bluuebunny/crossref_metadata_2025_split huggingface dataset:
Red flowers differ in shades between pollination systems and across continents
Authors: Chen Zhe , Niu Yang , Liu Chang-Qiu , Sun Hang 
Published: May 2020

AbstractBackground and AimsFloral colour is a primary signal in plant–pollinator interactions. The association between red flowers and bird pollination is well known, explained by the ‘bee avoidance’ and ‘bird attraction’ hypotheses. Nevertheless, the relative importance of these two hypotheses has rarely been investigated on a large scale, even in terms of colour perception per se.MethodsWe collected reflectance spectra for 130 red flower species from different continents and ascertained their pollination systems. The spectra were analysed using colour vision models for bees and (three types of) birds, to estimate colour perception by these pollinators. The differences in colour conspicuousness (chromatic and achromatic contrast, purity) and in spectral properties between pollination systems and across continents were analysed.Key ResultsCompared with other floral colours, red flowers are very conspicuous to birds and much less conspicuous to bees. The red flowers pollinated by bees and by birds are more conspicuous to their respective pollinators. Compared with the bird flowers in the Old World, the New World ones are less conspicuous to bees and may be more conspicuous not only to violet-sensitive but also to ultraviolet-sensitive birds. These differences can be explained by the different properties of the secondary reflectance peak (SP). SP intensity is higher in red flowers pollinated by bees than those pollinated by birds (especially New World bird flowers). A transition from high SP to low SP in red flowers can induce chromatic contrast changes, with a greater effect on reducing attraction to bees than enhancing attraction to birds.ConclusionsShades of red flowers differ between pollination systems. Moreover, red bird flowers are more specialized in the New World than in the Old World. The evolution towards colour specialization is more likely to result in higher efficiency of bee avoidance than bird attraction
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons
Authors: Wei Xiaoqiong , Zhang Chengxin , Freddolino Peter L , Zhang Yang 
Published: May 2020

Abstract

Motivation
Many protein function databases are built on automated or semi-automated curations and can contain various annotation errors. The correction of such misannotations is critical to improving the accuracy and reliability of the databases.

Results
We proposed a new approach to detect potentially incorrect Gene Ontology (GO) annotations by comparing the ratio of annotation rates (RAR) for the same GO term across different taxonomic groups, where those with a relatively low RAR usually correspond to incorrect annotations. As an illustration, we applied the approach to 20 commonly studied species in two recent UniProt-GOA releases and identified 250 potential misannotations in the 2018-11-6 release, where only 25% of them were corrected in the 2019-6-3 release. Importantly, 56% of the misannotations are ‘Inferred from Biological aspect of Ancestor (IBA)’ which is in contradiction with previous observations that attributed misannotations mainly to ‘Inferred from Sequence or structural Similarity (ISS)’, probably reflecting an error source shift due to the new developments of function annotation databases. The results demonstrated a simple but efficient misannotation detection approach that is useful for large-scale comparative protein function studies.

Availability and implementation
https://zhanglab.ccmb.med.umich.edu/RAR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Role of AMP-activated protein kinase during postovulatory aging of mouse oocytes†
Authors: Sun Guang-Yi , Gong Shuai , Kong Qiao-Qiao , Li Zhi-Bin , Wang Jia , Xu Ming-Tao , Luo Ming-Jiu , Tan Jing-He 
Published: May 2020

Abstract
Studies suggested that postovulatory oocyte aging might be prevented by maintaining a high maturation-promoting factor (MPF) activity. Whether AMP-activated protein kinase (AMPK) plays any role in postovulatory oocyte aging is unknown. Furthermore, while activation of AMPK stimulates meiotic resumption in mouse oocytes, it inhibits meiotic resumption in pig and bovine oocytes. Thus, the species difference in AMPK regulation of oocyte MPF activities is worth in-depth studies. This study showed that AMPK activation with metformin or 5-aminoimidazole- 4-carboxamide- 1-beta-d- ribofuranoside and inactivation with compound C significantly increased and decreased, respectively, the activation susceptibility (AS) and other aging parameters in aging mouse oocytes. While AMPK activity increased, MPF activity and cyclic adenosine monophosphate (cAMP) decreased significantly with time post ovulation. In vitro activation and inactivation of AMPK significantly decreased and increased the MPF activity, respectively. MPF upregulation with MG132 or downregulation with roscovitine completely abolished the effects of AMPK activation or inactivation on AS of aging oocytes, respectively. AMPK facilitated oocyte aging with increased reactive oxygen species (ROS) and cytoplasmic calcium. Furthermore, treatment with Ca2+/calmodulin-dependent protein kinase (CaMK) inhibitors significantly decreased AS and AMPK activation. Taken together, the results suggested that AMPK facilitated oocyte aging through inhibiting MPF activities, and postovulatory oocyte aging activated AMPK with decreased cAMP by activating CaMKs via increasing ROS and cytoplasmic calcium.
Environmental Factors Shape Sleep EEG Connectivity During Early Adolescence
Authors: Markovic Andjela , Kaess Michael , Tarokh Leila 
Published: May 2020

Abstract
Quantifying the degree to which genetic and environmental factors shape brain network connectivity is critical to furthering our understanding of the developing human brain. Sleep, a state of sensory disengagement, provides a unique opportunity to study brain network activity noninvasively by means of sleep electroencephalography (EEG) coherence. We conducted a high-density sleep EEG study in monozygotic (MZ; n = 38; mean age = 12.46; 20 females) and dizygotic (DZ; n = 24; mean age = 12.50; 12 females) twins to assess the heritability of sleep EEG coherence in early adolescence—a period of significant brain rewiring. Structural equation modeling was used to estimate three latent factors: genes, environmental factors shared between twins and environmental factors unique to each twin. We found a strong contribution of unique environmental factors (66% of the variance) and moderate genetic influence (19% of the variance) on sleep EEG coherence across frequencies and sleep states. An exception to this was sleep spindle activity, an index of the thalamocortical network, which showed on average a genetic contribution of 48% across connections. Furthermore, we observed high intraindividual stability of coherence across two consecutive nights suggesting that despite only a modest genetic contribution, sleep EEG coherence is like a trait. Our findings in adolescent humans are in line with earlier findings in animals that show the primordial cerebral map and its connections are plastic and it is through interaction with the environment that the pattern of brain network connectivity is shaped. Therefore, even in twins living together, small differences in the environment may cascade into meaningful differences in brain connectivity.
Lower Rate of Seropositivity to Measles Among Young Healthcare Personnel in New York City
Authors: Lucca Anabella , Bayoumi Nagla , Ramanathan Lakshmi V , Sepkowitz Kent , Kamboj Mini 
Published: May 2020

Abstract
We examined the prevalence of measles antibody among 12 349 newly hired HCP between 2009 and 2019. Younger HCP were significantly more likely to have no immunity. Compared with a 92.2% seropositive rate among 1057 persons hired at age &gt;50 years, only 84.4% of approximately 10 000 HCP aged &lt;40 years had protective antibody.
Gut Microbiota Features on Nursing Home Admission Are Associated With Subsequent Acquisition of Antibiotic-resistant Organism Colonization
Authors: Wang Joyce , Cassone Marco , Gibson Kristen , Lansing Bonnie , Mody Lona , Snitkin Evan S , Rao Krishna 
Published: May 2020

Abstract
Nursing home (NH) patients often acquire colonization with antibiotic-resistant organisms (AROs). We show that patients exposed to broad-spectrum antibiotics during previous hospitalizations have elevated enterococcal relative abundances on NH admission and higher risk of subsequent ARO acquisition. Our findings suggest that interventions preventing ARO spread should extend beyond NH doors.
Within-Season Producer Response to Warmer Temperatures: Defensive Investments by Kenyan Farmers
Authors: Jagnani Maulik , Barrett Christopher B , Liu Yanyan , You Liangzhi 
Published: May 2020

AbstractWe present evidence that farmers adjust agricultural inputs in response to within-season temperature variation, undertaking defensive investments to reduce the adverse agro-ecological impacts of warmer temperatures. Using panel data from Kenyan maize-growing households, we find that higher temperatures early in the growing season increase the use of pesticides, while reducing fertiliser use. Warmer temperatures throughout the season increase weeding effort. These adjustments arise because greater heat increases the incidence of pests, crop diseases and weeds, compelling farmers to divert investment from productivity-enhancing technologies such as fertiliser to adaptive, loss-reducing, defensive inputs such as pesticides and weeding labour.
Reproductive system infections in women: upper genital tract, fetal, neonatal and infant syndromes
Authors: Brunham Robert C , Paavonen Jorma 
Published: May 2020

ABSTRACT
Lower genital tract infection and bloodborne spread of infection are the two principal modes for infection of the upper genital tract or for infection of the fetus, neonate or infant. Treponema pallidum and human immunodeficiency virus (HIV) are the two most common bloodborne pathogens that infect the fetus, neonate or infant. Most infections of the upper genital tract, however, spread along epithelial surfaces from the vagina or cervix to the upper genital tract or chorioamnion, fetus, neonate or infant. These infections are caused by either pathogens associated with a dysbiotic vaginal microbiome or those that are sexually transmitted. The clinical syndromes that these pathogens produce in the lower genital tract were discussed in part one of this review. We now discuss the syndromes and pathogens that affect the upper genital tract of both non-pregnant and pregnant women as well as fetus, neonate and infant.
Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets
Authors: Smith Brian Tilston , Mauck William M , Benz Brett W , Andersen Michael J 
Published: May 2020

Abstract
The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9× more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.
Prediction of Balance Perturbations and Falls on Stairs in Older People Using a Biomechanical Profiling Approach: A 12-Month Longitudinal Study
Authors: Ackermans Thijs , Francksen Natasha , Lees Carolyn , Papatzika Fyllis , Arampatzis Adamantios , Baltzopoulos Vasilios , Lisboa Paulo , Hollands Mark , O’Brien Thomas , Maganaris Constantinos 
Published: May 2020

Abstract

Background
Stair falls are a major health problem for older people, but presently, there are no specific screening tools for stair fall prediction. The purpose of the present study was to investigate whether stair fallers could be differentiated from nonfallers by biomechanical risk factors or physical/psychological parameters and to establish the biomechanical stepping profile posing the greatest risk for a stair fall.

Methods
Eighty-seven older adults (age: 72.1 ± 5.2 years) negotiated an instrumented seven-step staircase and performed a range of physical/psychological tasks. k-Means clustering was used to profile the overall stair negotiation behavior with biomechanical parameters indicative of fall risk as input. Falls and events of balance perturbation (combined “hazardous events”) were then monitored during a 12-month follow-up. Cox-regression analysis was performed to examine whether physical/psychological parameters or biomechanical outcome measures could predict future hazardous events. Kaplan–Meier survival curves were obtained to identify the stepping strategy posing a risk for a hazardous event.

Results
Physical/psychological parameters did not predict hazardous events and the commonly used Fall Risk Assessment Tool classified only 1/17 stair fallers at risk for a fall. Single biomechanical risk factors could not predict hazardous events on stairs either. On the contrary, two particular clusters identified by the stepping profiling method in stair ascent were linked with hazardous events.

Conclusion
This highlights the potential of the stepping profiling method to predict stair fall risk in older adults against the limited predictability of single-parameter approaches currently used as screening tools.
The challenges of detecting and attributing ocean acidification impacts on marine ecosystems
Authors: Doo Steve S , Kealoha Andrea , Andersson Andreas , Cohen Anne L , Hicks Tacey L , Johnson Zackary I , Long Matthew H , McElhany Paul , Mollica Nathaniel , Shamberger Kathryn E F , Silbiger Nyssa J , Takeshita Yuichiro , Busch D Shallin 
Published: May 2020

AbstractA substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
The use of extracorporeal membrane oxygenation in the setting of postinfarction mechanical complications: outcome analysis of the Extracorporeal Life Support Organization Registry
Authors: Matteucci Matteo , Fina Dario , Jiritano Federica , Meani Paolo , Raffa Giuseppe Maria , Kowalewski Mariusz , Aldobayyan Ibrahim , Turkistani Mohammad , Beghi Cesare , Lorusso Roberto 
Published: May 2020

Abstract

OBJECTIVES
Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) has been recently considered and used for patients with post-acute myocardial infarction mechanical complications (post-AMI MC); however, information in this respect is scarce. The purpose of this study was to evaluate the in-hospital outcomes of patients with post-AMI MC submitted to VA-ECMO, and enrolled in the Extracorporeal Life Support Organizations (ELSO)’s data Registry.

METHODS
This was a retrospective review of the ELSO Registry to identify adult (&gt;18 years old) patients with post-AMI MC who underwent VA-ECMO support between 2007 and 2018. The primary end point of this study was in-hospital survival. ECMO complications were also evaluated.

RESULTS
The patient cohort available for this study included 158 patients. The median age was 62.4 years (range 20–80). The most common post-AMI MC was ventricular septal rupture (n = 102; 64.5%), followed by papillary muscle rupture (n = 42; 26.6%) and ventricular free-wall rupture (n = 14; 8.9%). Approximately a quarter of patients (n = 41; 25.9%) had cardiac arrest before VA-ECMO institution. The median duration of VA-ECMO was 5.9 days (range 1 h–40.3 days). ECMO complications occurred in 119 patients (75.3%). Overall, survival to hospital discharge for the entire patient cohort was 37.3%. Patients who had ventricular septal rupture as primary diagnosis had higher in-hospital mortality (n = 66; 64.7%).

CONCLUSIONS
In patients with post-AMI MC, VA-ECMO provides haemodynamic stabilizations and carries a potential to reverse otherwise lethal course. ECMO complications, however, remain an important limitation. Further investigations are required to better evaluate the efficacy and safety of ECMO in this context.
A 0.6-protamine/heparin ratio in cardiac surgery is associated with decreased transfusion of blood products
Authors: Goedhart Anne L M , Gerritse Bastiaan M , Rettig Thijs C D , van Geldorp Martijn W A , Bramer Sander , van der Meer Nardo J M , Boonman-de Winter Leandra J , Scohy Thierry V 
Published: May 2020

Abstract

OBJECTIVES
In cardiac surgery, adequate heparinization is necessary to prevent thrombus formation in the cardiopulmonary bypass (CPB). To counteract the heparin effect after weaning from CPB, protamine is administered. The optimal protamine/heparin ratio is still unknown.

METHODS
In this before–after study, we evaluated the effect of a 0.6/1-protamine/heparin ratio implementation as of May 2017 versus a 0.8/1-protamine/heparin ratio on the 12-h postoperative blood loss and the amount of blood and blood component transfusions (fresh frozen plasma, packed red blood cells, fibrinogen concentrate, platelet concentrate and prothrombin complex concentrate) after cardiac surgery. A total of 2051 patients who underwent cardiac surgery requiring CPB between May 2016 and May 2018 were included.

RESULTS
In the 0.6/1-protamine/heparin ratio group, only 28.8% of the patients received blood component transfusion, compared to 37.9% of the patients in the 0.8/1-ratio group (P &lt; 0.001). The median 12-h postoperative blood loss was 230 ml (interquartile range 140–320) in the 0.6/1-ratio group versus 260 ml (interquartile range 155–365) in the 0.8/1-ratio group (P &lt; 0.001).

CONCLUSIONS
A 0.6/1-protamine/heparin ratio after weaning from CPB is associated with a significantly reduced 12-h postoperative blood loss and blood components transfusion.
Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial
Authors: Novitsky Vlad , Zahralban-Steele Melissa , Moyo Sikhulile , Nkhisang Tapiwa , Maruapula Dorcas , McLane Mary Fran , Leidner Jean , Bennett Kara ,   PANGEA Consortium, Abeler-Dörner Lucie , Bonsall David , Fraser Christophe , Golubchik Tanya , Ayles Helen , Bowden Rory , Calvez Vincent , Fidler Sarah , Grabowski Kate , Kagaayi Joseph , Hayes Richard , Seeley Janet , Herbeck Joshua , Lingappa Jairam , Kaleebu Pontiano , Ssemwanga Deogratius , Pillay Deenan , Tanser Frank , Quinn Thomas , Rambaut Andrew , Leigh-Brown Andrew , Ratmann Oliver , Wawer Maria , Cohen Myron , Dennis Ann , D’Oliveira Tulio , Frampton Dan , Hoppe Anne , Kellam Paul , Kityo Cissy , Paton Nick , Wirth Kathleen E , Gaolathe Tendani , Kadima Etienne , Chakalisa Unoda , Pretorius Holme Molly , Lockman Shahin , Mmalane Mompati , Makhema Joseph , Gaseitsiwe Simani , DeGruttola Victor , Essex M 
Published: May 2020

AbstractBackgroundPhylogenetic mapping of HIV-1 lineages circulating across defined geographical locations is promising for better understanding HIV transmission networks to design optimal prevention interventions.MethodsWe obtained near full-length HIV-1 genome sequences from people living with HIV (PLWH), including participants on antiretroviral treatment in the Botswana Combination Prevention Project, conducted in 30 Botswana communities in 2013–2018. Phylogenetic relationships among viral sequences were estimated by maximum likelihood.ResultsWe obtained 6078 near full-length HIV-1C genome sequences from 6075 PLWH. We identified 984 phylogenetically distinct HIV-1 lineages (molecular HIV clusters) circulating in Botswana by mid-2018, with 2–27 members per cluster. Of these, dyads accounted for 62%, approximately 32% (n = 316) were found in single communities, and 68% (n = 668) were spread across multiple communities. Men in clusters were approximately 3 years older than women (median age 42 years, vs 39 years; P &lt; .0001). In 65% of clusters, men were older than women, while in 35% of clusters women were older than men. The majority of identified viral lineages were spread across multiple communities.ConclusionsA large number of circulating phylogenetically distinct HIV-1C lineages (molecular HIV clusters) suggests highly diversified HIV transmission networks across Botswana communities by 2018.