bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upgrade of Tile Calorimeter of the ATLAS Detector for the High Luminosity LHC.
Authors: Santurio Eduardo Valdes 
Published: November 2017

Abstract
The Tile Calorimeter (TileCal) is the hadronic calorimeter of ATLAS covering the central region of the ATLAS experiment. TileCal is a sampling calorimeter with steel as absorber and scintillators as active medium. The scintillators are read out by wavelength shifting fibers coupled to photomultiplier tubes (PMT). The analogue signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The High Luminosity Large Hadron Collider (HL-LHC) will have a peak luminosity of 5 × 1034
cm
−2
s
−1, five times higher than the design luminosity of the LHC. TileCal will undergo a major replacement of its on- and off-detector electronics for the high luminosity programme of the LHC in 2026. The calorimeter signals will be digitized and sent directly to the off-detector electronics, where the signals are reconstructed and shipped to the first level of trigger at a rate of 40 MHz. This will provide a better precision of the calorimeter signals used by the trigger system and will allow the development of more complex trigger algorithms. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. Field Programmable Gate Arrays (FPGAs) are extensively used for the logic functions of the off- and on-detector electronics. One hybrid demonstrator prototype module with the new calorimeter module electronics, but still compatible with the present system, may be inserted in ATLAS at the end of 2016.
Möbius orthogonality for the Zeckendorf sum-of-digits function
Authors: Drmota Michael , Müllner Clemens , Spiegelhofer Lukas 
Published: November 2017

We show that the (morphic) sequence

(
−
1

)

s
φ

(
n
)

(-1)^{s_\varphi (n)}

is asymptotically orthogonal to all bounded multiplicative functions, where

s
φ

s_\varphi

denotes the Zeckendorf sum-of-digits function. In particular we have

∑

n
>
N

(
−
1

)

s
φ

(
n
)

μ
(
n
)
=
o
(
N
)

\sum _{n>N} (-1)^{s_\varphi (n)} \mu (n) = o(N)

, that is, this sequence satisfies the Sarnak conjecture.
Multi-omics integration—a comparison of unsupervised clustering methodologies
Authors: Tini Giulia , Marchetti Luca , Priami Corrado , Scott-Boyer Marie-Pier 
Published: November 2017

AbstractWith the recent developments in the field of multi-omics integration, the interest in factors such as data preprocessing, choice of the integration method and the number of different omics considered had increased. In this work, the impact of these factors is explored when solving the problem of sample classification, by comparing the performances of five unsupervised algorithms: Multiple Canonical Correlation Analysis, Multiple Co-Inertia Analysis, Multiple Factor Analysis, Joint and Individual Variation Explained and Similarity Network Fusion. These methods were applied to three real data sets taken from literature and several ad hoc simulated scenarios to discuss classification performance in different conditions of noise and signal strength across the data types. The impact of experimental design, feature selection and parameter training has been also evaluated to unravel important conditions that can affect the accuracy of the result.
Integrating protein engineering with process design for biocatalysis
Authors: Woodley John M. 
Published: November 2017

Biocatalysis uses enzymes for chemical synthesis and production, offering selective, safe and sustainable catalysis. While today the majority of applications are in the pharmaceutical sector, new opportunities are arising every day in other industry sectors, where production costs become a more important driver. In the early applications of the technology, it was necessary to design processes to match the properties of the biocatalyst. With the advent of protein engineering, organic chemists started to develop and improve enzymes to suit their needs. Likewise in industry, although not widespread, a new paradigm was already implemented several years ago to engineer enzymes to suit process needs. Today, a new era is entered, where the effectiveness with which such integrated protein and process engineering is achieved becomes critical to implementation. In this paper, the development of a tool to improve the effectiveness of this approach is discussed, namely the use of target-setting based on process requirements, to guide the necessary protein engineering.This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.
Is the LAN effect in morphosyntactic processing an ERP artifact?
Authors: Caffarra Sendy , Mendoza Martha , Davidson Doug 
Published: November 2017

AbstractThe left anterior negativity (LAN) is an ERP component that has been often associated with morphosyntactic processing, but recent reports have questioned whether the LAN effect, in fact, exists. The present project examined whether the LAN effect, observed in the grand average response to local agreement violations, is the result of the overlap between two different ERP effects (N400, P600) at the level of subjects (n=80), items (n=120), or trials (n=6160). By-subject, by-item, and by-trial analyses of the ERP effect between 300 and 500 ms showed a LAN for 55% of the participants, 46% of the items, and 49% of the trials. Many examples of the biphasic LAN-P600 response were observed. Mixed-linear models showed that the LAN effect size was not reduced after accounting for subject variability. The present results suggest that there are cases where the grand average LAN effect represents the brain responses of individual participants, items, and trials.
Experimental evidence that female rhesus macaques (Macaca mulatta) perceive variation in male facial masculinity
Authors: Rosenfield Kevin A. , Semple Stuart , Georgiev Alexander V. , Maestripieri Dario , Higham James P. , Dubuc Constance 
Published: November 2017

AbstractAmong many primate species, face shape is sexually dimorphic, and male facial masculinity has been proposed to influence female mate choice and male-male competition by signalling competitive ability. However, whether conspecifics pay attention to facial masculinity has only been assessed in humans. In a study of free-ranging rhesus macaques, Macaca mulatta, we used a two-alternative look-time experiment to test whether females perceive male facial masculinity. We presented 107 females with pairs of images of male faces – one with a more masculine shape and one more feminine – and recorded their looking behaviour. Females looked at the masculine face longer than at the feminine face in more trials than predicted by chance. Although there was no overall difference in average look-time between masculine and feminine faces across all trials, females looked significantly longer at masculine faces in a subset of trials for which the within-pair difference in masculinity was most pronounced. Additionally, the proportion of time subjects looked toward the masculine face increased as the within-pair difference in masculinity increased. This study provides evidence that female macaques perceive variation in male facial shape, a necessary condition for intersexual selection to operate on such a trait. It also highlights the potential impact of perceptual thresholds on look-time experiments.
The feasibility and stability of large complex biological networks: a random matrix approach
Authors: Stone Lewi 
Published: November 2017

AbstractIn his theoretical work of the 70’s, Robert May introduced a Random Matrix Theory (RMT) approach for studying the stability of large complex biological systems. Unlike the established paradigm, May demonstrated that complexity leads to instability in generic models of biological networks. The RMT approach has since similarly been applied in many disciplines. Central to the approach is the famous “circular law” that describes the eigenvalue distribution of an important class of random matrices. However the “circular law” generally does not apply for ecological and biological systems in which density-dependence (DD) operates. Here we directly determine the far more complicated eigenvalue distributions of complex DD systems. A simple mathematical solution falls out, that allows us to explore the connection between feasible systems (i.e., having all equilibrium populations positive) and stability. In particular, for these RMT systems, almost all feasible systems are stable. The degree of stability, or resilience, is shown to depend on the minimum equilibrium population, and not directly on factors such as network topology.
Brain-Computer Interfaces for Post-Stroke Motor Rehabilitation: A Meta-Analysis
Authors: Cervera Maria A. , Soekadar Surjo R. , Ushiba Junichi , Millán José del R. , Liu Meigen , Birbaumer Niels , Garipelli Gangadhar 
Published: November 2017

ABSTRACTObjectiveBrain-computer interfaces (BCIs) can provide sensory feedback of ongoing brain oscillations enabling stroke survivors to modulate their sensorimotor rhythms purposefully. A number of recent clinical studies indicate that repeated use of such BCIs might trigger neurological recovery and hence improvement in motor function. Here we provide a first meta-analysis evaluating the clinical effectiveness of BCI-based post-stroke motor rehabilitation.MethodsTrials were identified using MEDLINE, CENTRAL, PEDro and by inspection of references in several review articles. We selected randomized controlled trials that used BCIs for post-stroke motor rehabilitation and provided motor impairment scores before and after the intervention. A random-effects inverse variance method was used to calculate the summary effect size.ResultsWe initially identified 524 articles and, after removing duplicates, we screened titles and abstracts of 473 articles. We found 26 articles corresponding to BCI clinical trials, of these, there were nine studies that involved a total of 235 post-stroke survivors fulfilling the inclusion criterion (randomized controlled trials that examined motor performance as an outcome measure) for the meta-analysis. Motor improvements, mostly quantified by the upper limb Fugl-Meyer Assessment (FMA-UE), exceeded the minimal clinical important difference (MCID=5.25) in six BCI studies, while such improvement was reached only in three control groups. Overall, the BCI training was associated with a standardized mean difference (SMD) of 0.79 (95% CI: 0.37 to 1.20) in FMA-UE compared to control conditions, which is in the range of medium to large summary effect size. In addition, several studies indicated BCI-induced functional and structural neuroplasticity at a sub-clinical level.InterpretationWe found a medium to large effect size of BCI therapy compared to controls. This suggests that BCI technology might be an effective intervention for post-stroke upper limb rehabilitation. However, more studies with larger sample size are required to increase the reliability of these results.
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria
Authors: Frénoy Antoine , Bonhoeffer Sebastian 
Published: November 2017

AbstractThe stress-induced mutagenesis paradigm postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to withstand the stress. This has implications for antibiotic treatment: exposure to sub-inhibitory doses of antibiotics has been reported to increase bacterial mutation rates, and thus probably the rate at which resistance mutations appear and lead to treatment failure.Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet sub-inhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus giving more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress.We developed a system using plasmid segregation to measure death and growth rates simultaneously in bacterial populations. We use it to replicate classical experiments reporting antibiotic-induced mutagenesis. We found that a substantial death rate occurs at the tested sub-inhibitory concentrations, and taking this death into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover even when antibiotics increase mutation rate, sub-inhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics.Beside showing that population dynamic is a crucial but neglected parameter affecting evolvability, we provide better experimental and computational tools to study evolvability under stress, leading to a re-assessment of the magnitude and significance of the stress-induced mutagenesis paradigm.
Antigen B from Echinococcus granulosus enters mammalian cells by endocytic pathways
Authors: da Silva Edileuza Danieli , Cancela Martin , Monteiro Karina Mariante , Ferreira Henrique Bunselmeyer , Zaha Arnaldo 
Published: November 2017

AbstractCystic hydatid disease is a zoonosis caused by the larval stage (hydatid cyst) of Echinococcus granulosus (Cestoda, Taeniidae). The hydatid cyst develops in the viscera of intermediate host as a unilocular structure filled by the hydatid fluid, which contains parasitic excretory/secretory products. Antigen B (AgB) is the major component of E. granulosus metacestode hydatid fluid. Functionally, AgB has been implicated in immunomodulation and lipid transport. However, the mechanisms underlying AgB functions are not completely known. In this study, we investigated AgB interactions with different mammalian cell types and the pathways involved in its internalization. AgB uptake was observed in four different cell lines, NIH-3T3, A549, J774 and RH. Inhibition of raft-mediated endocytosis causes about 50 and 69% decrease in AgB internalization by RH and A549 cells, respectively. Interestingly, AgB colocalized with the raft endocytic marker, but also showed a partial colocalization with the clathrin endocytic marker. The results indicate that raft-mediated endocytosis is the main route to AgB internalization, and that a clathrin-mediated entry may also occur at a lower frequency. Cellular internalization could be a requirement for AgB functions as a lipid carrier and/or immunomodulatory molecule, contributing to create a more permissive microenvironment to metacestode development and survival.Author summaryAntigen B (AgB) is an oligomeric lipoprotein highly abundant in Echinococcus granulosus hydatid fluid. AgB has already been characterized as an immunomodulatory protein, capable of inducing a permissive immune response to parasite development. Also, an important role in lipid acquisition is attributed to AgB, because it has been found associated to different classes of host lipids. However, the mechanisms of interaction employed by AgB to perform its functions remain undetermined. In this study, we demonstrate that mammalian cells are able to internalize E. granulosus AgB in culture and found that specific mechanisms of endocytosis are involved. Our results extend the understanding of AgB biological role indicating cellular internalization as a mechanism of interaction, which in turn, may represent a target to intervention.
Functional Plasticity of the gut and the Malpighian tubules underlies cold acclimation and mitigates cold-induced hyperkalemia inDrosophila melanogaster
Authors: Yerushalmi Gil Y. , Misyura Lidiya , MacMillan Heath A. , Donini Andrew 
Published: November 2017

AbstractAt low temperatures,Drosophila, like most insects, lose the ability to regulate ion and water balance across the gut epithelia, which can lead to a lethal increase of [K+] in the hemolymph (hyperkalemia). Cold-acclimation, the physiological response to low temperature exposure, can mitigate or entirely prevent these ion imbalances, but the physiological mechanisms that facilitate this process are not well understood. Here, we test whether plasticity in the ionoregulatory physiology of the gut and Malpighian tubules ofDrosophilamay aid in preserving ion homeostasis in the cold. Upon adult emergence,D. melanogasterfemales were subjected to seven days at warm (25°C) or cold (10°C) acclimation conditions. The cold acclimated flies had a lower critical thermal minimum (CTmin), recovered from chill coma more quickly, and better maintained hemolymph K+ balance in the cold. The improvements in chill tolerance coincided with increased Malpighian tubule fluid secretion and better maintenance of K+secretion rates in the cold, as well as reduced rectal K+reabsorption in cold-acclimated flies. To test whether modulation of ion-motive ATPases, the main drivers of epithelial transport in the alimentary canal, mediate these changes, we measured the activities of Na+-K+-ATPase and V-type H+-ATPase at the Malpighian tubules, midgut, and hindgut. Na+/K+-ATPase and V-type H+-ATPase activities were lower in the midgut and the Malpighian tubules of cold-acclimated flies, but unchanged in the hindgut of cold acclimated flies, and were not predictive of the observed alterations in K+transport. Our results suggest that modification of Malpighian tubule and gut ion and water transport likely prevents cold-induced hyperkalemia in cold-acclimated flies and that this process is not directly related to the activities of the main drivers of ion transport in these organs, Na+/K+- and V-type H+-ATPases.Summary StatementAt low temperatures,insectslose the ability to regulate ion and water balance and can experience a lethal increase in hemolymph [K+]. Previous exposure to low temperatures can mitigate this effect and improve chill tolerance. Here, we show that plasticity of ion and fluid transport across the Malpighian tubule and rectal epithelia likely drive this response.
DECENT: Differential Expression with Capture Efficiency adjustmeNT for single-cell RNA-seq data
Authors: Ye Chengzhong , Speed Terence P , Salim Agus 
Published: November 2017

AbstractDropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed affects the validity of the statistical analyses. Despite this, few current methods for differential expression (DE) analysis of scRNA-seq data explicitly model the dropout process. We develop DECENT, a DE method for scRNA-seq data that explicitly models the dropout process and performs statistical analyses on the inferred pre-dropout counts. We demonstrate using simulated and real datasets the superior performance of DECENT compared to existing methods. DECENT does not require spike-in data, but spike-ins can be used to improve performance when available. The method is implemented in a publicly-available R package.
Pay or preserve: a new approach to valuing cultural heritage
Authors: Boujdad Mkadem Abdelhamid , Zakriti Abderrahman , Nieuwenhuysen Paul 
Published: November 2017

Purpose
The purpose of this paper is to initiate a new approach to cultural heritage value through the highly revealing example of Chefchaouen city, Morocco. This study relates to approaching the valuation of cultural heritage per se. It does not evaluate or assess the economic value or the economic impacts of the cultural heritage. It tries to assess and measure the “culturality” of heritage based on local population opinion about urban heritage of the medina. This paper aims at obtaining information about their feeling and perceptions in respect of this heritage which may be useful for people democratic participation in decision making about heritage.

Design/methodology/approach
A survey using direct interviews with a sample of lower middle-class citizens coupled with direct administration of a questionnaire is carried out. The medina (but not the city) of Chefchaouen is the basis of the surveys conducted recently. The interviews are centered on the idea of preservation and participation instead of any monetized valuation.

Findings
The study has shown that there is a strong commitment of social category to participate in any type of activity leading to preserve the medina because it is their source of living and a source of profound affection. Therefore, this “willingness to preserve” may be seen as a key to define a new variable or attribute to measure the intrinsic value of heritage assets and justify the introduction in the national and international heritage list.

Research limitations/implications
This study should have been achieved with much larger target population and preferably through a funded project destined to preserve work and training. Funding for better experiences is severely lacking.

Practical implications
Local authorities may use this research and be inspired by it new and open dimensions. Serious collaboration between authorities and people should have the most promising results.

Social implications
Local authorities are more sensitive to population; therefore, they may include them in preservation planning and create employment by using the available funding.

Originality/value
This paper tries to enhance heritage study field at methodological level. It suggests a parameter shift to a more simple approach based on the local population opinion toward their heritage. Decision making about heritage should include people opinions and not people’s wishes.
Nobody deserves this fate: the vicious cycle of low human development in Guinea-Bissau
Authors: Só Bassiro , Franco Eduardo Ferreira , Carvalho Hamilton Coimbra , Santos Joaquim Rocha dos , Armenia Stefano 
Published: November 2017

PurposeThis paper aims to understand and explore the causal relationship of elements responsible for the macro vicious cycle of poverty in Guinea-Bissau, and discuss policies to break it.Design/methodology/approachThe methodology used in this study is based on the system dynamics simulation paradigm.FindingsBreaking the Guinean poverty cycle requires a multifaceted approach involving more resources and the building of several national capabilities. Traditional approaches tend to fail.Research limitations/implicationsLimitations come from the level of abstraction used in the model, which does not detail the processes for building specific capabilities and their interrelationships, and the necessary exclusion of variables that may have an impact in the process. Considering implications, the study models the evolution of human development index (HDI) in Guinea-Bissau, linking it to the economy and political sectors and allowing the simulation of different scenarios.Practical implicationsThe study presents a critical stance towards common recommendations from international agencies, and it provides a blueprint for development of more effective public policies.Social implicationsOvercoming the poverty trap in sub-Saharan countries remains a challenge for the international community. The study aims at helping in the process of integrating different frameworks into a compact and manageable model.Originality/valueThe study contributes to the system dynamics and economic development literatures by presenting an integrative model of human development in Guinea-Bissau. There is no study in the system dynamics literature modelling the relationship of HDI to economy and political sectors while different and contradictory points of view characterize the economics literature, leaving well-meaning public officials in Guinea-Bissau at a loss of mental models to tackle the poverty trap in the country.