bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling Climate Change Impacts on an Arctic Polygonal Tundra: 1. Rates of Permafrost Thaw Depend on Changes in Vegetation and Drainage
Authors: Grant R. F. , Mekonnen Z. A. , Riley W. J.
Published: March 2019

Model projections of permafrost thaw during the next century diverge widely. Here we used ecosys to examine how climate change will affect permafrost thaw in a polygonal tundra at Barrow AK. The model was tested against diurnal and seasonal variation in energy exchange, soil heat flux, soil temperature (Ts), and active layer depth (ALD) measured during 2014 and 2015, and interannual variation in ALD measured from 1991 to 2015. During RCP 8.5 climate change from 2015 to 2085, increases in Ta and precipitation (P) to 6.2 °C and 27% above current values, and in atmospheric CO2 concentrations (Ca) to763 μmol mol−1, altered energy exchange by increasing leaf area index of dominant sedge relative to that of moss. Increased Ca and sedge leaf area index imposed greater stomatal control of transpiration and reduced soil heat fluxes, slowing soil warming, limiting increases in evapotranspiration, and thereby causing gradual soil wetting. Consequently, increases in surface Ts and ALD of 2.4–4.7 °C and 21–24 cm above current values were modeled after 70 years. ALD increase was slowed if model boundary conditions were altered to improve landscape drainage. These rates were smaller than those of earlier modeling studies, some of which did not account for changes in vegetation, but are closer to those derived from current studies of warming impacts in the region. Therefore, accounting for climate change effects on vegetation density and composition, and consequent effects on surface energy budgets, will cause slower increases in Ts and ALD to be modeled during climate change simulations.
A novel D–π–A blue fluorophore based on [1,2,4]triazolo[1,5-a]pyridine as an electron acceptor and its application in organic light-emitting diodes
Authors: Cao Chen , Chen Wen-Cheng , Tian Shuang , Chen Jia-Xiong , Wang Zhong-Yi , Zheng Xu-Hui , Ding Chong-Wei , Li Jing-Hong , Zhu Jie-Ji , Zhu Ze-Lin , Tong Qing-Xiao , Lee Chun-Sing
Published: March 2019

A novel luminophore based on [1,2,4]triazolo[1,5-a]pyridine has been utilized as an emitter and host for high-efficiency deep-blue fluorescence and orange phosphorescence OLEDs, respectively.
Ruthenium(ii)/acetate catalyzed intermolecular dehydrogenative ortho C–H silylation of 2-aryl N-containing heterocycles
Authors: Liu Shun , Lin Qiao , Liao Chunshu , Chen Jing , Zhang Kun , Liu Qiang , Li Bin
Published: March 2019

The application of a RuHCl(CO)(PPh3)3–OAc catalytic system for the selective intermolecular mono C–H silylation of 2-aryl heterocycles using HSiEt3 as the silylating reagent is described for the first time.
Achieving highly efficient CO2 to CO electroreduction exceeding 300 mA cm−2 with single-atom nickel electrocatalysts
Authors: Jeong Hui-Yun , Balamurugan Mani , Choutipalli Venkata Surya Kumar , Jeong Eun-suk , Subramanian Venkatesan , Sim Uk , Nam Ki Tae
Published: March 2019

A high CO2 to CO electroreduction rate exceeding 300 mA cm−2 was achieved with single atom nickel and nitrogen doped three-dimensional porous carbon electrocatalysts.
Single‐inductor multiple‐output DC–DC converter with duty‐cycle‐constrained comparator control
Authors: Chen Zhijian , Li Cuiwen , Leung Ka Nang , Zheng Yanqi
Published: March 2019

An auto‐buck–boost single‐inductor multiple‐output (SIMO) dc–dc converter with duty‐cycle‐constrained comparator control is presented in this Letter. Combined both comparator‐based and duty‐cycle‐constrained controllers enable the dc–dc converter attaining fast transient response and low cross‐regulation (CR). The proposed algorithm is independent of the precision of current sensor and suppresses CR robustly with the proposed tri‐feedback loop control of comparator‐based voltage control, duty‐cycle‐constrained distribution and average current control. The proposed scheme is suitable for auto‐buck–boost SIMO dc–dc converter design for dynamic voltage scaling applications.
Comparison analysis of low‐switching‐frequency‐based IPMSM sensorless drives considering regulators, observer and inverter non‐linearity
Authors: Zhang Hang , Liu Weiguo , Chen Zhe , Jiao Ningfei , Zhao Dongdong
Published: March 2019

This study proposes an integration design of sensorless closed‐loop drives for rail transit application employing interior permanent magnet synchronous machine (IPMSM), which works under low switching frequency. Due to the long signal sampling period in high‐speed region, the individual back‐EMF observer cannot ensure the sensorless closed‐loop control stability. In order to increase the speed dynamic response and decouple the d–q axes currents accurately, a fast non‐singular terminal sliding mode control is designed. It combines a linear sliding mode factor with conventional non‐singular terminal sliding mode and is applied uniformly to position observer, speed and currents regulators. Then, considering the effect of inverter non‐linearity on position observer, the observed position error caused by dead‐time is analysed, and a compensation method based on q‐axis voltage error is proposed. Based on the above methods, a comparison analysis of position observer, speed and currents regulators is given. Finally, a 3.7 kW IPMSM is tested to verify the feasibility of the improved sensorless method.
Dendritic silver hierarchical structures for anode materials in Li ion batteries
Authors: Li Jing , Fa Wenjun , Zhao Hongxiao , Zhu Congxu , Jia Huimin , Gu Longyan
Published: March 2019

Dendritic silver hierarchical structures were prepared via a simple electrochemical deposition method in the presence of citric acid. The influence of the molar ratio of citric acid and AgNO3, the deposition time and the deposition current on the crystalline and morphology of the products were studied by X‐ray diffraction and scanning electron microscopy. Dendritic silver hierarchical structures consist of a long trunk with secondary branches, which grew in a parallel direction with a definite angle to the trunk. The average diameter of the trunk is 230–320 nm, that of the secondary branches is about 250 nm and the length of the branches is about 850 nm. The charge specific capacity of dendritic silver hierarchical structures was stable at around 250 mAh g−1 after 500 cycles at 0.1C. They also exhibited excellent rate capability at the various current rates from 0.1 to 5C.
Effect of compaction pressure on the densification, microstructure, and mechanical properties of Ti‐1Al‐8V‐5Fe alloy based on TiH2 and HDH‐Ti powders
Authors: Zhang Yanan , Guo Xing , Chen Yungui , Li Qiangguo
Published: March 2019

The high‐strength of Ti‐1Al‐8V‐5Fe (Ti‐185) alloy is due to TiH2 powders produced at different compaction pressures and compared with hydride–dehydride‐Ti powders. The objective of this work was to investigate the microstructural evolution and mechanical properties of Ti‐185 alloy under different compaction pressures. The dehydrogenation characteristics of TiH2‐185 and the oxygen contents of sintered samples were evaluated by thermogravimetric analysis and mass spectrometer (TG‐MS) and oxygen/nitrogen (O/N) analysers. The corresponding microstructural evolution and change in mechanical properties were analysed by means of scanning electron microscopy, X‐ray diffraction, electro‐universal tester, and hardness tester, respectively. Results show that with the increase in compaction pressure, the green and sintered density and densification rates increase, but the volume fraction of α‐phase decreases. The TiH2‐185 samples have higher densification and sintered density, lower oxygen content than Ti‐185 samples, which is attributed to its better compressibility and superior self‐cleaning ability as well as more water produced. In addition, the sintered TiH2‐185 samples exhibit higher yield strength and hardness in comparison with the sintered Ti‐185 samples. The enhanced mechanical properties are attributed to its higher density and less soft α‐phase in the microstructure.
Disease mortality in domesticated animals is predicted by host evolutionary relationships
Authors: Farrell Maxwell J. , Davies T. Jonathan
Published: March 2019

Infectious diseases of domesticated animals impact human well-being via food insecurity, loss of livelihoods, and human infections. While much research has focused on parasites that infect single host species, most parasites of domesticated mammals infect multiple species. The impact of multihost parasites varies across hosts; some rarely result in death, whereas others are nearly always fatal. Despite their high ecological and societal costs, we currently lack theory for predicting the lethality of multihost parasites. Here, using a global dataset of >4,000 case-fatality rates for 65 infectious diseases (caused by microparasites and macroparasites) and 12 domesticated host species, we show that the average evolutionary distance from an infected host to other mammal host species is a strong predictor of disease-induced mortality. We find that as parasites infect species outside of their documented phylogenetic host range, they are more likely to result in lethal infections, with the odds of death doubling for each additional 10 million years of evolutionary distance. Our results for domesticated animal diseases reveal patterns in the evolution of highly lethal parasites that are difficult to observe in the wild and further suggest that the severity of infectious diseases may be predicted from evolutionary relationships among hosts.
Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model
Authors: Angelbello Alicia J. , Rzuczek Suzanne G. , Mckee Kendra K. , Chen Jonathan L. , Olafson Hailey , Cameron Michael D. , Moss Walter N. , Wang Eric T. , Disney Matthew D.
Published: March 2019

Myotonic dystrophy type 1 (DM1) is an incurable neuromuscular disorder caused by an expanded CTG repeat that is transcribed into r(CUG)
exp
. The RNA repeat expansion sequesters regulatory proteins such as Muscleblind-like protein 1 (MBNL1), which causes pre-mRNA splicing defects. The disease-causing r(CUG)
exp
has been targeted by antisense oligonucleotides, CRISPR-based approaches, and RNA-targeting small molecules. Herein, we describe a designer small molecule, Cugamycin, that recognizes the structure of r(CUG)
exp
and cleaves it in both DM1 patient-derived myotubes and a DM1 mouse model, leaving short repeats of r(CUG) untouched. In contrast, oligonucleotides that recognize r(CUG) sequence rather than structure cleave both long and short r(CUG)-containing transcripts. Transcriptomic, histological, and phenotypic studies demonstrate that Cugamycin broadly and specifically relieves DM1-associated defects in vivo without detectable off-targets. Thus, small molecules that bind and cleave RNA have utility as lead chemical probes and medicines and can selectively target disease-causing RNA structures to broadly improve defects in preclinical animal models.
Analysis of an improved Cyanophora paradoxa genome assembly
Authors: Price Dana C , Goodenough Ursula W , Roth Robyn , Lee Jae-Hyeok , Kariyawasam Thamali , Mutwil Marek , Ferrari Camilla , Facchinelli Fabio , Ball Steven G , Cenci Ugo , Chan Cheong Xin , Wagner Nicole E , Yoon Hwan Su , Weber Andreas P M , Bhattacharya Debashish
Published: March 2019

Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage.
Decolonizing Eastern Europe: A global perspective on 1989 and the world it made
Authors: Fowkes James , Hailbronner Michaela
Published: March 2019

The end of the Cold War can be usefully understood as a moment of decolonization, and the post-1989 experience, for many states, as a postcolonial one. But we do not usually think in these terms when it comes to Eastern Europe, even though it has faced similar challenges to countries further South. Among those challenges has been the search for a new national and constitutional identity—a task complicated by a colonized past, yielding not a few identity-builders to resort to what we call constitutional kitsch. But we wonder whether Eastern Europeans have been afforded less space to build their own post-1989 identities, compared to places further South. And we wonder if this has to do with our greater sensitivity to this postcolonial need in places where we find such terms more natural, while Eastern Europe may have been too close to Europe for that need to be taken as seriously.
Discovery of False Elite Controllers: HIV Antibody-Positive RNA-Negative Blood Donors Found To Be on Antiretroviral Therapy
Authors: Sykes Wendy , Van den Berg Karin , Jacobs Genevieve , Jauregui Adam , Roubinian Nareg , Wiesner Lubbe , Maartens Gary , Swanevelder Ronel , Custer Brian , Busch Michael , Jentsch Ute , Murphy Edward L , Vermeulen Marion ,   NHLBI Recipient Epidemiology and Donor Evaluation Study-III (REDS-III)
Published: March 2019

Background

An increase in potential HIV elite controllers (EC) and anecdotal reports of antiretroviral therapy (ART) use among South African blood donors led us to verify EC status.

Methods

Stored plasma samples from potential EC were tested for ART drugs. Demographic and temporal associations were examined using multivariable logistic regression.

Results

Of 226 potential EC, 150 (66.4%) had detectable ART with increasing prevalence by year (OR = 7.57 for 2016 vs 2010, 95% confidence interval, 1.96–32.17).

Discussion

False presumptive EC status due to undisclosed ART represents a growing proportion of potential EC donors in South Africa coincident with the country’s ART rollout.
Seasonal Occurrence of Haemaphysalis longicornis (Acari: Ixodidae) and Haemaphysalis flava, Vectors of Severe Fever With Thrombocytopenia Syndrome (SFTS) in South Korea
Authors: Jung Minhyung , Kho Jung-Wook , Lee Wook-Gyo , Roh Jong Yul , Lee Doo-Hyung
Published: March 2019

The seasonal abundance of Haemaphysalis longicornis Neumann and H. flava Neumann (Acari: Ixodidae) was monitored from 2015 through 2017 in Gyeonggi-do, South Korea. The hard ticks were surveyed monthly using CO2 bait traps from April to November and flagging from July to September in a coniferous forest, a deciduous forest, shrubs, and a grassland vegetation types. Haemaphysalis longicornis and H. flava were most abundant in the grassland and shrubs, which yielded over 50% of the total number of ticks in all 3 yr. Furthermore, H. longicornis comprised up to 90% of the ticks collected. Generally, peaks of nymph, adult, and larva numbers were observed from April to June, from June to July, and from August to September, respectively. Half of the ticks were pooled and tested for the presence of the SFTS virus with negative results.
Therapeutic Uses of the Flute Within Music Therapy Practice
Authors: Burns Cecilia E
Published: March 2019

The purpose of this study was to describe flute usage among current, professional music therapists. The broad term “flute” included any instrument with sound created by blowing air across or into an aperture hole. Members of the American Music Therapy Association (AMTA) were sent an electronic survey consisting of 25 questions pertaining to the flute and music therapy. Descriptive statistics describe how flutes were being used in music therapy sessions, and chi-square tests were used to determine whether music therapists who studied flute as a primary instrument used the flute as an instrument within a music therapy setting more frequently. Results showed that 42.4% of the 387 respondents were actively using flute music in some way within music therapy sessions while 67.8% of respondents reported using flute music at some point in the past. Flute-playing music therapists reported using flutes more frequently in a music therapy context than music therapists who did not study flute as a primary instrument. It appears that the flute is a viable instrument for music therapy practice.
Physical Therapist Education and the Labor Market in Brazil: Advances and Challenges
Authors: Sampaio Rosana F , Wan Der Maas Lucas , Marães Vera R F S , Neves Jorge A , Vaz Daniela V , Nóbrega Rodrigo A A , Ocarino Juliana M
Published: March 2019

Background

In Brazil, the number of physical therapy education programs and, consequently, of professionals has been growing for the past 20 years.

Objectives

The objective of the study was to describe the evolution and distribution of physical therapist education programs in Brazil and to analyze the impact of workforce growth on the labor market for these professionals.

Design

This was a descriptive, exploratory, quantitative study.

Methods

Secondary data collected from official sources in Brazil were used.

Results

The first physical therapist education program was created in 1958, and, after significant growth, 536 programs were active in 2014. The historical series (1996–2014) shows a corresponding increase in the number of admissions by higher educational institutions. This expansion resulted in an increase in the number of professionals, with an impact on the labor market. The workforce in physical therapy is predominantly female, and women increased their participation in this labor market from 59% in 1996 to 81% in 2014. An increase in nominal monthly salaries was observed over the years from US $797.00 in 1996 to US $1056.00 in 2014. Nevertheless, the real average salaries, that is, salaries adjusted to inflation, have followed a trend of devaluation.

Limitations

Results of this study must be interpreted in terms of overall trends rather than as precise absolute numbers due to the inherent nature of the varied secondary data sources.

Conclusions

These data can support further discussion on training and the labor market in the field of physical therapy.
Quadratic points of surfaces in projective 3-space
Authors: Craizer Marcos , Garcia Ronaldo A
Published: March 2019

Quadratic points of a surface in the projective 3-space are the points which can be exceptionally well approximated by a quadric. They are also singularities of a 3-web in the elliptic part and of a line field in the hyperbolic part of the surface. We show that generically the index of the 3-web at a quadratic point is ±1/3, while the index of the line field is ±1. Moreover, for an elliptic quadratic point whose cubic form is semi-homogeneous, we can use Loewner’s conjecture to show that the index is at most 1. From the above local results, we can conclude some global results: A generic compact elliptic surface has at least 6 quadratic points, a compact elliptic surface with semi-homogeneous cubic forms has at least 2 quadratic points and the number of quadratic points in a hyperbolic disc is odd. By studying the behavior of the cubic form in a neighborhood of the parabolic curve, we also obtain a relation between the indices of the quadratic points of a generic surface with non-empty elliptic and hyperbolic regions.
Tackling the outcome bias related to the effectiveness of antibiotics against the common cold: results of a randomized controlled trial applying the Solomon four-group design
Authors: Ludolph Ramona , Schulz Peter J
Published: March 2019

In recent years, antimicrobial resistance (AMR) has become an international public health priority. In the area of human medicine, the mis- and overuse of antibiotics is an important contributor to the development of AMR. Such a non-prudent use of antibiotics is especially prevalent in the treatment of viral infections such as the common cold. The present study aims to address the misconception, also known as outcome bias, that antibiotics may be an effective treatment against the common cold by providing a “debiasing” risk communication intervention. It aims at conveying the non-existence of a cause–effect relationship between antibiotics and the reduction of cold-related symptoms through a visual aid and simple explanatory text. A Solomon four-group design was employed to test for within- and between-subjects effects of the intervention as well as potential sensitization effects of the repeated measurement. A total of 311 participants residing in Germany were randomly assigned to receiving (1) a pretest, the debiasing intervention and post-test (2), a pretest, a control stimulus and post-test (3), the debiasing intervention and post-test, or (4) the post-test only. Outcome measures included knowledge about the effectiveness of antibiotics, the attitude toward using it as treatment against the common cold and the evaluation of a scenario describing an irresponsible use of antibiotics. Within-subjects comparisons found that participants receiving the pre- and post-test and intervention showed improved knowledge (t(77) = -2.53, p = .014), attitude (t(77) = -2.09, p = .040), and evaluation measures (t(77) = -2.23, p = .028). The pretest might, however, have caused a sensitization of participants for knowledge-related questions (t(77) = 2.207, p = .029). Between-subjects comparisons found differences in knowledge levels between the post-test only group and both groups receiving the intervention (F(3, 307) = 5.63, p = .001, η2p = .05]. There were no differences between the intervention and control groups with regard to attitude and evaluation of the scenario. While the risk communication intervention led to an increase in knowledge, the outcomes related to attitude and evaluation of a scenario were only affected positively in one group. Therefore, it seems that communication interventions based on visual aids are a simple method to promote the understanding of the true relationship between antibiotic treatment and the decrease of cold-related symptoms. Variables such as attitude and evaluation of a scenario presenting the irresponsible use of antibiotics require, however, additional interventions facilitating a translation of accurate understanding into respective attitudes and judgments.
Reappraisal of respiratory syncytial virus as an aetiology of severe acute lower respiratory tract infections in children younger than 5 years in Nigeria
Authors: Oladele Damilola M , Oladele Dimeji P , Ibraheem Rasheedat M , Abdulkadir Mohammed B , Raheem Rasaki Adewole , Gobir Aishat A , Adedoyin Olarenwaju T , Johnson Abdul-Wahab B R
Published: March 2019

Background

Acute lower respiratory tract infections (ALRIs) especially severe ALRIs, constitute a global high burden of morbidity and mortality in children <5 y of age and respiratory syncytial virus (RSV) has been documented to a play a major aetiological role. However, Nigerian reports on severe childhood RSV ALRIs are rare and most reports are old. With recent advances in RSV preventive strategy, arises the need for a recent appraisal of RSV infection in children with severe ALRI. The current study thus set out to determine the prevalence of RSV infection among hospitalized children <5 y of age and describe the related social determinants.

Methods

We performed a descriptive cross-sectional study conducted over 1 y of 120 children, ages 2–59 months, diagnosed with ALRI. Relevant data were obtained and an antigen detection assay was used for viral studies.

Results

The prevalence of RSV infection was 34.2% and its peak was in the rainy months. The proportion of infants in the RSV-positive group was significantly higher than that in the RSV-negative group (82.9% vs 54.4%; p=0.002). These findings were largely consistent with those of earlier reports.

Conclusions

RSV has remained a common cause of severe ALRI in infants, especially during the rainy months in Nigeria. It is thus suggested that more effort be focused towards implementing the current global recommendations for the prevention of RSV-associated LRI, particularly in infants.
DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network
Authors: Meng Jing , Victor Brandon , He Zhen , Salim Agus
Published: March 2019

Motivation

It is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, they take into consideration only limited information about the reference and potential variant allele in both samples at a candidate somatic site. Also, they differ in how biological and technological noises are addressed. Hence, they are expected to produce divergent outputs.

Results

To overcome the drawbacks of existing somatic callers, we develop a deep learning-based tool called DeepSSV, which employs a convolutional neural network (CNN) model to learn increasingly abstract feature representations from the raw data in higher feature layers. DeepSSV creates a spatially-oriented representation of read alignments around the candidate somatic sites adapted for the convolutional architecture, which enables it to expand to effectively gather scattered evidences. Moreover, DeepSSV incorporates the mapping information of both reference-allele-supporting and variant-allele-supporting reads in the tumor and normal samples at a genomic site that are readily available in the pileup format file. Together, the CNN model can process the whole alignment information. Such representational richness allows the model to capture the dependencies in the sequence and identify context-based sequencing artifacts, and alleviates the need of post-call filters that heavily depend on prior knowledge. We fitted the model on ground truth somatic mutations, and did benchmarking experiments on simulated and real tumors. The benchmarking results demonstrate that DeepSSV outperforms its state-of-the-art competitors in overall F1score.

Availability and Implementation

https://github.com/jingmeng-bioinformatics/DeepSSV

Contact

a.salim@latrobe.edu.au

Supplementary information

Supplementary data are available at online.
An essential RNA-binding lysine residue in the Nab3 RRM domain undergoes mono and trimethylation
Authors: Lee Kwan Yin , Chopra Anand , Biggar Kyle , Meneghini Marc D.
Published: March 2019

The Nrd1-Nab3-Sen1 (NNS) complex integrates molecular inputs to direct termination of noncoding transcription in budding yeast. NNS is positively regulated by methylation of histone H3 lysine-4 as well as through Nrd1 binding to the initiating form of RNA PolII. These cues collaborate with Nrd1 and Nab3 binding to target RNA sequences in nascent transcripts through their RRM RNA recognition motifs. In this study, we identify nine lysine residues distributed amongst Nrd1, Nab3, and Sen1 that are mono-, di-, or trimethylated, suggesting novel molecular inputs for NNS regulation. One of these methylated residues, Nab3 lysine-363 (K363), resides within its RRM, and is known to physically contact target RNA. Although mutation of Nab3-K363 to arginine (Nab3-K363R) causes a severe growth defect, it nevertheless produces a stable protein that is incorporated into the NNS complex, suggesting that RNA binding through Nab3-K363 is crucial for NNS function. Consistent with this hypothesis, K363R mutation decreases RNA binding of the Nab3 RRMin vitroand causes transcription termination defectsin vivo.These findings reveal crucial roles for Nab3-K363 and suggest that methylation of this residue may modulate NNS activity through its impact on Nab3 RNA binding.
PhenoMS-ML: Phenotypic Screening by Mass Spectrometry and Machine Learning
Authors: van Oosten Luuk N. , Klein Christian D.
Published: March 2019

Protein mass fingerprinting by MALDI-TOF MS in combination with machine learning (PhenoMS-ML) permits the identification of response signatures generated in cell cultures upon exposure to well-characterized drugs. PhenoMS-ML is capable to identify and classify the mode of action of unknown antibacterial agents in wild-type Escherichia coli and Staphylococcus aureus. It allows the sensitive, specific, and high-throughput identification of drug target mechanisms that are difficult to assess by other methods.
Empirical determination of severe trauma in seals from collisions with tidal turbine blades
Authors: Onoufriou Joe , Brownlow Andrew , Moss Simon , Hastie Gordon , Thompson Dave
Published: March 2019

Tidal energy converters (turbines) are being developed in many countries as part of attempts to reduce reliance on hydrocarbon fuels. However, the moving blades of tidal turbines pose potential collision risks for marine animals. Accurate assessment of mortality risk as a result of collisions is essential for risk management during planning and consenting processes for marine energy developments. In the absence of information on the physical consequences of such collisions, predicting likely risks relies on theoretical collision risk models. The application of these at a population level usually assumes that all collisions result in mortality. This is unlikely and the approach therefore produces upwardly biased estimates of population consequences.

In this study, we estimate the pathological consequences of direct collisions with tidal turbines using seal carcasses and physical models of tidal turbine blades. We quantify severe trauma at a range of impact speeds and to different areas of seal carcasses. A dose–response model was developed with associated uncertainty to determine an impact speed threshold of severe trauma to use in future collision risk models.

Results showed that severe trauma was restricted to the thoracic region, with no evidence of injury to the lumbar or cervical spine. Pathological indicators of mortality were only predicted to occur in collision speeds in excess of 5.1 m/s (95% C.I. 3.2–6.6) and was affected by body condition; increasing blubber depth reduced the likelihood of severe trauma.

Synthesis and applications. This study provides important information for policy makers and regulators looking to predict the potential impacts of tidal turbines on marine mammals. We demonstrate that the probability of severe trauma in seals due to collisions with turbine blades is highly dependent upon collision speed, and that the majority of predicted collisions are unlikely to cause fatal skeletal trauma. We recommend that collision risk models incorporate appropriate mortality assumptions to ensure accurate estimates of the population consequences are produced in risk assessments for tidal turbine deployments.
A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability
Authors: Mahaut Lucie , Gaba Sabrina , Fried Guillaume
Published: March 2019

Combining several crop species and associated agricultural practices in a crop sequence has the potential to control weed abundance while promoting weed diversity in arable fields. However, how the variability in environmental conditions that arise from crop sequences affects weed diversity and abundance remains poorly understood, with most studies to‐date simply opposing weed communities in monoculture and in crop rotation. Here, we describe crop sequences along gradients of disturbance and resource variability using a crop functional trait and associated agricultural practices. We tested the hypothesis that in disturbances reduces weed abundance, whereas variability in resources promotes weed diversity.

We used functional Hill's numbers to compute crop sequence functional diversity based on sowing date, herbicide spectrum and crop height—these are the respective proxies of disturbance timings, disturbance types and light availability. Using a large‐scale weed monitoring database, we assessed crop sequence diversity for 1,045 crop sequences of five consecutive cropping seasons. We computed weed richness and abundance at pluri‐annual (pool of weeds observed across five cropping seasons) and annual (pool of weeds observed during a winter cereal cropping season preceded by five cropping seasons) scales. We also accounted for herbicide and tillage intensities to test whether management intensity affects the response of weed diversity and abundance to crop sequence diversity.

At the pluri‐annual scale, weed richness increased with the diversity of crop height and sowing date, whereas weed abundance decreased with sowing date diversity. Annual weed richness decreased with sowing date diversity, whereas annual weed abundance poorly relied on crop sequence diversity.

Synthesis and applications. This study establishes a scientific basis for designing crop sequences according to specific weed management goals. We show that farmers may enhance arable weed diversity on a pluri‐annual scale by sequentially sowing crop species that differ in their competitive ability and sowing date. They may also achieve a better control of weed abundance by increasing the diversity of crop sowing dates across the crop sequence.
Phenotypic and community consequences of captive propagation in mosquitofish
Authors: Wood Zachary T. , Fryxell David C. , Robinson Rebecca R. , Palkovacs Eric P. , Kinnison Michael T.
Published: March 2019

Captive propagation can lead to phenotypic change in fish populations, but the broader community‐level consequences of captive phenotypes remain largely unknown.

We investigate the degree to which captive propagation alters the phenotypes and ecological roles of fish stocked into wild communities. We focus on captive propagation of western mosquitofish (Gambusia affinis) for biocontrol, which represents one of the largest scale production efforts for any fish released into the wild.

Captive propagation in mosquitofish consistently generated novel mixtures of morphological and behavioural traits that deviate from those of wild populations.

A mesocosm experiment showed that mosquitofish from captive propagation facilities differ from wild fish in their effects on aquatic community structure by shifting their consumption to less‐mobile, benthic prey.

Synthesis and applications. Captive‐propagated and translocated wild fish stocks not only differ in phenotype, but can have substantially different ecological effects on the communities into which they are introduced. Therefore, captive propagation programmes involving continual release should expand their concerns beyond altered phenotypes and fitness to include whether propagated fish actually provide the intended ecological roles and services associated with their wild counterparts. Infusions of wild alleles and captive environments that mimic wild conditions are recommended strategies to retain the desired ecological role of captive‐propagated fish.
Metagenomic and metatranscriptomic responses of natural oil degrading bacteria in the presence of dispersants
Authors: Tremblay Julien , Fortin Nathalie , Elias Miria , Wasserscheid Jessica , King Thomas L. , Lee Kenneth , Greer Charles W.
Published: March 2019

Oil biodegradation has been extensively studied in the wake of the deepwater horizon spill, but the application of dispersant to oil spills in marine environments remains controversial. Here, we report metagenomic (MG) and metatranscriptomic (MT) data mining from microcosm experiments investigating the oil degrading potential of Canadian west and east coasts to estimate the gene abundance and activity of oil degrading bacteria in the presence of dispersant. We found that the addition of dispersant to crude oil mainly favours the abundance of Thalassolituus in the summer and Oleispira in the winter, two key natural oil degrading bacteria. We found a high abundance of genes related not only to n‐alkane and aromatics degradation but also associated with transporters, two‐component systems, bacterial motility, secretion systems and bacterial chemotaxis.
From Merkel to Kramp‐Karrenbauer: Can German Christian Democracy Reinvent Itself?
Authors: Dostal Jörg Michael
Published: March 2019

Germany's Christian Democrats have started preparing for the time after Angela Merkel. After ten years as German chancellor facing a weak opposition, Merkel unexpectedly split the country in late 2015 and early 2016 because of her ‘open border’ policies that allowed more than 1 million refugees and migrants to rapidly enter Germany. Her management of the subsequent crisis was largely considered a failure and her party suffered a series of dramatic election defeats. Reacting to the negative electoral feedback, and in particular the breakthrough of the rightist and anti‐immigration Alternative for Germany (AfD), the Christian Democratic Union organised an intra‐party contest to replace Merkel as party leader. Three candidates with different political profiles, Annegret Kramp‐Karrenbauer, Friedrich Merz and Jens Spahn, contested the election. By voting for Kramp‐Karrenbauer, the CDU membership voiced support for maintaining a large‐scale political coalition based on efforts to find compromises between different party wings and social and cultural interests.
Bias correction of estimated proportions using inverse binomial group testing
Authors: Hepworth Graham
Published: March 2019

Group testing, in which individuals are pooled together and tested as a group, can be combined with inverse sampling to estimate the prevalence of a disease. Alternatives to the MLE are desirable because of its severe bias. We propose an estimator based on the bias correction method of Firth (1993), which is almost unbiased across the range of prevalences consistent with the group testing design. For equal group sizes, this estimator is shown to be equivalent to that derived by applying the correction method of Burrows (1987), and better than existing methods. For unequal group sizes, the problem has some intractable elements, but under some circumstances our proposed estimator can be found, and we show it to be almost unbiased. Calculation of the bias requires computer‐intensive approximation because of the infinite number of possible outcomes.
A comparative study of robot‐assisted and open radical prostatectomy in 10 790 men treated by highly trained surgeons for both procedures
Authors: Haese Alexander , Knipper Sophie , Isbarn Hendrik , Heinzer Hans , Tilki Derya , Salomon Georg , Michl Uwe , Steuber Thomas , Budäus Lars , Maurer Tobias , Tennstedt Pierre , Huland Hartwig , Graefen Markus
Published: March 2019

Objective

To compare oncological, functional and surgical outcomes of open retropubic radical prostatectomy (ORP) vs robot‐assisted laparoscopic radical prostatectomy (RARP).

Patients and methods

We identified 10 790 consecutive treated patients within our prospective database (2008–2016) who underwent either ORP (7007 patients) or RARP (3783). All procedures were performed by seven highly trained surgeons performing both surgical approaches regularly. Oncological (48‐month biochemical recurrence [BCR] rate), functional (urinary continence, erectile function), and surgical outcomes (rate of nerve‐sparing [NS] procedures, lymph node yield, surgical margin [SM] status, length of hospital stay [LOS], operation time, blood loss, transfusion rate, time to catheter removal) were assessed. Kaplan–Meier, multivariable Cox and logistic regression models were used to test for BCR and functional outcome differences.

Results

No statistically significant difference regarding oncological outcome distinguished between ORP vs RARP. For functional outcomes, the 1‐week continence rates were higher in the ORP group (25.8% vs 21.8%, P < 0.001). At 3 months, no statistically significant differences were observed. At 12 months, continence rates were modestly higher in the RARP group (90.3% vs 88.8%, P = 0.01). This effect was no longer observed after stratification for age‐groups. The 12‐month potency rates were similar in ORP vs RARP (80.3% vs 83.6%, P = 0.33). For surgical outcomes, there was no significant difference in the rates of NS procedures, lymph node yield, SM status, and LOS. Conversely, operation time was shorter in ORP, and blood loss, transfusion rates and time to catheter removal were significantly lower in RARP.

Conclusions

Both surgical approaches, performed in a high‐volume centre by the same surgeons, achieve excellent, comparable oncological and functional outcomes. However, a modest advantage for RARP for surgical outcomes was observed, most likely attributable to its minimally invasive nature, and better teaching capabilities. Consequently, more than the surgical approach itself, the well‐trained surgeon remains the most important factor to achieve satisfactory outcomes.
The impact of post‐transplant diabetes mellitus on liver transplant outcomes
Authors: Lieber Sarah R. , Lee Ruth‐Ann , Jiang Yue , Reuter Claire , Watkins Randall , Szempruch Kristen , Gerber David A. , Desai Chirag S. , DeCherney G. Stephen , Barritt A. Sidney
Published: March 2019

Background

Post‐transplant diabetes mellitus (PTDM) is common after liver transplantation (LT). Yet, how PTDM relates to graft outcomes and survival needs elucidation as more individuals are transplanted for nonalcoholic fatty liver disease (NAFLD).

Methods

This single‐center, retrospective study of adult LT recipients (2003‐2016) identified PTDM incidence and associations with graft steatosis, rejection, and post‐LT patient survival. Multivariable analysis investigated predictors of PTDM. Kaplan‐Meier curves depicted patient survival 5 years post‐LT.

Results

Among 415 adult LT recipients, 23% had pre‐LT DM and 13% were transplanted for NAFLD. PTDM incidence was 34.7%, 46.9%, and 56.2% and overall survival was 90%, 80.9%, and 71.7% at 1, 3, and 5 years, respectively. Over a third of non‐NAFLD patients developed PTDM. Half of PTDM cases developed by 6 months and 75% by 12 months. The PTDM group had more rejection episodes compared to no PTDM (31.9% vs 21.8%, P = 0.055), with trends toward worse patient survival 5 years post‐LT (log‐rank test P = 0.254). Age was the only significant predictor of PTDM.

Conclusions

Post‐transplant diabetes mellitus occurs rapidly in the post‐LT period and is a significant problem for both NAFLD and non‐NAFLD LT recipients. Age is a significant risk factor for PTDM. Outcomes trended toward increased rejection and worse survival among PTDM individuals, suggesting the benefit of early strategies targeting glucose control.
Long non‐coding RNA ES1 controls the proliferation of breast cancer cells by regulating the Oct4/Sox2/miR‐302 axis
Authors: Keshavarz Mostafa , Asadi Malek Hossein
Published: March 2019

ES1 is a long non‐coding RNA (lncRNA) that regulates pluripotency of human embryonic stem cells, which is known to be a downstream target of stemness factors Oct4 and Nanog, and serves as a modular scaffold for Sox2. However, the role of ES1 in cancer biology is not fully characterized. The results of our study show that ES1 transcript is upregulated in both high‐grade and P53‐mutated breast tumor tissues. Knockdown experiments show that ES1 suppression in breast cancer cells restricts cancer cell proliferation and cell cycle progression. Moreover, ES1 inhibition can also induce apoptosis and cellular senescence. Additionally, our data reveal that ES1 transcript promotes cell migration as well as the epithelial to mesenchymal transition of breast cancer cells. Furthermore, loss of ES1 expression downregulates the expression of Oct4/Sox2 and consequently leads to downregulation of their targets, miR‐302 and miR‐106b. Altogether, for the first time, our findings reveal that ES1 controls the proliferation and death of breast cancer cells by regulating the Oct4/Sox2/miR‐302/miR‐106b axis.
Stress – (self) eating: Epigenetic regulation of autophagy in response to psychological stress
Authors: Puri Deepika , Subramanyam Deepa
Published: March 2019

Autophagy is a constitutive and cytoprotective catabolic process. Aberrations in autophagy lead to a multitude of degenerative disorders, with neurodegeneration being one of the most widely studied autophagy‐related disorders. While the field has largely been focusing on the cytosolic constituents and processes of autophagy, recent studies are increasingly appreciating the role of chromatin modifications and epigenetic regulation in autophagy maintenance. Autophagy has been implicated in the regulation of neurogenesis, and disruption of neurogenesis in response to psychological stress is a proximal risk factor for development of neuropsychiatric disorders such as major depressive disorder (MDD). In this review, we will discuss the regulation of autophagy in normal neurogenesis as well as during chronic psychological stress, focusing on the epigenetic control of autophagy in these contexts, and also highlight the lacunae in our understanding of this process. The systematic study of these regulatory mechanisms will provide a novel therapeutic strategy, based on the use epigenetic regulators of autophagy to enhance neurogenesis and potentially alleviate stress‐related behavioral disorders.
Reproductive fitness consequences of progenesis: Sex‐specific pay‐offs in safe and risky environments
Authors: Denoël Mathieu , Drapeau Laura , Winandy Laurane
Published: March 2019

Progenesis is considered to have an important role in evolution because it allows the retention of both a larval body size and shape in an adult morphology. However, the cost caused by the adoption of a progenetic process in both males and females remains to be explored to explain the success of progenesis and particularly its biased prevalence across the sexes and environments. Here, through an experimental approach, we used a facultative progenetic species, the palmate newt (Lissotriton helveticus) that can either mature at a small size and retain gills or mature after metamorphosis, to test three hypotheses for sex‐specific pay‐offs of progenesis in safe versus risky habitats. Goldfish were used because they caused a higher decline in progenetic than metamorphic newts. We determined that progenetic newts have a lower reproductive fitness than metamorphic newts. We also found that, when compared to metamorphs, progenetic males have lower reproductive activity than progenetic females and that predatory risk affects more progenetic than metamorphic newts. By identifying ultimate causes of the female‐biased sex ratios found in nature, these results support the male escape hypothesis, that is the higher metamorphosis rate of progenetic males. They also highlight that although progenesis is advantageous in advancing the age at first reproduction, it also brings an immediate fitness cost and this, particularly, in hostile predatory environments. This means that whereas some environmental constraints could favour facultative progenesis, some others, such as predation, can ultimately counter‐select progenesis. Altogether, these results improve our understanding of how developmental processes can affect the sexes differently and how species invasions can impair the success of alternative developmental phenotypes.