bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of the relative richness of naturalized and invasive plant species on Earth
Authors: Essl Franz , Dawson Wayne , Kreft Holger , Pergl Jan , Pyšek Petr , Van Kleunen Mark , Weigelt Patrick , Mang Thomas , Dullinger Stefan , Lenzner Bernd , Moser Dietmar , Maurel Noëlie , Seebens Hanno , Stein Anke , Weber Ewald , Chatelain Cyrille , Inderjit  , Genovesi Piero , Kartesz John , Morozova Olga , Nishino Misako , Nowak Pauline M , Pagad Shyama , Shu Wen-Sheng , Winter Marten 
Published: August 2019

AbstractBiological invasions are a defining feature of the Anthropocene, but the factors that determine the spatially uneven distribution of alien plant species are still poorly understood. Here, we present the first global analysis of the effects of biogeographic factors, the physical environment and socio-economy on the richness of naturalized and invasive alien plants. We used generalized linear mixed-effects models and variation partitioning to disentangle the relative importance of individual factors, and, more broadly, of biogeography, physical environment and socio-economy. As measures of the magnitude of permanent anthropogenic additions to the regional species pool and of species with negative environmental impacts, we calculated the relative richness of naturalized (= RRN) and invasive (= RRI) alien plant species numbers adjusted for the number of native species in 838 terrestrial regions. Socio-economic factors (per-capita gross domestic product (GDP), population density, proportion of agricultural land) were more important in explaining RRI (~50 % of the explained variation) than RRN (~40 %). Warm-temperate and (sub)tropical regions have higher RRN than tropical or cooler regions. We found that socio-economic pressures are more relevant for invasive than for naturalized species richness. The expectation that the southern hemisphere is more invaded than the northern hemisphere was confirmed only for RRN on islands, but not for mainland regions nor for RRI. On average, islands have ~6-fold RRN, and >3-fold RRI compared to mainland regions. Eighty-two islands (=26 % of all islands) harbour more naturalized alien than native plants. Our findings challenge the widely held expectation that socio-economic pressures are more relevant for plant naturalization than for invasive plants. To meet international biodiversity targets and halt the detrimental consequences of plant invasions, it is essential to disrupt the connection between socio-economic development and plant invasions by improving pathway management, early detection and rapid response.
What makes motion dazzle markings effective against predation?
Authors: Kodandaramaiah Ullasa , Palathingal Shuaib , Bindu Kurup Gayathri , Murali Gopal 
Published: August 2019

AbstractMotion dazzle markings comprise patterns such as stripes and zig-zags that are postulated to protect moving prey by making predators misjudge the prey’s speed or trajectory. Recent experiments have provided conflicting results on their effect on speed perception and attack success. We focus on motion dazzle stripes and investigate the influence of four parameters—stripe orientation, stripe contrast, target size, and target speed—on perceived speed and attack success using a common experimental paradigm involving human “predators” attacking virtual moving targets on a computer touchscreen. We found that high-contrast stripes running parallel or perpendicular to the direction of motion reduce attack success compared to conspicuous uniform targets. Surprisingly, parallel stripes induced underestimation of speed, while perpendicular stripes induced overestimation of speed in relation to uniform black, suggesting that misjudgment of speed per se is sufficient to reduce attack accuracy. Across all the experiments, we found some support for parallel stripes inducing underestimation of target speed but these stripes reduced attack success only when targets were small, moved at an intermediate speed, and had high internal contrast. We suggest that prey features (e.g., size or speed) are an important determinant of capture success and that distortion of speed perception by a color pattern does not necessarily translate to reduced capture success of the prey. Overall, our results support the idea that striped patterns in prey animals can reduce capture in motion but are effective under a limited set of conditions.
HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs
Authors: Whitwell Harry J , DiMaggio Peter 
Published: August 2019

Abstract

Motivation
Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy/light pair are assigned. In such cases, having a pair of MS/MS spectra that differ due to an isotopic label can assist in identifying the relevant m/z values that support the correct peptide annotation or can be used for de novo sequencing.

Results
We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS/MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra. The result is a tool to visually compare two spectra, and downloadable peaks lists that can be used to support de novo sequencing.

Availability and implementation
HiLight-PTM is released using shinyapps.io by RStudio, and can be accessed from any internet browser at https://harrywhitwell.shinyapps.io/hilight-ptm/.

Supplementary information
Supplementary data are available at Bioinformatics online.
CRDS: Consensus Reverse Docking System for target fishing
Authors: Lee Aeri , Kim Dongsup 
Published: August 2019

AbstractMotivationIdentification of putative drug targets is a critical step for explaining the mechanism of drug action against multiple targets, finding new therapeutic indications for existing drugs and unveiling the adverse drug reactions. One important approach is to use the molecular docking. However, its widespread utilization has been hindered by the lack of easy-to-use public servers. Therefore, it is vital to develop a streamlined computational tool for target prediction by molecular docking on a large scale.ResultsWe present a fully automated web tool named Consensus Reverse Docking System (CRDS), which predicts potential interaction sites for a given drug. To improve hit rates, we developed a strategy of consensus scoring. CRDS carries out reverse docking against 5254 candidate protein structures using three different scoring functions (GoldScore, Vina and LeDock from GOLD version 5.7.1, AutoDock Vina version 1.1.2 and LeDock version 1.0, respectively), and those scores are combined into a single score named Consensus Docking Score (CDS). The web server provides the list of top 50 predicted interaction sites, docking conformations, 10 most significant pathways and the distribution of consensus scores.Availability and implementationThe web server is available at http://pbil.kaist.ac.kr/CRDS.Supplementary informationSupplementary data are available at Bioinformatics online.
Monocentric chromosomes in Juncus (Juncaceae) and implications for the chromosome evolution of the family
Authors: Guerra Marcelo , Ribeiro Tiago , Felix Leonardo P 
Published: August 2019

AbstractHolocentric chromosomes are rare among angiosperms, but have been suggested to be shared by all or most of the species of Cyperaceae and Juncaceae. However, no clear demonstration of the centromere type in Juncus, the largest genus of Juncaceae, has so far been published. Thus, we conducted a detailed chromosomal investigation of four Juncus spp. aiming to identify their centromere type. Mitotic chromosomes were analysed using the fluorochromes CMA and DAPI, fluorescent in situ hybridization (FISH) with rDNA probes and immunodetection of histones H3 phosphorylated at serine 10 (H3-S10ph) and H2A phosphorylated at threonine 133 (H2A-T133ph). DAPI-stained chromosomes of all species displayed typical primary constrictions, which were not related to AT-poor CMA+ heterochromatin or rDNA sites (usually negatively stained with DAPI). Immunodetection with H3-S10ph and H2A-T133ph revealed hyperphosphorylation of pericentromeric and centromeric regions, respectively, in a restricted area, as observed in monocentric chromosomes. Meiotic analyses in J. microcephalus showed no indication of inverted meiosis, commonly found in plants with holocentric chromosomes. Since the species investigated here belong to four different sections of Juncus and all of them display typical monocentric chromosomes, it seems that this kind of centromere is common in the genus and may represent the standard centromere organization for Juncus. If Juncus has monocentric chromosomes, there is no reason to hypothesize that other genera of Juncaceae for which centromeres have not been carefully investigated have holocentric chromosomes.
A Desirable Future: Uber as Image-Making in Winnipeg
Authors: Gibbings Sheri L , Taylor Jessica 
Published: August 2019

AbstractThis paper investigates the sociotechnical imaginary surrounding Uber’s supposedly imminent arrival in Winnipeg, through an examination of communication in the public sphere. We examine how actors mobilized their communicative resources in efforts to either bring ride-hailing or keep it away. For some advocates, ride-hailing technology was less important than Uber’s symbolic value of building Winnipeg’s image as an innovative city. Media coverage contrasted innovation and Uber with Winnipeg’s anxieties about being behind other cities and its taxi industry’s reputation as stuck in the past. These visions of Winnipeg’s future addressed an unspoken White, middle-class city dweller. While Winnipeg’s transportation industry was shaped by the socially located experiences of racialized immigrant men as taxi drivers and Indigenous women as passengers, these actors had less power to shape the imaginary. Our analysis suggests that cities like Winnipeg view Uber as an image-making product as much as a beneficial service for their citizens.
Tight Coupling between Morphological Features of the Central Sulcus and Somatomotor Body Representations: A Combined Anatomical and Functional MRI Study
Authors: Germann Jürgen , Chakravarty M Mallar , Collins D Louis , Petrides Michael 
Published: August 2019

Abstract
Pioneering research established the concept of somatotopic organization of the primary motor and somatosensory cortex along the central sulcus as depicted in the widely known schematic illustration (the “homunculus”) by Penfield and colleagues. With the exception of the hand, however, a precise relationship between morphological features of the central sulcus and the representation of various parts of the body has not been addressed. To investigate whether such relations between anatomical features and functional body representations exist, we first examined central sulcus morphology in detail and then conducted a functional magnetic resonance imaging experiment to establish somatomotor representations. This study established that the central sulcus is composed of five distinct sulcal segments and demonstrated that each segment relates systematically to the sensorimotor representation of distinct parts of the body. Thus, local morphology predicts the localization of body representations with precision, raising fundamental questions regarding functional and morphological differentiation.
What Do We Really Know about the Transatlantic Current Account?
Authors: Braml Martin T , Felbermayr Gabriel J 
Published: August 2019

Abstract
Do the USA have a current account surplus or a deficit with the EU? Since 2009, official sources disagree: The U.S. Department of Commerce claims a consistent US surplus while Eurostat reports the opposite. International transactions are notoriously difficult to measure accurately, but the size of the transatlantic discrepancy is extremely substantial: over the last 10 years, it has grown to a cumulated 1 Trillion USD. In times of severe trade policy disagreements across the Atlantic, this gap is obviously problematic. This article tries to dissect the transatlantic reporting gap. Two country-pairs—USA-UK and USA-Netherlands—account for almost the entire transatlantic discrepancy, which, in 2017, stood at about 180 billion USD. In the former case, national statistics on net services trade disagree by as much as 55 billion USD; in the latter case, there is a reporting difference in net primary income of about 60 billion USD. In contrast, data provided by the Bundesbank for the German-US current account closely mirror US data. Nonrandom measurement error and, possibly, deliberate manipulation seem to cause the observed discrepancies. (JEL codes: F14, F32, H26)
Polypharmacy and Drug–Drug Interactions in People Living With Human Immunodeficiency Virus in the Region of Madrid, Spain: A Population-Based Study
Authors: López-Centeno Beatriz , Badenes-Olmedo Carlos , Mataix-Sanjuan Ángel , McAllister Katie , Bellón José M , Gibbons Sara , Balsalobre Pascual , Pérez-Latorre Leire , Benedí Juana , Marzolini Catia , Aranguren-Oyarzábal Ainhoa , Khoo Saye , Calvo-Alcántara María J , Berenguer Juan 
Published: August 2019

Abstract

Background
Drug–drug interactions (DDIs) that involve antiretrovirals (ARVs) tend to cause harm if unrecognized, especially in the context of comorbidity and polypharmacy.

Methods
A linkage was established between the drug dispensing registry of Madrid and the Liverpool human immunodeficiency virus (HIV) DDI database (January 2017–June 2017). Polypharmacy was defined as the use of ≥5 non-HIV medications, and DDIs were classified by a traffic-light ranking for severity.

Results
A total of 22 945 people living with HIV (PLWH) and 6 613 506 individuals without HIV had received medications. ARV regimens were predominantly based on integrase inhibitors (51.96%). Polypharmacy was higher in PLWH (32.94%) than individuals without HIV (22.16%; P &lt; .001); this difference was consistently observed across all age strata except for individuals ≥75 years. Polypharmacy was more common in women than men in both PLWH and individuals without HIV. The prevalence of contraindicated combinations involving ARVs was 3.18%. Comedications containing corticosteroids, quetiapine, or antithrombotic agents were associated with the highest risk for red-flag DDI, and the use of raltegravir- or dolutegravir-based antiretroviral therapy was associated with an adjusted odds ratio of 0.72 (95% confidence interval, .60–.88; P = .001) for red-flag DDI.

Conclusions
Polypharmacy was more frequent among PLWH across all age groups except those aged ≥75 years and was more common in women. The detection of contraindicated medications in PLWH suggests a likely disconnect between hospital and community prescriptions. Switching to alternative unboosted integrase regimens should be considered for patients with risk of harm from DDIs.
Determinants of Latent Tuberculosis Treatment Acceptance and Completion in Healthcare Personnel
Authors: Swift Melanie D , Molella Robin G , Vaughn Andrew I S , Breeher Laura E , Newcomb Richard D , Abdellatif Shahnaz , Murad M Hassan 
Published: August 2019

Abstract

Background
US public health strategy for eliminating tuberculosis (TB) prioritizes treatment of latent TB infection (LTBI). Healthcare personnel (HCP) are less willing to accept treatment than other populations. Little is known about factors associated with HCP LTBI therapy acceptance and completion.

Methods
We conducted a retrospective chart review to identify all employees with LTBI at time of hire at a large academic medical center during a 10-year period. Personal demographics, occupational factors, and clinic visit variables were correlated with LTBI treatment acceptance and completion rates using multivariate logistic regression.

Results
Of 470 HCP with LTBI for whom treatment was recommended, 193 (41.1%) accepted treatment, while 137 (29.1%) completed treatment. Treatment adherence was better with 4 months of rifampin than 9 months of isoniazid (95% vs 68%, P &lt; .005). Increased age of the healthcare worker was independently associated with lower rates of treatment acceptance (odds ratio [95% confidence interval]: 0.97 [0.94–0.99] per year), as was having an occupation of clinician (0.47 [0.26–0.85]) or researcher (0.34 [0.19–0.64]). Male gender was associated with higher treatment acceptance (1.90 [1.21–2.99]). Treatment completion was associated with being from a low- (9.49 [2.06–43.73]) or medium- (8.51 [3.93–18.44]) TB-burden country.

Conclusions
Geographic and occupational factors affect acceptance and completion of LTBI therapy. Short-course regimens may improve adherence. Physicians, researchers, and HCP from high-TB-burden countries have lower treatment rates than other HCP. Improving LTBI treatment in HCP will require attending to cultural and occupational differences.
Sex steroid hormones and behavior reveal seasonal reproduction in a resident fin whale population
Authors: Carone Erica , Pardo Mario A , Atkinson Shannon , Mashburn Kendall , Pérez-Puig Héctor , Enríquez-Paredes Luis , Gendron Diane 
Published: August 2019

AbstractFin whales in the Gulf of California constitute a resident population genetically isolated from the rest of the North Pacific Ocean. Its small population size and the scarce information available about its dynamics in a semi-enclosed sea underline the importance of conducting studies about its reproduction. Given the monsoonal regime that dominates the oceanographic habitat of this region, we hypothesized seasonality in the population’s reproductive activity. To test this, we validated and assayed testosterone and progesterone from blubber biopsies of free-ranging individuals. Lactating females exhibited low progesterone concentrations, whereas a group of females of unknown reproductive stage, but with extremely high progesterone concentrations, showed strong evidence of separation and were considered to be likely ovulating or pregnant. A seasonal model of testosterone concentrations showed a high peak during the late summer. This trend was supported by the first documentation of courtship events and by the recording of a female with high progesterone concentration during summer and re-sighted with a calf 1 year later. Therefore, the breeding in this resident population would be seasonal, as it is in migratory baleen whales, but occurring during the summer/autumn, which is the least productive season in the Gulf of California. Our study represents an important input to assist in future management policies of this protected population.
Fasting in the ureotelic Lake Magadi tilapia, Alcolapia grahami, does not reduce its high metabolic demand, increasing its vulnerability to siltation events
Authors: De Boeck Gudrun , Wood Chris M , Brix Kevin V , Sinha Amit K , Matey Victoria , Johannsson Ora E , Bianchini Adalto , Bianchini Lucas F , Maina John N , Kavembe Geraldine D , Papah Michael B , Kisipan Mosiany L , Ojoo Rodi O 
Published: August 2019

AbstractLake Magadi, Kenya, is one of the most extreme aquatic environments on Earth (pH~10, anoxic to hyperoxic, high temperatures). Recently, increased water demand and siltation have threatened the viable hot springs near the margins of the lake where Alcolapia grahami, the only fish surviving in the lake, live. These Lake Magadi tilapia largely depend on nitrogen-rich cyanobacteria for food and are 100% ureotelic. Their exceptionally high aerobic metabolic rate, together with their emaciated appearance, suggests that they are energy-limited. Therefore, we hypothesized that during food deprivation, Magadi tilapia would economize their energy expenditure and reduce metabolic rate, aerobic performance and urea-N excretion. Surprisingly, during a 5-day fasting period, routine metabolic rates increased and swimming performance (critical swimming speed) was not affected. Urea-N excretion remained stable despite the lack of their N-rich food source. Their nitrogen use switched to endogenous sources as liver and muscle protein levels decreased after a 5-day fast, indicating proteolysis. Additionally, fish relied on carbohydrates with lowered muscle glycogen levels, but there were no signs indicating use of lipid stores. Gene expression of gill and gut urea transporters were transiently reduced as were gill rhesus glycoprotein Rhbg and Rhcg-2. The reduction in gill glutamine synthetase expression concomitant with the reduction in Rh glycoprotein gene expression indicates reduced nitrogen/ammonia metabolism, most likely decreased protein synthesis. Additionally, fish showed reduced plasma total CO2, osmolality and Na+ (but not Cl−) levels, possibly related to reduced drinking rates and metabolic acidosis. Our work shows that Lake Magadi tilapia have the capacity to survive short periods of starvation which could occur when siltation linked to flash floods covers their main food source, but their seemingly hardwired high metabolic rates would compromise long-term survival.
How free-ranging ungulates with differing water dependencies cope with seasonal variation in temperature and aridity
Authors: Boyers Melinda , Parrini Francesca , Owen-Smith Norman , Erasmus Barend F N , Hetem Robyn S 
Published: August 2019

AbstractLarge mammals respond to seasonal changes in temperature and precipitation by behavioural and physiological flexibility. These responses are likely to differ between species with differing water dependencies. We used biologgers to contrast the seasonal differences in activity patterns, microclimate selection, distance to potential water source and body temperature of the water-independent gemsbok (Oryx gazella gazella) and water-dependent blue wildebeest (Connochaetes taurinus), free-living in the arid Kalahari region of Botswana. Gemsbok were more active nocturnally during the hot seasons than in the cold-dry season, while wildebeest showed no seasonal difference in their nocturnal activity level. Both species similarly selected shaded microclimates during the heat of the day, particularly during the hot seasons. Wildebeest were further than 10 km from surface water 30% or more of the time, while gemsbok were frequently recorded >20 km from potential water sources. In general, both species showed similar body temperature variation with high maximum 24-h body temperature when conditions were hot and low minimum 24-h body temperatures when conditions were dry, resulting in the largest amplitude of 24-h body temperature rhythm during the hot-dry period. Wildebeest thus coped almost as well as gemsbok with the fairly typical seasonal conditions that occurred during our study period. They do need to access surface water and may travel long distances to do so when local water sources become depleted during drought conditions. Thus, perennial water sources should be provided judiciously and only where essential.