bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ligand promiscuity in the tryptophan repressor – from structural understanding towards rational design
Authors: Stiel Andre C. , Shanmugaratnam Sooruban , Herud-Sikimic Ole , Jürgens Gerd , Höcker Birte 
Published: January 2020

AbstractReceptors that promiscuously bind a range of ligands provide insights into how nature mediates affinity and biological functioning. Moreover, such receptors provide vantage points for the rational design of specific binding for biotechnological applications. Here we describe the molecular details of the ligand binding promiscuity of the well-known tryptophan repressor TrpR. We elucidated high-resolution structures of TrpR bound to the co-repressors 5-methyl-tryptophan and 5-methyl-tryptamine as well as the pseudo-repressors indole-3-propionic and indole-3-acetic acid. Furthermore, using isothermal titration calorimetry we procure the corresponding thermodynamic parameters. Together this data provides molecular explanations for the strongly varied affinities and biological effects of the ligands providing insights into how nature shapes specificity and affinity. Beyond this we use these insights to exemplarily showcase knowledge-based design of TrpR by swapping its specificity from its native ligand tryptophan to indole-3-acetic acid. Finally, we elucidate the structures of the variant bound to indole-3-acetic and indole-3-propionic acid to retrace our design rationale.
Mesopredators display behaviourally plastic responses to dominant competitors when scavenging and communicating
Authors: Wang Yiwei , Allen Maximilian L. , Wilmers Christopher C. 
Published: January 2020

AbstractMesopredators face interspecific competition and intraguild predation when sharing resources with apex predators or more dominant mesopredators. We theorize that mesopredators use a variety of tactics to avoid competitively dominant predators at shared locations, such as scavenging and communication sites, that provide a mix of risks and rewards to these smaller predators. We examined whether mesopredator species employed behavioural tactics to reduce risks from dominant pumas when exploiting resources. We monitored carcasses in the Santa Cruz Mountains, CA across a gradient of human development and treated half of the carcasses with puma sign. Bobcats visited treated carcasses significantly later and for less time. Contrary to our expectations, coyotes and grey foxes were more likely to visit treated carcasses, although foxes were significantly less likely to visit a carcass also used by coyotes. Bobcats and foxes were less likely to visit carcasses at higher development levels whereas raccoons exhibited the opposite pattern. At communication sites, we observed temporal segregation among mesopredators and pumas. Coyotes and small predators exhibited the most segregation, followed by coyotes and pumas, and raccoons and pumas. Our results suggest subordinate predators employ a combination of spatial and temporal avoidance to minimize competitive interactions at shared sites.
Transcriptomic homogeneity and an age-dependent onset of hemoglobin expression characterize morphological PV types
Authors: Que Lin , Lukacsovich David , Földy Csaba 
Published: January 2020

AbstractThe diversity created by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. For example, parvalbumin interneurons (PV-INs) comprise of a main transcriptomic cluster within all inhibitory cells. However, transcriptomics alone has not resolved the different morphological PV types that exist. To close this gap, we used single-cell RNA-seq in morphologically identified PV-INs, sampled from 10 days to 3 months-old mice and studied their transcriptomic states in the morphological, physiological, and developmental domains. Our findings reveal novel genes whose expression separately identify morphological types but corroborate an overall transcriptomic homogeneity among PV-INs. Surprisingly, morphological PV types display uniform cell adhesion molecule (CAM) profiles, suggesting that CAMs do not actively maintain their specificity of wiring after development. Finally, our results reveal a pronounced change of transcriptomic states between postnatal days 20 and 25, during which PV-INs display a rapid and unexpected onset of hemoglobin gene expression which remains stable in later development.
LuxHS: DNA methylation analysis with spatially varying correlation structure
Authors: Halla-aho Viivi , Lähdesmäki Harri 
Published: January 2020

ABSTRACTBisulfite sequencing (BS-seq) is a popular method for measuring DNA methylation in basepair-resolution. Many BS-seq data analysis tools utilize the assumption of spatial correlation among the neighboring cytosines’ methylation states. While being a fair assumption, most existing methods leave out the possibility of deviation from the spatial correlation pattern. Our approach builds on a method which combines a generalized linear mixed model (GLMM) with a likelihood that is specific for BS-seq data and that incorporates a spatial correlation for methylation levels. We propose a novel technique using a sparsity promoting prior to enable cytosines deviating from the spatial correlation pattern. The method is tested with both simulated and real BS-seq data and compared to other differential methylation analysis tools.
Research on component synthesis active vibration suppression method for flexible spacecraft attitude maneuver with reaction jet actuators
Authors: Xu Jiangtao , Luo Na , Liu Shaojie , Zhao Baoshan , Qi Fang , Lian Yinjun , Wang Litong 
Published: January 2020

Purpose
The purpose of this paper is to design a component synthesis method to suppress the vibration of the flexible spacecraft, which has the constant amplitude force/moment actuator.

Design/methodology/approach
The authors proposed a method to construct constant amplitude of time delay and composite coefficient sequences based on the principles of the component synthesis vibration suppression (CSVS). The associated design strategy of the CSVS torque control is also developed. The dynamic model consisting of a single axis rotating rigid central body and a fixed flexibility panel is used to validate the proposed method. Constraint modal and free modal method are both tested to analyse the natural frequencies of the panel and dynamic properties of rigid–flexible decoupling system, under the conditions of known and unknown frequencies. The feasibility of constructing CSVS control force based on the constraint modal frequency is also analysed.

Findings
The proposed method can suppress multistage vibration and has arbitrary order robustness for each order frequencies simultaneously. Simulation results show that only the duration time of the actuator has to be set for the proposed method, reasonable vibration suppression effect can be achieved.

Practical implications
The method can be used in spacecraft, especially flexible spacecraft to suppress the vibration; the approach is convenient for engineering application and can be easily designed.

Originality/value
The authors proposed a method to construct constant amplitude of time delay and composite coefficient sequences based on the principles of the CSVS.
Unexplained wealth and for what purpose: a Sri Lankan perspective
Authors: Abeyagoonasekera Asanga 
Published: January 2020

Purpose
Explore perspective from Sri Lanka on unexplained wealth and why it should be taken as a pivotal measure to fight corruption in the society.

Design/methodology/approach
Qualitative and referenced work to explain the viewpoint.

Findings
The prevailing political will in achieving goals to fight economic crime is questionable. The entire society has a role to play when fighting corruption, which is not only limited to regulators, bribery commissions and the state sector. Private sector and individual voices in the society, including whistle blowers, could play a leading role in combating cases of unexplained wealth.

Originality/value
This study highlights political corruption in Sri Lanka with a unique viewpoint connecting political lobbying and unexplained wealth.
Capable guardianship against identity theft
Authors: Ylang Norah 
Published: January 2020

Purpose
This paper aims to examine demographic differences between individuals who do not take measures to protect themselves from identity theft victimization and those who do. A majority of the research on identity theft has focused on predictors of victimization, reporting behaviors of the victims and their health and mental outcomes. However, little remains known about the individuals who choose to take any identity-theft measures despite concerns over this fast-growing breed of crime.

Design/methodology/approach
Guided by Felson and Cohen’s routine activities theoretical framework (1979), this study uses the 2014 Identity Theft Supplement of the National Crime Victimization Survey to identify the demographic characteristics that influence the use of self-protection measures among individuals in the general population.

Findings
This study finds that these individuals are much more likely to be white, older, female and highly educated. The decision to undertake protection against identity theft is also influenced by the following factors: prior experience of misuse, possession of a bank account in the prior 12 months, current possession of at least one credit card and awareness that one is entitled to a free copy of one’s credit report.

Originality/value
This study addresses the gap in scholarship on identity theft prevention by applying the concept of guardianship in Cohen and Felson’s routine activity theory (1979) to the usage of self-protection measures in a general population. Future findings will identify the areas which agencies and researchers can focus on to inform policies that foster individuals’ own initiatives to take self-protection measures against potential identity theft.
The effect of samara wing presence on predation of Acer pseudoplatanus (Sapindaceae) seeds on the ground
Authors: der Weduwen Dagmar , Ruxton Graeme D. 
Published: January 2020

AbstractThe key selective pressure shaping the morphology of samaras is seen as enhancing primary wind‐borne dispersal from the parent plant to the ground. However, the consequences of the samara wing of primarily wind‐dispersed tree species for post‐dispersal processes has not been well studied. We explored whether the presence of this wing in Acer pseudoplatanus either deters or promotes predation after dispersal, either by increasing the time and energy required to predate the seed or by increasing the seed's visibility to predators. We found that wing‐removed fruits were preferred, suggesting that the presence of samaras makes seed handling more expensive for granivores. Further, we found that fewer seeds were consumed from treatments that contained the most winged seeds, thus there was no evidence of the samaras making seed finding easier for granivores. We conclude that the presence of the wing may offer an anti‐predatory benefit as well as aiding primary dispersal.
Identifying anaerobic amino acids degraders through the comparison of short‐term and long‐term enrichments
Authors: Mei Ran , Nobu Masaru K. , Liu Wen‐Tso 
Published: January 2020

SummaryDegradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well‐recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short‐term enrichment (SE) and long‐term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long‐term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.
Violence, Power and Meaning: The Moral Logic of Terrorism
Authors: Johnston Nicolas , Bose Srinjoy 
Published: January 2020

AbstractDominant orthodoxies within the study of terrorism have developed and promoted a strategic understanding of terrorism which has, in effect, reinforced the very conflict it seeks to explain. In response, this article develops the challenge of critical terrorism studies to propose a new strategic approach to terrorism. It posits that, while unable to achieve a Clausewitzian victory over the state per se, terrorism is able to politically paralyse the state's overwhelming power by shifting the moral horizons of that state's constituency. We explore two mutually reinforcing mechanisms by which terrorism achieves this objective and explore a number of strategic policy implications of each. This new approach is needed as current approaches misrepresent the challenge the global community currently faces, creating a self‐perpetuating loop of conflict and grievance which promises no end to terrorist violence.
Social participation, health‐related behavior, and depression of older adults living alone in Korea
Authors: Won Seojin , Kim Hyemee 
Published: January 2020

AbstractThis study aims to identify the effects of social participation on depression among adults over 60 years old living alone in Korea, focusing on the mediating effect of health‐related behavior on the social participation–depression relationship. The study relies on secondary data analysis using the 6th wave of the Korea Longitudinal Study of Ageing, and structural equation modeling method was employed for analyses. The findings indicate that older adults' participation in religious and social gatherings decreases depressive symptoms. The study also finds that regular eating behavior, drinking, and exercise also act as significant mediators, as older adults' participation in social gatherings is associated with those health‐related behaviors and that they also reduce depression. The results suggest that social participation by older adults who live alone is crucial not only for providing them with support but also for encouraging health‐related activities that can have direct effects on their mental health. Implications for social work practice are also discussed.
Reduced‐gate convolutional long short‐term memory using predictive coding for spatiotemporal prediction
Authors: Elsayed Nelly , Maida Anthony S. , Bayoumi Magdy 
Published: January 2020

AbstractSpatiotemporal sequence prediction is an important problem in deep learning. We study next‐frame(s) video prediction using a deep‐learning‐based predictive coding framework that uses convolutional LSTM (convLSTM) modules. We introduce a novel rgcLSTM architecture that requires a significantly lower parameter budget than a comparable convLSTM. By using a single multifunction gate, our reduced‐gate model achieves equal or better next‐frame(s) prediction accuracy than the original convolutional LSTM while using a smaller parameter budget, thereby reducing training time and memory requirements. We tested our reduced gate modules within a predictive coding architecture on the moving MNIST and KITTI datasets. We found that our reduced‐gate model has a significant reduction of approximately 40% of the total number of training parameters and a 25% reduction in elapsed training time in comparison with the standard convolutional LSTM model. The performance accuracy of the new model was also improved. This makes our model more attractive for hardware implementation, especially on small devices. We also explored a space of 20 different gated architectures to get insight into how our rgcLSTM fits into that space.
Self‐rated health scores predict mortality among people with type 2 diabetes differently across three different country groupings: findings from the ADVANCE and ADVANCE‐ON trials
Authors: Hua X. , Lung T. W. C. , Woodward M. , Salomon J. A. , Hamet P. , Harrap S. B. , Mancia G. , Poulter N. , Chalmers J. , Clarke P. M. 
Published: January 2020

AbstractAimsTo explore whether there is a different strength of association between self‐rated health and all‐cause mortality in people with type 2 diabetes across three country groupings: nine countries grouped together as 'established market economies'; Asia; and Eastern Europe.MethodsThe ADVANCE trial and its post‐trial follow‐up were used in this study, which included 11 140 people with type 2 diabetes from 20 countries, with a median follow‐up of 9.9 years. Self‐rated health was reported on a 0–100 visual analogue scale. Cox proportional hazard models were fitted to estimate the relationship between the visual analogue scale score and all‐cause mortality, controlling for a range of demographic and clinical risk factors. Interaction terms were used to assess whether the association between the visual analogue scale score and mortality varied across country groupings.ResultsThe visual analogue scale score had different strengths of association with mortality in the three country groupings. A 10‐point increase in visual analogue scale score was associated with a 15% (95% CI 12–18) lower mortality hazard in the established market economies, a 25% (95% CI 21–28) lower hazard in Asia, and an 8% (95% CI 3–13) lower hazard in Eastern Europe.ConclusionsSelf‐rated health appears to predict 10‐year all‐cause mortality for people with type 2 diabetes worldwide, but this relationship varies across groups of countries.
Population‐level variation of digestive physiology costs of mounting an immune response in damselflies
Authors: Tye Simon P. , Blaske Benjamin K. , Siepielski Adam M. 
Published: January 2020

1. Trade‐offs are often predicted to occur between energetically costly activities, such as somatic growth and eliciting immune responses to parasites. Although parasitism frequently reduces growth via lowered consumption, it remains unclear if the energetic demands of generating immune responses also affect the digestive physiological processes necessary for growth. Moreover, as local environmental conditions affect energetic investment towards growth and immune responses, the extent of any digestive–immune response trade‐offs may vary among populations and not be fixed at the species‐level.2. To test these ideas, melanisation – a general innate immune response – was first induced in damselfly larvae (Enallagma vesperum) from two populations. The study then quantified growth and consumption rates, assimilation and production efficiencies, and daily metabolic rates to determine if digestive–immune response trade‐offs were present and, if so, whether they differed between populations.3. There was no evidence of any trade‐offs between immune responses and digestive physiology components in either population. However, the results did show that populations differentially allocated energy towards different digestive physiology components after an immune response was elicited: one population increased their relative consumption and daily metabolic rates, while the other population had lower assimilation efficiencies and consumption rates.4. Although researchers lack a mechanistic understanding of the observed population‐level differences, these results suggest that accounting for population‐level variation in digestive physiology and immune responses is critical to inferences about how immunological defences to parasitism may affect the ability for organisms to both acquire and utilise resources.
Comparison of xylazine and detomidine in combination with midazolam/ketamine for field castration in Quarter Horses
Authors: Smith Mindy C. , Bass Luke , Damone James , Mama Khursheed , Rao Sangeeta 
Published: January 2020

AbstractBackgroundThe ideal field anaesthetic protocol for castration will offer an adequate duration and depth of anaesthesia using a single injection without compromising safety or recovery quality.ObjectivesThe objective of this study was to compare intravenous (IV) xylazine and detomidine as sedatives in combination with midazolam and ketamine for induction of anaesthesia in horses undergoing field castration.Study designRandomised, blinded, clinical study.MethodsFifty‐seven male Quarter Horses were randomly assigned to receive xylazine (group X) (1.1 mg/kg bwt) or detomidine (group D) (0.03 mg/kg bwt) as premedication with midazolam (0.05 mg/kg bwt) and ketamine (2.2 mg/kg bwt) anaesthesia. Using simple descriptive scales, quality of sedation, induction, surgical conditions and recovery were scored by blinded observers. Induction, surgery, recovery time and time from induction to standing were recorded.ResultsThere were a greater number of horses with lower sedation score in group D when compared with horses in group X at 5 minutes after the first dose of sedation (11.1%, 66.7% and 2.2% of horses from group D with sedation scores of 1, 2 and 3, vs 0%, 52% and 48% from group X, respectively,P = .05). A significant (P < .01) difference was found between surgical condition scores for group D (63%, 14.8%, 11.1% and 11.1% with surgery scores of 1, 2, 3 and 4, respectively) and group X (28%, 4%, 28% and 40%). Horses in Group D were less likely to require maintenance doses of ketamine (P = .05) with only 26% (7 of 27 horses) in this group requiring additional doses compared to 68% (17 of 25 horses) in group X. Recovery time in minutes (Group D: 24.74 ± 14.80, Group X: 13.08 ± 8.00;P < .01) and induction to standing time in minutes (Group D: 42.2 ± 13.8, Group X: 29.8 ± 8.2;P < .01) were significantly longer for horses in group D compared with group X.Main limitationsMultiple surgeons and multiple blinded observers.ConclusionsDetomidine as compared with xylazine as premedication results in good quality sedation and surgical conditions and prolonged surgical plane of anaesthesia, without significant differences in induction or recovery quality.
Mean stress effect on Gaßner curves interpreted as shifted Wöhler curves and application to smooth and notched geometries
Authors: D'Antuono Pietro , Ciavarella Michele 
Published: January 2020

AbstractRecently, the authors proposed the simple idea that Gaßner curves can be interpreted as shifted Wöhler curves if the Palmgren‐Miner rule is applied. The idea is extended here to the general case of nonzero mean stress fatigue loading applied to smooth or notched specimens. The mean stress effect has been addressed through the corrections proposed by Smith‐Watson‐Topper and by Walker. In this way, a new expression for the shift factorGhas been obtained. Through the application of the theory of the critical distances in its point variant,Gis demonstrated to be valid for both smooth and notched geometries. A comparison with the Society of Automotive Engineers (SAE) Keyhole test program data is added to substantiate the findings.