bluuebunny/crossref_metadata_2025 huggingface dataset:
Crimes of the Senses: Yarn Bombing and Aesthetic Criminology
Authors: Millie Andrew
Published: April 2019

Yarn bombing involves the display of knitted or crocheted items in public space, often without permission. This article draws on interviews with yarn bombers in the North West of England and considers who the yarn bombers are, their motivations and experiences and their views on the legal status of yarn bombing. Although the visual is important for yarn bombing—and it is therefore of interest to visual criminology—this article also looks further to consider other sensory experience. In this way, it contributes to an emerging aesthetic criminology concerned with broader sensory, affective and emotive experience. Drawing on Thrift’s work on urban affect or mood, as well as Anderson and Young on affective atmospheres, yarn bombing is regarded as a crime of the senses affecting both the look and the feel of the city. The scope for further development of an aesthetic criminology is suggested, including specific methodologies that embrace the full range of sensory experiences associated with crime, disorder or social harm.
Labour share decline, financialisation and structural change
Authors: Pariboni Riccardo , Tridico Pasquale
Published: April 2019

The purpose of this article is to explain the determinants behind the decline of labour share in the last three to four decades in OECD countries. In our view, this decline was determined by financialisation and was deepened by the structural changes that occurred almost simultaneously in those economies. Financialisation, or finance-dominated capitalism, from the 1980s onwards, was a key element in the strategic offensive of the advanced countries’ dominant classes to appropriate higher shares of national income and to restore their control over the political process, a control that had been threatened by a generalised advancement of the labour movement in the 1970s. The development of a finance-dominated capitalism was helped by the process of globalisation, which affected not only OECD countries but also many others. A new, though unstable, macroeconomic model emerged, which we will call financial capitalism. In financial capitalism, trade unions lost power vis-à-vis capital, labour flexibility increased enormously, and a structural change from manufacturing to services was accelerated in rich countries. This resulted in negative consequences for labour share and income inequality. After having provided a theoretical discussion of the determinants of the compression of the wage share, making reference to the relevant literature, we submit our hypotheses to empirical scrutiny, performing a panel data analysis on 28 OECD Countries. The results of the estimations provide support to the theoretical argument.
A New Real-Time Link Prediction Method Based on User Community Changes in Online Social Networks
Authors: Mahmoudi Amin , Yaakub Mohd Ridzwan , Abu Bakar Azuraliza
Published: April 2019

The link prediction problem is becoming an important area of online social network (OSN) research. The existing methods that have been developed to address this problem mostly try to predict links based on structural information about the whole of the user lifespan. In addition, most of them do not consider user attributes such as user weight, density of interaction and geo-distance, all of which have an influence on the prediction of future links in OSNs due to the human-centric nature of these networks. Moreover, an OSN is a dynamic environment because users join and leave communities based on their interests over time. Therefore, it is necessary to predict links in real time. Therefore, the current study proposes a new method based on time and user attributes to predict links based on changes in user communities, where the changes in the user communities are indicative of users’ interests. The proposed method is tested on the UKM dataset and its performance is compared with that of 10 well-known methods and another community-based method. The area-under-the-curve results show that the proposed method is more accurate than all of the compared methods.
Headgear compliance as assessed by a temperature-sensitive recording device: a prospective clinical study
Authors: Huanca Ghislanzoni Luis , Ameur Sofian , Antonarakis Gregory S , Kiliaridis Stavros
Published: April 2019

Objective

To accurately describe compliance in headgear wearing time by using a temperature- and force-sensitive device over an 8 month period of use in a prospective clinical manner.

Materials and methods

Twenty children with Class II malocclusion aged 8–12 years were randomly selected for treatment with cervical headgear. The headgears were equipped with an electronic module, which measured temperature and force, and patients were instructed to wear the headgear 12 hours daily. The recorded values were analysed to determine the number of days the headgear was used, the number of hours per day it was worn, and the percentage of compliance (100 per cent corresponding to 12 hours daily).

Results

The average treatment period was 8.4 months with 5.8 months of effective use. When effectively used, headgear was worn 8.7 hours a day (compliance of 73 per cent). Including days where it was not worn, compliance was 6.4 hours (54 per cent). The appliance was used on average 0.5 hours during the day (8 am–8 pm) and 5.9 hours during the night (8 pm–8 am). Very low compliance was recorded during July and August.

Conclusion

The average compliance with cervical headgear use was 54 per cent of the 12 hour prescription. The headgear was effectively used only 5.8 months over the study period, with roughly 30 per cent of no use. Headgear was used almost exclusively during evening and night-time. During the summer period, compliance was particularly poor.
Free-living amoebae and squatters in the wild: ecological and molecular features
Authors: Samba-Louaka Ascel , Delafont Vincent , Rodier Marie-Hélène , Cateau Estelle , Héchard Yann
Published: April 2019

Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.
Endometrial preparation methods for frozen-thawed embryo transfer are associated with altered risks of hypertensive disorders of pregnancy, placenta accreta, and gestational diabetes mellitus
Authors: Saito Kazuki , Kuwahara Akira , Ishikawa Tomonori , Morisaki Naho , Miyado Mami , Miyado Kenji , Fukami Maki , Miyasaka Naoyuki , Ishihara Osamu , Irahara Minoru , Saito Hidekazu
Published: April 2019

STUDY QUESTION

What were the risks with regard to the pregnancy outcomes of patients who conceived by frozen-thawed embryo transfer (FET) during a hormone replacement cycle (HRC-FET)?

SUMMARY ANSWER

The patients who conceived by HRC-FET had increased risks of hypertensive disorders of pregnancy (HDP) and placenta accreta and a reduced risk of gestational diabetes mellitus (GDM) in comparison to those who conceived by FET during a natural ovulatory cycle (NC-FET).

WHAT IS KNOWN ALREADY

Previous studies have shown that pregnancy and live-birth rates after HRC-FET and NC-FET are comparable. Little has been clarified regarding the association between endometrium preparation and other pregnancy outcomes.

STUDY DESIGN, SIZE, DURATION

A retrospective cohort study of patients who conceived after HRC-FET and those who conceived after NC-FET was performed based on the Japanese assisted reproductive technology registry in 2014.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The pregnancy outcomes were compared between NC-FET (n = 29 760) and HRC-FET (n = 75 474) cycles. Multiple logistic regression analyses were performed to investigate the potential confounding factors.

MAIN RESULTS AND THE ROLE OF CHANCE

The pregnancy rate (32.1% vs 36.1%) and the live birth rate among pregnancies (67.1% vs 71.9%) in HRC-FET cycles were significantly lower than those in NC-FET cycles. A multiple logistic regression analysis showed that pregnancies after HRC-FET had increased odds of HDPs [adjusted odds ratio, 1.43; 95% confidence interval (CI), 1.14–1.80] and placenta accreta (adjusted odds ratio, 6.91; 95% CI, 2.87–16.66) and decreased odds for GDM (adjusted odds ratio, 0.52; 95% CI, 0.40–0.68) in comparison to pregnancies after NC-FET.

LIMITATIONS, REASONS FOR CAUTION

Our study was retrospective in nature, and some cases were excluded due to missing data. The implication of bias and residual confounding factors such as body mass index, alcohol consumption, and smoking habits should be considered in other observational studies.

WIDER IMPLICATIONS OF THE FINDINGS

Pregnancies following HRC-FET are associated with higher risks of HDPs and placenta accreta and a lower risk of GDM. The association between the endometrium preparation method and obstetrical complication merits further attention.

STUDY FUNDING/COMPETING INTEREST(S)

No funding was obtained for this work. The authors declare no conflicts of interest in association with the present study.

TRIAL REGISTRATION NUMBER

Not applicable.
Hospitalization Outcomes for Inflammatory Bowel Disease in Teaching vs Nonteaching Hospitals
Authors: Dalal Rahul S , Vajravelu Ravy K , Lewis James D , Lichtenstein Gary R
Published: April 2019

Teaching hospitals are known for higher inpatient costs compared to community centers. We therefore assessed the impact of hospital teaching status on IBD hospitalization outcomes and found that increased resource utilization is driven by disease complexity, not hospital teaching status.
Energy assessment of the implementation of renewable energies in a Portuguese household
Authors: Palmero-Marrero Ana I , Pinheiro Ricardo , Oliveira Armando C
Published: April 2019

This paper presents a detailed energy analysis of a 37-year-old house, located near Porto, Portugal. The current situation leads to overheating in the Summer and low temperatures during the Winter, causing high levels of discomfort to the occupants. With the aim to improve the overall comfort, several passive/active solar systems were proposed, and a complete energetic analysis was made. The only air conditioning system used in the house is a wood-burning fireplace that distributes warm air through the rooms. During the Summer, no air conditioning is used. Throughout the year, comfortable conditions are not achieved for the occupants. Building energy requirements for the household in the cooling and heating seasons were quantified. The study was extended throughout a whole year: for the heating season and for the cooling season. Also, indoor temperatures were calculated through numerical simulations. The household and its components were modeled with the TRNSYS 17 program. The results show that the integration of passive and active solar systems, guarantee an improvement in comfort and energy savings. The amount of energy required by the household is covered, to a very significant extent (approximately 71%), by energy from renewable sources. The renewable sources considered were solar energy and biomass. As passive measures, a change of the windows and the increase in wall insulation were considered. For the solar active systems, the application of solar thermal collectors for Domestic Hot Water (DHW) and photovoltaic collectors for electricity generation at the household were analyzed. The consumption of biomass in the burning fireplace was also assessed.
War as Symbolic Politics
Authors: Kaufman Stuart J
Published: April 2019

This article uses Kaufman's symbolic politics theory of ethnic war as the basis for a broader theory integrating most existing insights about the causes of international and civil war. It starts with findings from psychology showing that people are intuitive thinkers whose decisions result less from rational calculation than from symbolic predispositions—biases such as ideology and prejudice. Studies also show that increased feelings of threat lead to increased aggressive attitudes and behavior. Symbolic politics theory explains how individual attitudes can result in collective action using mobilization theory, with social organization and framing by leaders explaining which attitudes become political action. According to symbolist logic, important causes of war include aggressive symbolic predispositions among leaders or mass publics, heightened threat perceptions, and strong political organizations backing aggressive leaders. Crises and enduring rivalries make war more likely because they strengthen hostile predispositions and threat perceptions, thereby promoting mobilization for war. Cooperative transnational ties and democratic political institutions are among the factors that tend to promote peace.
Effects of increased energy and amino acid intake in late gestation on reproductive performance, milk composition, metabolic, and redox status of sows1
Authors: Che Lianqiang , Hu Liang , Wu Ceng , Xu Qin , Zhou Qiang , Peng Xie , Fang Zengfeng , Lin Yan , Xu Shenyu , Feng Bin , Li Jian , Tang Jiayong , Zhang Reinan , Li Hua , Theil Peter Kappel , Wu De
Published: April 2019

The objective of this study was to determine the effects of increased AA and energy intake during late gestation on reproductive performance, milk composition, and metabolic and redox status of sows. A total of 118 Yorkshire sows (third through sixth parity) were randomly assigned to dietary treatments from day 90 of gestation until farrowing. Dietary treatments consisted of combinations of 2 standardized ileal digestible (SID) AA levels [14.7 or 20.6 g/d SID Lys, SID Lys and other AA met or exceeded the NRC (2012) recommendations] and 2 energy levels (28.24 or 33.78 MJ/d intake of NE) in a 2 × 2 factorial design. After parturition, all sows were fed a standard lactation diet. Blood samples were collected and analyzed for parameters on metabolism, redox status, and amino acid profile. The data were analyzed using the generalized linear mixed models to reveal the impact of dietary levels of energy, AA, and their interaction. Sows with increased intake of AA had greater BW gain (P < 0.01) during late gestation. Furthermore, the BW loss during lactation was increased in sows with increasing intake of energy (P < 0.05) or AA (P < 0.05). Sows fed high energy had higher total litter birth weights (20.2 kg vs. 18.4 kg, P < 0.05) and shorter duration of farrowing (261 min vs. 215 min, P < 0.05), compared with those fed low energy, which likely was due to higher (P < 0.05) plasma glucose and lower (P < 0.05) plasma lactate prior to parturition. High AA intake in late gestation increased the ADG of piglets during the following lactation (P < 0.05), and increased the concentrations of plasma urea, and the following AA: Lys, Met, Thr, Val, Ile, Leu, Phe, Asp, Ser, and Arg at farrowing (P < 0.05). In conclusion, the increased intake of energy increased total litter weight of newborns and shortened the farrowing duration, which likely was due to improved energy status at farrowing. Furthermore, sows with increased intake of AA led to higher growth rate of piglets during the following lactation, accompanying with the increasing levels of plasma urea and amino acids. Therefore, the higher energy intake in late gestation appeared to improve litter weight and farrowing duration, while higher AA intake may have positive effect on piglets performance in lactation.
Comparison of Different Trap Designs for Capture of Noctuid Moths (Lepidoptera: Noctuidae) With Pheromone and Floral Odor Attractants
Authors: Whitfield E Charles , Lobos Enrique , Cork Alan , Hall David R
Published: April 2019

Six trap designs were assessed for capturing noctuid moths in field trials in the United Kingdom and Argentina. The traps were baited with either a sex pheromone for Autographa gamma in the UK trials and Helicoverpa gelotopoeon (Dyar) (Lepidoptera: Noctuidae) in Argentina, or a floral odor blend. In the UK trials the Universal Trap and a funnel sleeve trap were compared; in Argentina the funnel sleeve trap, a homemade bucket trap, and (L.) (Lepidoptera: Noctuidae) three sticky traps: LepTrap, wing trap, and delta trap were compared. Comparisons were made between the traps and attractants and captures of noctuid moths and nontarget insects. Traps baited with the floral attractant caught a lower number but a wider range of noctuid species including Helicoverpa, Spodoptera, Rachiplusia, Dargida, Mythimna, Chrysodeixis, Agrotis, and Autographa spp., and nontarget insects. In the UK trials, the funnel sleeve trap caught significantly more A. gamma than the Universal Trap. The addition of an insecticide to the Universal Trap marginally increased trap catches. In the Argentinian trials, the homemade bucket and the sleeve traps outperformed all sticky traps in most situations regardless of crop environment and attractant type. The homemade bucket and the funnel sleeve traps are also considerably cheaper than the other trap designs. Of the sticky traps the LepTrap caught more noctuids than the wing and delta traps. The results suggest that the bucket trap and the sleeve trap have a much greater maximum capacity and possibly a greater retention efficiency for noctuid moths compared to the sticky traps.
‘If We Hadn’t Left … We Would Have All Died’: Escaping Famine on the Greek Island of Chios, 1941–44
Authors: Hionidou Violetta
Published: April 2019

The decision-making processes of historical famine-induced migration movements have rarely been examined in detail. This article discusses such a movement from the Greek island of Chios and into Turkey in the early 1940s using first-hand accounts of famine survivors collected in the period 1999–2009. This article outlines the unfolding famine situation, describes the point at which individuals made the decision to leave or to stay and examines how that decision was implemented. The decision-making involved an elaborate process where pros and cons were assessed, where the wishes of individual family members were taken into consideration and where the long-term wellbeing of the family unit was the most important factor in any decision made. Difficult decisions, some of which may today appear irrational, were made. The article argues that individuals, even in crises situations, demonstrate agency and plan their actions and future, albeit within the constraints of a given situation.
On the millimetre continuum flux–radius correlation of proto-planetary discs
Authors: Rosotti Giovanni P , Booth Richard A , Tazzari Marco , Clarke Cathie , Lodato Giuseppe , Testi Leonardo
Published: April 2019

A correlation between proto-planetary disc radii and sub-mm fluxes has been recently reported. In this letter, we show that the correlation is a sensitive probe of grain growth processes. Using models of grain growth and drift, we have shown in a companion paper that the observed disc radii trace where the dust grains are large enough to have a significant sub-mm opacity. We show that the observed correlation emerges naturally if the maximum grain size is set by radial drift, implying relatively low values of the viscous α parameter ≲0.001. In this case, the relation has an almost universal normalization, while if the grain size is set by fragmentation the flux at a given radius depends on the dust-to-gas ratio. We highlight two observational consequences of the fact that radial drift limits the grain size. The first is that the dust masses measured from the sub-mm could be overestimated by a factor of a few. The second is that the correlation should be present also at longer wavelengths (e.g. 3mm), with a normalization factor that scales as the square of the observing frequency as in the optically thick case.
The RNA workbench 2.0: next generation RNA data analysis
Authors: Fallmann Jörg , Videm Pavankumar , Bagnacani Andrea , Batut Bérénice , Doyle Maria A , Klingstrom Tomas , Eggenhofer Florian , Stadler Peter F , Backofen Rolf , Grüning Björn
Published: April 2019

RNA has become one of the major research topics in molecular biology. As a central player in key processes regulating gene expression, RNA is in the focus of many efforts to decipher the pathways that govern the transition of genetic information to a fully functional cell. As more and more researchers join this endeavour, there is a rapidly growing demand for comprehensive collections of tools that cover the diverse layers of RNA-related research. However, increasing amounts of data, from diverse types of experiments, addressing different aspects of biological questions need to be consolidated and integrated into a single framework. Only then is it possible to connect findings from e.g. RNA-Seq experiments and methods for e.g. target predictions. To address these needs, we present the RNA Workbench 2.0 , an updated online resource for RNA related analysis. With the RNA Workbench we created a comprehensive set of analysis tools and workflows that enables researchers to analyze their data without the need for sophisticated command-line skills. This update takes the established framework to the next level, providing not only a containerized infrastructure for analysis, but also a ready-to-use platform for hands-on training, analysis, data exploration, and visualization. The new framework is available at https://rna.usegalaxy.eu , and login is free and open to all users. The containerized version can be found at https://github.com/bgruening/galaxy-rna-workbench.
INGA 2.0: improving protein function prediction for the dark proteome
Authors: Piovesan Damiano , Tosatto Silvio C E
Published: April 2019

Our current knowledge of complex biological systems is stored in a computable form through the Gene Ontology (GO) which provides a comprehensive description of genes function. Prediction of GO terms from the sequence remains, however, a challenging task, which is particularly critical for novel genomes. Here we present INGA 2.0, a new version of the INGA software for protein function prediction. INGA exploits homology, domain architecture, interaction networks and information from the ‘dark proteome’, like transmembrane and intrinsically disordered regions, to generate a consensus prediction. INGA was ranked in the top ten methods on both CAFA2 and CAFA3 blind tests. The new algorithm can process entire genomes in a few hours or even less when additional input files are provided. The new interface provides a better user experience by integrating filters and widgets to explore the graph structure of the predicted terms. The INGA web server, databases and benchmarking are available from URL: https://inga.bio.unipd.it/.
Big Three Dragons: A z = 7.15 Lyman-break galaxy detected in [O iii] 88 μm, [C ii] 158 μm, and dust continuum with ALMA
Authors: Hashimoto Takuya , Inoue Akio K , Mawatari Ken , Tamura Yoichi , Matsuo Hiroshi , Furusawa Hisanori , Harikane Yuichi , Shibuya Takatoshi , Knudsen Kirsten K , Kohno Kotaro , Ono Yoshiaki , Zackrisson Erik , Okamoto Takashi , Kashikawa Nobunari , Oesch Pascal A , Ouchi Masami , Ota Kazuaki , Shimizu Ikkoh , Taniguchi Yoshiaki , Umehata Hideki , Watson Darach
Published: April 2019

We present new ALMA observations and physical properties of a Lyman break galaxy at z = 7.15. Our target, B14-65666, has a bright ultra-violet (UV) absolute magnitude, MUV ≈ −22.4, and has been spectroscopically identified in Lyα with a small rest-frame equivalent width of ≈4 Å. A previous Hubble Space TElescope (HST) image has shown that the target is composed of two spatially separated clumps in the rest-frame UV. With ALMA, we have newly detected spatially resolved [O iii] 88 μm, [C ii] 158 μm, and their underlying dust continuum emission. In the whole system of B14-65666, the [O iii] and [C ii] lines have consistent redshifts of 7.1520 ± 0.0003, and the [O iii] luminosity, (34.4 ± 4.1) × 108 L⊙, is about three times higher than the [C ii] luminosity, (11.0 ± 1.4) × 108 L⊙. With our two continuum flux densities, the dust temperature is constrained to be Td ≈ 50–60 K under the assumption of a dust emissivity index of βd = 2.0–1.5, leading to a large total infrared luminosity of LTIR ≈ 1 × 1012 L⊙. Owing to our high spatial resolution data, we show that the [O iii] and [C ii] emission can be spatially decomposed into two clumps associated with the two rest-frame UV clumps whose spectra are kinematically separated by ≈200 km s−1. We also find these two clumps have comparable UV, infrared, [O iii], and [C ii] luminosities. Based on these results, we argue that B14-65666 is a starburst galaxy induced by a major merger. The merger interpretation is also supported by the large specific star formation rate (defined as the star formation rate per unit stellar mass), sSFR $= 260^{+119}_{-57}\:$Gyr−1, inferred from our SED fitting. Probably, a strong UV radiation field caused by intense star formation contributes to its high dust temperature and the [O iii]-to-[C ii] luminosity ratio.
On Local definability of holomorphic functions
Authors: Jones Gareth , Kirby Jonathan , Le Gal Olivier , Servi Tamara
Published: April 2019

Given a collection $\mathcal {A}$ of holomorphic functions, we consider how to describe all the holomorphic functions locally definable from $\mathcal {A}$. The notion of local definability of holomorphic functions was introduced by Wilkie, who gave a complete description of all functions locally definable from $\mathcal {A}$ in the neighbourhood of a generic point. We prove that this description is no longer complete in the neighbourhood of non-generic points. More precisely, we produce three examples of holomorphic functions that suggest that at least three new operations need to be added to Wilkie’s description in order to capture local definability in its entirety. The constructions illustrate the interaction between resolution of singularities and definability in the o-minimal setting.
AIDS, Antiretrovirals, Brazil and the International Politics of Global Health, 1996–2008
Authors: Cueto Marcos , Lopes Gabriel
Published: April 2019

In the mid-1990s, Brazil became a player in the global politics of AIDS through its participation in debates on whether antiretroviral drugs were commodities or public goods. Brazilian actors not only challenged powerful pharmaceutical companies but the assumption that international health policies were solely defined in developed countries. After 1996, a coalition of Brazilian officers, health activists, people living with Aids and medical scientists advocated for universal access to generic medication (instead of costly patented drugs) and publicized its achievements at home and abroad, such as a marked decline in AIDS cases. However, during the first decade of the twenty-first century increased costs, little attention to prevention and the persistence of homophobia hindered treatment. Moreover, unilateral US programmes and conservative evangelicals glorifying sexual abstinence sabotaged anti-AIDS work. After the financial crisis of 2008, universal access to ARVs lost political momentum and sustaining treatment became difficult in Brazil.
Addressing common errors and misconceptions in integral calculus with clickers and classroom voting
Authors: Cline Kelly , Zullo Holly , Huckaby David A
Published: April 2019

Common student errors and misconceptions can be addressed through the method of classroom voting, in which the instructor presents a multiple-choice question to the class, and after a few minutes for consideration and small-group discussion, each student votes on the correct answer, using a clicker or a phone. If a large number of students have voted for one particular incorrect answer, the instructor can recognize and address the issue. In order to identify multiple-choice questions that are especially effective at provoking common errors and misconceptions, we recorded the percentages of students voting for each option on each question used in 25 sections of integral calculus, taught by 7 instructors, at 4 institutions, over the course of 12 years, on a collection of 172 questions. We restricted our analysis to the 115 questions which were voted on by at least 5 different classes. We present the six questions that caused the largest percentages of students to vote for a particular incorrect answer, discuss how we used these questions in the classroom, and examine the common features of these questions. Further, we look for correlations between question characteristics and the mean percentage of students voting for common errors on these questions, and we find that questions based on general cases have higher percentages of students voting for common errors.
Spatial epidemiology of cutaneous leishmaniasis in Colombia: socioeconomic and demographic factors associated with a growing epidemic
Authors: Hernández Andrés M , Gutierrez Juan D , Xiao Yanyu , Branscum Adam J , Cuadros Diego F
Published: April 2019

Background

Despite the identification of some environmental factors linked to the cutaneous leishmaniasis (CL) epidemic, little is known about the impact of environmental disturbances caused by human activities. We assessed the association between socioeconomic and demographic factors with the spatial structure of the CL epidemic in Colombia.

Methods

Using data from more than 65 000 CL cases collected across the entire country from publicly available sources, we conducted a spatial clustering analysis to identify high burden areas (clusters) of CL. Associations between CL clusters and socioeconomic variables were investigated.

Results

We identified seven statistically significant clusters of CL located across all Colombian biomes. Deforestation and livestock were statistically significantly associated with the spatial clustering of CL. Urbanization, time spent traveling to main cities and water bodies were other factors linked with the clustering of CL.

Conclusions

This study found that human activities such as deforestation linked to agriculture, livestock production and mining activities are key drivers of the spatial distribution of the CL epidemic. The intensity of these human activities, which are projected to increase because of social and economic transformations in progress in Colombia, will potentially exacerbate the already growing CL epidemic in the country.
A Daily Diary Study of Responses to Age Meta-stereotypes
Authors: Finkelstein Lisa M , Voyles Elora C , Thomas Courtney L , Zacher Hannes
Published: April 2019

An age meta-stereotype occurs when we activate the idea that another age group is holding a stereotype of our age group, but what happens after this occurs? We used experience sampling methodology to explore reactions to, and subsequent behaviors associated with, positive and negative age meta-stereotypes occurring over the course of a work week. One hundred eighty-five employees from various organizations across the United States responded to a daily survey tapping into activation of positive and negative age meta-stereotypes, reactions (threat, challenge, or boost), and interpersonal behaviors (avoidance, conflict, and engagement). Hypotheses regarding relationships among reactions and behaviors were largely supported, but there were some unexpected findings regarding reactions to positive and negative age meta-stereotypes. Of particular interest: (a) younger respondents experienced more negative age meta-stereotypes than older respondents, even those that have been shown to be typically older meta-stereotypes, and (b) experiencing older negative meta-stereotypes, regardless of the age of the respondent, was related to challenge reactions while experiencing younger negative meta-stereotypes, regardless of the age of respondent, was related to threat. Our findings demonstrate advantages to studying age meta-stereotypes using experience sampling methods, and point to a need for more theoretical refinement to account for different reactions and behaviors depending on respondent age and type of meta-stereotype.
Gait Variability in Women With Hip Osteoarthritis Before and After Total Hip Replacement
Authors: Wada Osamu , Asai Tsuyoshi , Hiyama Yoshinori , Nitta Shingo , Mizuno Kiyonori
Published: April 2019

Objective

Gait variability changes before and after total hip arthroplasty are unclear. This study aimed to investigate gait variability changes in hip osteoarthritis patients before and after total hip arthroplasty and to examine the relationships between gait variability changes and hip function.

Design

Twenty-three female patients with hip osteoarthritis (61.0 ± 7.1 yrs) and 10 healthy female participants (57.8 ± 3.9 yrs) were assessed 1 mo before and 12 mos after surgery. Heel and lower trunk accelerations were measured using two triaxial accelerometers. The coefficient of variation of stride time for gait variability of lower limb motions and the harmonic ratio for trunk variability were calculated. Radiographic leg-length discrepancy, hip abductor strength, hip abduction, extension range of motion, and pain level during gait were measured.

Results

The coefficient of variation was significantly decreased after total hip arthroplasty and was comparable with that in healthy individuals. Although postoperative harmonic ratios were greater than preoperative harmonic ratios, they were not comparable with those in healthy individuals. The coefficient of variation changes were associated with pain relief during gait. Harmonic ratio changes were associated with hip abductor strength, extension range of motion, and limb lengthening.

Conclusion

Gait variability improved after total hip arthroplasty due to improved hip function. However, trunk variability was insufficient compared with that in healthy individuals.
Bone Marrow Edema
Authors: Pimenta Tiago , Parada Fernando , Rocha J. Afonso
Published: April 2019

Bone marrow edema represents a typical pattern on magnetic resonance imaging consisting of an area of abnormal bone signal with low to intermediate intensity on T1-weighted images and a high intensity on fat-suppressed T2-weighted images. Bone marrow edema syndromes are a group of entities characterized by idiopathic bone marrow edema and osteoporosis. Regional migratory osteoporosis is a bone marrow edema syndrome characterized by a self-limited migrating arthralgia of the lower limbs not related to trauma or other events. Its clinical presentation is variable and may include a less frequent form of migration of the bone marrow edema within the same joint, illustrated here by means of a case report. Conservative treatment is the preferred approach to this condition, and usually, it resolves completely and with no sequelae. Physicians should be made aware of this condition to avoid unnecessary and costly diagnostic and therapeutic measures.
Integrated Hypertension and HIV Care Cascades in an HIV Treatment Program in Eastern Uganda: A Retrospective Cohort Study
Authors: Muddu Martin , Tusubira Andrew K. , Sharma Srish K. , Akiteng Ann R. , Ssinabulya Isaac , Schwartz Jeremy I.
Published: April 2019

Background:

Persons living with HIV (PLHIV) are at increased risk of cardiovascular disease. Integration of services for hypertension (HTN), the primary cardiovascular disease risk factor, into HIV care programs is recommended in Uganda, though, uptake has been limited. We sought to compare the care cascades for HTN and HIV within an HIV program in Eastern Uganda.

Methods:

We conducted a retrospective cohort study of all PLHIV enrolled in 3 HIV clinics between 2014 and 2017. We determined the proportion of patients in the following cascade steps over 12 months: Screened, Diagnosed, Initiated on treatment, Retained, Monitored, and Controlled. Cascades were analyzed using descriptive statistics and compared using χ2 and t tests.

Results:

Of 1649 enrolled patients, 98.5% were initiated on HIV treatment, of whom 70.7% were retained in care, 100% had viral load monitoring, and 90.3% achieved control (viral suppression). Four hundred fifty-six (27.7%) participants were screened for HTN, of whom 46.9% were diagnosed, 88.1% were initiated on treatment, 57.3% were retained in care, 82.7% were monitored, and 24.3% achieved blood pressure control. There were no differences in any HIV cascade step between participants with HIV alone and those with both conditions.

Conclusions:

The HIV care cascade approached global targets, whereas the parallel HTN care cascade demonstrated notable quality gaps. Management of HTN within this cohort did not negatively impact HIV care. Our findings suggest that models of integration should focus on screening PLHIV for HTN and retention and control of those diagnosed to fully leverage the successes of HIV programs.
Bayesian inference of distributed time delay in transcriptional and translational regulation
Authors: Choi Boseung , Cheng Yu-Yu , Cinar Selahittin , Ott William , Bennett Matthew R. , Josić Krešimir , Kim Jae Kyoung
Published: April 2019

Motivation

Advances in experimental and imaging techniques have allowed for unprecedented insights into the dynamical processes within individual cells. However, many facets of intracellular dynamics remain hidden, or can be measured only indirectly. This makes it challenging to reconstruct the regulatory networks that govern the biochemical processes underlying various cell functions. Current estimation techniques for inferring reaction rates frequently rely on marginalization over unobserved processes and states. Even in simple systems this approach can be computationally challenging, and can lead to large uncertainties and lack of robustness in parameter estimates. Therefore we will require alternative approaches to efficiently uncover the interactions in complex biochemical networks.

Results

We propose a Bayesian inference framework based on replacing uninteresting or unobserved reactions with time delays. Although the resulting models are non-Markovian, recent results on stochastic systems with random delays allow us to rigorously obtain expressions for the likelihoods of model parameters. In turn, this allows us to extend MCMC methods to efficiently estimate reaction rates, and delay distribution parameters, from single-cell assays. We illustrate the advantages, and potential pitfalls, of the approach using a birth-death model with both synthetic and experimental data, and show that we can robustly infer model parameters using a relatively small number of measurements. We demonstrate how to do so even when only the relative molecule count within the cell is measured, as in the case of fluorescence microscopy.
Epigenome-wide analysis uncovers a blood-based DNA methylation biomarker of lifetime cannabis use
Authors: Markunas Christina A. , Hancock Dana B. , Xu Zongli , Quach Bryan C. , Sandler Dale P. , Johnson Eric O. , Taylor Jack A.
Published: April 2019

Cannabis use is highly prevalent and is associated with adverse and beneficial effects. To better understand the full spectrum of health consequences, biomarkers that accurately classify cannabis use are needed. DNA methylation (DNAm) is an excellent candidate, yet no blood-based epigenome-wide association studies (EWAS) in humans exist. We conducted an EWAS of lifetime cannabis use (ever vs. never) using blood-based DNAm data from a case-cohort study within Sister Study, a prospective cohort of women at risk of developing breast cancer (Discovery N=1,730 [855 ever users]; Replication N=853 [392 ever users]). We identified and replicated an association with lifetime cannabis use at cg15973234 (CEMIP): combined P=3.3×10−8. We found no overlap between published blood-based cis-meQTLs of cg15973234 and reported lifetime cannabis use-associated SNPs (P<0.05), suggesting that the observed DNAm difference was driven by cannabis exposure. We also developed a multi-CpG classifier of lifetime cannabis use using penalized regression of top EWAS CpGs. The resulting 49-CpG classifier produced an area under the curve (AUC)=0.74 (95% confidence interval [0.72, 0.76], P=2.00×10−5) in the discovery sample and AUC=0.54 ([0.51, 0.57], P=4.64×10−2) in the replication sample. Our EWAS findings provide evidence that blood-based DNAm is associated with lifetime cannabis use.
Phytolacca americana PaGT2 is an ambidextrous polyphenol glucosyltransferase
Authors: Maharjan Rakesh , Fukuda Yohta , Shimomura Naomichi , Nakayama Taisuke , Nakayama Toru , Hamada Hiroki , Inoue Tsuyoshi , Ozaki Shin-ichi
Published: April 2019

The health benefits of polyphenols have attracted their use as potential therapeutic agents, food additives, and cosmetics. However, low water solubility of polyphenols limits their cell absorbability, obscuring further exploration. Glycosylation is known to enhance the solubility of polyphenols preserving their pharmacological properties. Here, we show that a uridine diphosphate (UDP) glucosyltransferase from Phytolacca americana (PaGT2) regioselectively catalyzes the transfer of glucose from UDP-glucose to stilbenoids such as piceatannol and flavonoids such as kaempferol. To understand the structure-function relationship of PaGT2, we determined the crystal structure of PaGT2 as well as PaGT2 complexed with donor analogue UDP-2-fluoro glucose and stilbenoid acceptor analogues. While only one conserved histidine residue is recognized as a catalytic residue in known UGTs, the crystal structures of PaGT2 suggested the presence of two catalytically active residues (His18 and His81) at two sides of the catalytic pocket. Although the single catalytic residue mutant His18Ala or His81Ala did not completely impair the glucosylation activity of the enzyme, the double mutant His18Ala/His81Ala failed to form glucoside products. These results showed that both catalytic residues in PaGT2 actively and independently catalyze glucosylation, hence we called PaGT2 as an ambidextrous UGT. The information from PaGT2 will be advantageous for the engineering of efficient biocatalysts for production of therapeutic polyphenols.
In the absence of reproductive isolation – Extensive gene flow after speciation
Authors: Wang Xinfeng , Guo Zixiao , He Ziwen , Xu Shaohua , Shao Shao , Li Sen , Yang Ming , Chen Qipian , Zhong Cairong , Wu Zhongyi , Duke Norman C. , Shi Suhua
Published: April 2019

In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). However, species may also be delineated by merely a small set of “speciation genes” without full RI. It is thus important to know whether “good species” (defined by the “secondary sympatry” test) do continue to exchange genes. Here, we carry out sequencing andde novohigh-quality assembly of the genomes of two closely related mangrove species (Rhizophora mucronataandR. stylosa). Whole-genome re-sequencing of individuals across their range on the tropical coasts shows their genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species in contact. Nevertheless, their genomes harbor ∼ 4,000 to 10,000 introgression blocks, each averaging only about 3-4 Kb. These fine-grained introgressions indicate that gene flow has continued long after speciation. Non-introgressable “genomic islets,” averaging only 1.4 Kb, may contribute to speciation as they often harbor diverging genes underlying flower development and gamete production. In conclusion, RI needs not be the main criterion of species delineation even though all species would eventually be fully reproductively isolated.
Genetic diversity and domestication of hazelnut (Corylus avellana) in Turkey
Authors: Helmstetter Andrew J. , Oztolan-Erol Nihal , Lucas Stuart J. , Buggs Richard J. A.
Published: April 2019

Assessing and describing genetic diversity in crop plants is a crucial first step towards their improvement. The European hazelnut, Corylus avellana, is one of the most economically important tree nut crops worldwide. It is primarily produced in Turkey where rural communities depend on it for their livelihoods. Despite this we know little about hazelnut’s domestication history and the genetic diversity it holds.

We use double digest Restriction-site Associated DNA (ddRAD) sequencing to produce genome-wide dataset containing wild and domesticated hazelnut. We uncover patterns of population structure and diversity, determine levels of crop-wild gene flow and estimate the timing of key divergence events.

We find that genetic clusters of cultivars do not reflect their given names and that there is limited evidence for a reduction in genetic diversity in domesticated individuals. Admixture has likely occurred multiple times between wild and domesticated hazelnut. Domesticates appear to have first diverged from their wild relatives during the Mesolithic.

We provide the first genomic assessment of Turkish hazelnut diversity and suggest that it is currently in a partial stage of domestication. Our study provides a platform for further research that will protect this crop from the threats of climate change and an emerging fungal disease.
Decomposing variation in immune response in a wild rodent population
Authors: Wanelik Klara M. , Begon Mike , Arriero Elena , Bradley Janette E. , Friberg Ida M. , Jackson Joseph A. , Taylor Christopher H. , Paterson Steve
Published: April 2019

Individuals vary in their immune response and, as a result, some are more susceptible to infectious disease than others. Little is known about which components of immune pathways are responsible for this variation, but understanding these underlying processes could allow us to predict the outcome of infection for an individual, and to manage their health more effectively. In this study, we describe transcriptome-wide variation in immune response (to a standardised challenge) in a wild population of field voles (Microtus agrestis). We find that this variation can be categorised into three main types. We also identify markers, across these three categories, which display particularly strong individual variation in response. This work shows how a simple standardised challenge performed on a natural population can reveal complex patterns of natural variation in immune response.
DNA barcode-guided lentiviral CRISPRa tool to trace and isolate individual clonal lineages in heterogeneous cancer cell populations
Authors: Akimov Y , Bulanova D , Abyzova M , Wennerberg K , Aittokallio T
Published: April 2019

The genetic and functional heterogeneity of tumors imposes the challenge of understanding how a cancer progresses, evolves and adapts to treatment at the subclonal level. Therefore, there is a critical need for methods that enable profiling of individual cancer cell lineages. Here, we report a novel system that couples an established DNA barcoding technique for lineage tracing with a controlled DNA barcode-guided lineage isolation (B-GLI). B-GLI allows both high-complexity of lineage tracing and effective isolation of individual clones by CRISPRa-mediated induction of puromycin resistance, making it possible to unbiasedly trace, isolate, and study individual cancer cell lineages. We present experimental evaluation of the system performance in isolation of lineages and outline a comprehensive workflow for B-GLI applications. We believe the system has broad applications aimed at molecular and phenotypic profiling of individual lineages in heterogeneous cell populations.