The Beam Conditions Monitor of the LHCb Experiment

The LHCb experiment at the European Organization for Nuclear Research (CERN) is dedicated to precision measurements of CP violation and rare decays of B hadrons. Its most sensitive components are protected by means of a Beam Conditions Monitor (BCM), based on polycrystalline CVD diamond sensors. Its configuration, operation and decision logics to issue or remove the beam permit signal for the Large Hadron Collider (LHC) are described in this paper.Comment: Index Terms: Accelerator measurement systems, CVD, Diamond, Radiation detector

The MADP Toolbox: An Open-Source Library for Planning and Learning in (Multi-)Agent Systems

This article describes the MultiAgent Decision Process (MADP) toolbox, a software library to support planning and learning for intelligent agents and multiagent systems in un- certain environments. Some of its key features are that it sup- ports partially observable environments and stochastic tran- sition models; has unified support for single- and multiagent systems; provides a large number of models for decision- theoretic decision making, including one-shot decision mak- ing (e.g., Bayesian games) and sequential decision mak- ing under various assumptions of observability and coopera- tion, such as Dec-POMDPs and POSGs; provides tools and parsers to quickly prototype new problems; provides an ex- tensive range of planning and learning algorithms for single- and multiagent systems; and is written in C++ and designed to be extensible via the object-oriented paradigm

Bovine tuberculosis disturbs parasite functional trait composition in African buffalo

Novel parasites can have wide-ranging impacts, not only on host populations, but also on the resident parasite community. Historically, impacts of novel parasites have been assessed by examining pairwise interactions between parasite species. However, parasite communities are complex networks of interacting species. Here we used multivariate taxonomic and trait-based approaches to determine how parasite community composition changed when African buffalo (Syncerus caffer) acquired an emerging disease, bovine tuberculosis (BTB). Both taxonomic and functional parasite richness increased significantly in animals that acquired BTB than in those that did not. Thus, the presence of BTB seems to catalyze extraordinary shifts in community composition. There were no differences in overall parasite taxonomic composition between infected and uninfected individuals, however. The trait-based analysis revealed an increase in direct-transmitted, quickly replicating parasites following BTB infection. This study demonstrates that trait-based approaches provide insight into parasite community dynamics in the context of emerging infections

Improved performance of the LHCb Outer Tracker in LHC Run 2

The LHCb Outer Tracker is a gaseous detector covering an area of $5\times 6 m^2$ with 12 double layers of straw tubes. The performance of the detector is presented based on data of the LHC Run 2 running period from 2015 and 2016. Occupancies and operational experience for data collected in $p p$, pPb and PbPb collisions are described. An updated study of the ageing effects is presented showing no signs of gain deterioration or other radiation damage effects. In addition several improvements with respect to LHC Run 1 data taking are introduced. A novel real-time calibration of the time-alignment of the detector and the alignment of the single monolayers composing detector modules are presented, improving the drift-time and position resolution of the detector by 20\%. Finally, a potential use of the improved resolution for the timing of charged tracks is described, showing the possibility to identify low-momentum hadrons with their time-of-flight.Comment: 29 pages, 20 figures, minor changes to match the published versio

Evolution of naturally occurring 5' non-translated region variants of hepatitis C virus genotype 1b in selectable replicons

Quasispecies shifts are essential for the development of persistent hepatitis C virus (HCV) infection. Naturally occurring sequence variations in the 5' non-translated region (NTR) of the virus could lead to changes in protein expression levels, reflecting selective forces on the virus. The extreme 5' end of the virus' genome, containing signals essential for replication, is followed by an internal ribosomal entry site (IRES) essential for protein translation as well as replication. The 5' NTR is highly conserved and has a complex RNA secondary structure consisting of several stem-loops. This report analyses the quasispecies distribution of the 5' NTR of an HCV genotype 1b clinical isolate and found a number of sequences differing from the consensus sequence. The consensus sequence, as well as a major variant located in stem-loop IIIa of the IRES, was investigated using self-replicating HCV RNA molecules in human hepatoma cells. The stem-loop IIIa mutation, which is predicted to disrupt the stem structure, showed slightly lower translation efficiency but was severely impaired in the colony formation of selectable HCV replicons. Interestingly, during selection of colonies supporting autonomous replication, mutations emerged that restored the base pairing in the stem-loop. Recloning of these altered IRESs confirmed that these second site revertants were more efficient in colony formation. In conclusion, naturally occurring variants in the HCV 5' NTR can lead to changes in their replication ability. Furthermore, IRES quasispecies evolution was observed in vitro under the selective pressure of the replicon system

How Survey Design Affects Monkey Counts: A Case Study on Individually Recognized Spider Monkeys (Ateles geoffroyi).

The fast movement and high degree of fission-fusion dynamics of spider monkeys (Ateles spp.) make them notoriously difficult to survey. We examined which aspects of survey design affect spider monkey sightings along transects in a group of individually recognized spider monkeys (Ateles geoffroyi) in Punta Laguna, Yucatan, Mexico. We calculated the number of monkeys and subgroups sighted per transect walk. Using generalized linear models, we found no effect of the number of observers, transect type (new vs. existing), walking speed, or time of day on individual monkey counts or subgroup counts. Recounting of individuals was relatively rare and occurred when transects were walked relatively slowly. We missed more young than adult monkeys. The group composition based on survey data was similar to the known group composition. Based on our findings we recommend that surveys performed on relatively flat terrain be conducted at speeds similar to or faster than the moving speed of spider monkeys to minimize recounting of individuals and that young:adult female ratios based on survey data be interpreted as conservative indicators of population health. The novel methods presented to determine sources of bias in population estimates are applicable to a wide range of primates that are difficult to survey

Cancer risk in children, adolescents, and young adults conceived by ART in 1983-2011

STUDY QUESTION: Do children, adolescents, and young adults born after ART, including IVF, ICSI and frozen-thawed embryo transfer (FET), have an increased risk of cancer compared with children born to subfertile couples not conceived by ART and children from the general population? SUMMARY ANSWER: After a median follow-up of 18 years, the overall cancer risk was not increased in children conceived by ART, but a slight risk increase was observed in children conceived after ICSI. WHAT IS KNOWN ALREADY: There is growing evidence that ART procedures could perturb epigenetic processes during the pre-implantation period and influence long-term health. Recent studies showed (non-)significantly increased cancer risks after ICSI and FET, but not after IVF. STUDY DESIGN, SIZE, DURATION: A nationwide historical cohort study with prospective follow-up was carried out, including all live-born offspring from women treated with ART between 1983 and 2011 and subfertile women not treated with ART in one of the 13 Dutch IVF clinics and two fertility centers. PARTICIPANTS/MATERIALS, SETTING, METHODS: Children were identified through the mothers' records in the Personal Records Database. Information on the conception method of each child was collected through the mother's medical record. In total, the cohort comprises 89 249 live-born children of subfertile couples, of whom 51 417 were conceived using ART and 37 832 were not (i.e. conceived naturally, through ovulation induction, or after IUI). Cancer incidence was ascertained through linkage with the Netherlands Cancer Registry for the period 1989-2019. Cancer risk in children conceived using ART was compared with risk in children born to subfertile couples but not conceived by ART (hazard ratio (HR)) and children from the general population (standardized incidence ratios (SIRs)). MAIN RESULTS AND THE ROLE OF CHANCE: In total, 358 cancers were observed after a median follow-up of 18 years. Overall cancer risk was not increased in children conceived using ART, when compared with the general population (SIR = 0.96, 95% CI = 0.81-1.12) or with children from subfertile couples not conceived by ART (HR = 1.06, 95% CI = 0.84-1.33). Compared with children from subfertile couples not conceived by ART, the use of IVF or FET was not associated with increased cancer risk, but ICSI was associated with a slight risk increase (HR = 1.58, 95% CI = 1.08-2.31). Risk of cancer after ART did not increase at older ages (≥18 years, HR = 1.26, 95% CI = 0.88-1.81) compared to cancer risk in children not conceived by ART. LIMITATIONS, REASONS FOR CAUTION: The observed increased risk among children conceived using ICSI must be interpreted with caution owing to the small number of cases. WIDER IMPLICATIONS OF THE FINDINGS: After a median follow-up of 18 years, children conceived using ART do not have an increased overall cancer risk. Many large studies with prolonged follow-up are needed to investigate cancer risk in (young) adults conceived by different types of ART. In addition, international pooling of studies is recommended to provide sufficient power to study risk of specific cancer sites after ART. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by The Dutch Cancer Society (NKI 2006-3631) that funded the OMEGA-women's cohort, Children Cancer Free (KIKA; 147) that funded the OMEGA-I-II offspring cohort. The OMEGA-III offspring cohort was supported by a Postdoc Stipend of Amsterdam Reproduction &amp; Development, and the Eunice Kennedy Shriver National Institute of Child Health &amp; Human Development of the National Institutes of Health under Award Number R01HD088393. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors declare no competing interests. TRIAL REGISTRATION NUMBER:N/A.</p

Determination of the Michel Parameters rho, xi, and delta in tau-Lepton Decays with tau --> rho nu Tags

Using the ARGUS detector at the $e^+ e^-$ storage ring DORIS II, we have measured the Michel parameters $\rho$, $\xi$, and $\xi\delta$ for $\tau^{\pm}\to l^{\pm} \nu\bar\nu$ decays in $\tau$-pair events produced at center of mass energies in the region of the $\Upsilon$ resonances. Using $\tau^\mp \to \rho^\mp \nu$ as spin analyzing tags, we find $\rho_{e}=0.68\pm 0.04 \pm 0.08$, $\xi_{e}= 1.12 \pm 0.20 \pm 0.09$, $\xi\delta_{e}= 0.57 \pm 0.14 \pm 0.07$, $\rho_{\mu}= 0.69 \pm 0.06 \pm 0.08$, $\xi_{\mu}= 1.25 \pm 0.27 \pm 0.14$ and $\xi\delta_{\mu}= 0.72 \pm 0.18 \pm 0.10$. In addition, we report the combined ARGUS results on $\rho$, $\xi$, and $\xi\delta$ using this work und previous measurements.Comment: 10 pages, well formatted postscript can be found at http://pktw06.phy.tu-dresden.de/iktp/pub/desy97-194.p

Frequencies of circulating MAIT cells are diminished in chronic hCV, HIV and HCV/ HIV Co-Infection and do not recover during therapy

Objective Mucosal-associated invariant T (MAIT) cells comprise a subpopulation of T cells that can be activated by bacterial products and cytokines to produce IFN-&gamma;. Since little is known on MAIT cells during HCV infection, we compared their phenotype and function in comparison to HIV and HCV/HIV co-infected patients, and determined the effect of IFN-&alpha;-based and direct-acting antiviral therapy on MAIT cells of HCV patients. Methods Blood samples from patients with chronic HCV (CHCV), virologically suppressed HIV, acute HCV/HIV co-infection (AHCV/HIV) and healthy individuals were examined by flowcytometry for phenotype and function of MAIT and NK cells. Results and Conclusions Compared to healthy individuals, the frequency of CD161+ V&alpha;7.2+ MAIT cells was significantly decreased in patients with CHCV, HIV and AHCV/HIV co-infection. CD38 expression on MAIT cells was increased in AHCV/HIV patients. MAIT cells were responsive to IFN-&alpha; in vitro as evidenced by enhanced frequencies of IFN-&gamma; producing cells. IFN-&alpha;-based therapy for CHCV decreased the frequency of IFN-&gamma;+ MAIT cells, which was still observed 24 weeks after successful therapy. Importantly, even after successful IFN-&alpha;-based as well as IFN-&alpha;free therapy for CHCV, decreased frequencies of MAIT cells persisted. We show that the frequencies of MAIT cells are reduced in blood of patients with CHCV, HIV and in AHCV/ HIV co-infection compared to healthy individuals. Successful therapy for CHCV did not normalize MAIT cell frequencies at 24 weeks follow up. The impact of HIV and HCV infection on the numbers and function of MAIT cells warrant further studies on the impact of viral