2011 were followed after initial HA diagnosis over the first 200 exposure days. The first HA patient per family who presented for diagnosis was included in the present study.Results32 of 216 children [14.8%] tested for F5/F2 carried either the F5 or the F2 variant. HRI occurred in 14 out of 32F5/F2-carriers compared with 40 of 184 without F5/F2. Multivariate analysis adjusted for F8 genotype, treatment intensity, first-line use of plasma derived FVIII versus recombinant FVIII concentrates revealed that the presence of F5/F2 independently increases the risk of HRI development to odds [OR] of 3.4. Large deletions in the F8 gene [OR: 5.10], patients from Israel [OR: 4.0], the increase of FVIII per one IU/kgbw [OR: 1.05] and birth year [OR: 1.12] were significantly associated with the risk to develop HRI.ConclusionData presented here suggest that HRI development is of multifactorial origin and that F5 and F2 mutations may contribute to this risk

Clinical correlates of anti-SARS-CoV-2 antibody profiles in Spanish COVID-19 patients from a high incidence region

Laboratory testing for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consists of two pillars: the detection of viral RNA via rt-PCR as the diagnostic gold standard in acute cases, and the detection of antibodies against SARS-CoV-2. However, concerning the latter, questions remain about their diagnostic and prognostic value and it is not clear whether all patients develop detectable antibodies. We examined sera from 347 Spanish COVID-19 patients, collected during the peak of the epidemic outbreak in Spain, for the presence of IgA and IgG antibodies against SARS-CoV-2 and evaluated possible associations with age, sex and disease severity (as measured by duration of hospitalization, kind of respiratory support, treatment in ICU and death). The presence and to some degree the levels of anti-SARS-CoV-2 antibodies depended mainly on the amount of time between onset of symptoms and the collection of serum. A subgroup of patients did not develop antibodies at the time of sample collection. Compared to the patients that did, no differences were found. The presence and level of antibodies was not associated with age, sex, duration of hospitalization, treatment in the ICU or death. The case-fatality rate increased exponentially with older age. Neither the presence, nor the levels of anti-SARS-CoV-2 antibodies served as prognostic markers in our cohort. This is discussed as a possible consequence of the timing of the sample collection. Age is the most important risk factor for an adverse outcome in our cohort. Some patients appear not to develop antibodies within a reasonable time frame. It is unclear, however, why that is, as these patients differ in no respect examined by us from those who developed antibodies

Inherited thrombophilia in children with venous thromboembolism and the familial risk of thromboembolism: an observational study

Screening for inherited thrombophilia (IT) is controversial; persons at high risk for venous thromboembolism (VTE) who benefit from screening need to be identified. We tested 533 first-and second-degree relatives of 206 pediatric VTE patients for IT (antithrombin, protein C, protein S, factor V G1691A, factor II G20210A) and determined the incidence of symptomatic VTE relative to their IT status. The risk for VTE was significantly increased among family members with, versus without, IT (hazard ratio ‫؍‬ 7.6; 95% confidence interval [CI], 4.0-14.5; P &lt; .001) and highest among carriers of antithrombin, protein C, or protein S deficiency (hazard ratio ‫؍‬ 25.7; 95% CI, 12.2-54.2; P &lt; .001). Annual incidences of VTE were 2.82% (95% CI, 1.63%-4.80%) among family members found to be carriers of antithrombin, protein C, or protein S deficiency, 0.42% (0.12%-0.53%) for factor II G202010A, 0.25% (0.12%-0.53%) for factor V G1691A, and 0.10% (0.06%-0.17%) in relatives with no IT. Given the high absolute risk of VTE in relatives with protein C, protein S, and antithrombin deficiency, we suggest screening for these forms of hereditary thrombophilia in children with VTE and their relatives. Interventional studies are required to assess whether thromboembolism can be prevented in this highrisk population. (Blood. 2012;120(7): 1510-1515

Glatiramer Acetate Treatment Normalizes Deregulated microRNA Expression in Relapsing Remitting Multiple Sclerosis

The expression of selected microRNAs (miRNAs) known to be involved in the regulation of immune responses was analyzed in 74 patients with relapsing remitting multiple sclerosis (RRMS) and 32 healthy controls. Four miRNAs (miR-326, miR-155, miR-146a, miR-142-3p) were aberrantly expressed in peripheral blood mononuclear cells from RRMS patients compared to controls. Although expression of these selected miRNAs did not differ between treatment-naïve (n = 36) and interferon-beta treated RRMS patients (n = 18), expression of miR-146a and miR-142-3p was significantly lower in glatiramer acetate (GA) treated RRMS patients (n = 20) suggesting that GA, at least in part, restores the expression of deregulated miRNAs in MS

Introducing LoCo, a Logic for Configuration Problems

In this paper we present the core of LoCo, a logic-based high-level representation language for expressing configuration problems. LoCo shall allow to model these problems in an intuitive and declarative way, the dynamic aspects of configuration notwithstanding. Our logic enforces that configurations contain only finitely many components and reasoning can be reduced to the task of model construction.Comment: In Proceedings LoCoCo 2011, arXiv:1108.609

A new method for determination of varicella-zoster virus immunoglobulin G avidity in serum and cerebrospinal fluid

BACKGROUND: Avidity determination of antigen-specific immunoglobulin G (IgG) antibodies is an established serological method to differentiate acute from past infections. In order to compare the avidity of varicella-zoster virus (VZV) IgG in pairs of serum and cerebrospinal fluid (CSF) samples, we developed a new technique of avidity testing, the results of which are not influenced by the concentration of specific IgG. METHODS: The modifications introduced for the new VZV IgG avidity method included the use of urea hydrogen peroxide as denaturing reagent, the adaptation of the assay parameters in order to increase the sensitivity for the detection of low-level VZV IgG in CSF, and the use of a new calculation method for avidity results. The calculation method is based on the observation that the relationship between the absorbance values of the enzyme immunoassays with and without denaturing washing step is linear. From this relationship, a virtual absorbance ratio can be calculated. To evaluate the new method, a panel of serum samples from patients with acute and past VZV infection was tested as well as pairs of serum and CSF. RESULTS: For the serum panel, avidity determination with the modified assay gave results comparable to standard avidity methods. Based on the coefficient of variation, the new calculation method was superior to established methods of avidity calculation. CONCLUSIONS: The new avidity method permits a meaningful comparison of VZV IgG avidity in serum and CSF and should be of general applicability for easy determination of avidity results, which are not affected by the concentration of specific IgG

Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study

Background Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously described to positively modulate the gut microbiota, too. However, most previous studies mainly focused on either elite athletes or animal models. Thus, we conducted a randomised intervention study that focused on the effects of different types of training (endurance and strength) in previously physically inactive, healthy adults in comparison to controls that did not perform regular exercise. Overall study duration was ten weeks including six weeks of intervention period. In addition to 16S rRNA gene amplicon sequencing of longitudinally sampled faecal material of participants (six time points), detailed body composition measurements and analysis of blood samples (at baseline and after the intervention) were performed to obtain overall physiological changes within the intervention period. Activity tracker devices (wrist-band wearables) provided activity status and sleeping patterns of participants as well as exercise intensity and heart measurements. Conclusions We could show that different types of exercise have distinct but moderate effects on the overall physiology of humans and very distinct microbial changes in the gut. The observed overall changes during the intervention highlight the importance of physical activity on well-being. Future studies should investigate the effect of exercise on a longer timescale, investigate different training intensities and consider high-resolution shotgun metagenomics technology. Trial registration DRKS, DRKS00015873 . Registered 12 December 2018; Retrospectively registered

Antibodies to nodal/paranodal proteins in paediatric immune-mediated neuropathy

Altres ajuts: This work was partly supported by grants from the "Jubiläumsfonds der Österreichischen Nationalbank," project 16919 (R. Höftberger), the GBS/CIDP Foundation International (J. Wanschitz), Austrian Science Fund FWF, DOC 33-B27 (R. Höftberger, M. Winklehner) and I3334-B27 (R. Höftberger), Hertha Firnberg project number T996-B30 (I. Koneczny), the grant of the Fondo de Investigaciones Sanitarias-Instituto de Salud Carlos III (fondos FEDER) (L. Querol), personal grant of the Pla estratègic de Recerca i Innovació en Salut (PERIS), Departament de Salut, Generalitat de Catalunya (L. Querol), and the German Ministry of Education and Research (BMBF, 01 GM1908A)