bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction–Modification Systems and paraMORC ATPases in Bacteria
Authors: Bellieny-Rabelo Daniel , Pretorius Willem J S , Moleleki Lucy N 
Published: February 2021

AbstractTwo-component systems (TCS) are important types of machinery allowing for efficient signal recognition and transmission in bacterial cells. The majority of TCSs utilized by bacteria is composed of a sensor histidine kinase (HK) and a cognate response regulator (RR). In the present study, we report two newly predicted protein domains—both to be included in the next release of the Pfam database: Response_reg_2 (PF19192) and HEF_HK (PF19191)—in bacteria which exhibit high structural similarity, respectively, with typical domains of RRs and HKs. Additionally, the genes encoding for the novel predicted domains exhibit a 91.6% linkage observed across 644 genomic regions recovered from 628 different bacterial strains. The remarkable adjacent colocalization between genes carrying Response_reg_2 and HEF_HK in addition to their conserved structural features, which are highly similar to those from well-known HKs and RRs, raises the possibility of Response_reg_2 and HEF_HK constituting a new TCS in bacteria. The genomic regions in which these predicted two-component systems-like are located additionally exhibit an overrepresented presence of restriction–modification (R–M) systems especially the type II R–M. Among these, there is a conspicuous presence of C-5 cytosine-specific DNA methylases which may indicate a functional association with the newly discovered domains. The solid presence of R–M systems and the presence of the GHKL family domain HATPase_c_3 across most of the HEF_HK-containing genes are also indicative that these genes are evolutionarily related to the paraMORC family of ATPases.
Distinct error rates for reference and nonreference genotypes estimated by pedigree analysis
Authors: Wang Richard J , Radivojac Predrag , Hahn Matthew W 
Published: February 2021

AbstractErrors in genotype calling can have perverse effects on genetic analyses, confounding association studies, and obscuring rare variants. Analyses now routinely incorporate error rates to control for spurious findings. However, reliable estimates of the error rate can be difficult to obtain because of their variance between studies. Most studies also report only a single estimate of the error rate even though genotypes can be miscalled in more than one way. Here, we report a method for estimating the rates at which different types of genotyping errors occur at biallelic loci using pedigree information. Our method identifies potential genotyping errors by exploiting instances where the haplotypic phase has not been faithfully transmitted. The expected frequency of inconsistent phase depends on the combination of genotypes in a pedigree and the probability of miscalling each genotype. We develop a model that uses the differences in these frequencies to estimate rates for different types of genotype error. Simulations show that our method accurately estimates these error rates in a variety of scenarios. We apply this method to a dataset from the whole-genome sequencing of owl monkeys (Aotus nancymaae) in three-generation pedigrees. We find significant differences between estimates for different types of genotyping error, with the most common being homozygous reference sites miscalled as heterozygous and vice versa. The approach we describe is applicable to any set of genotypes where haplotypic phase can reliably be called and should prove useful in helping to control for false discoveries.
MB-GAN: Microbiome Simulation via Generative Adversarial Network
Authors: Rong Ruichen , Jiang Shuang , Xu Lin , Xiao Guanghua , Xie Yang , Liu Dajiang J , Li Qiwei , Zhan Xiaowei 
Published: February 2021

Abstract

Background
Trillions of microbes inhabit the human body and have a profound effect on human health. The recent development of metagenome-wide association studies and other quantitative analysis methods accelerate the discovery of the associations between human microbiome and diseases. To assess the strengths and limitations of these analytical tools, simulating realistic microbiome datasets is critically important. However, simulating the real microbiome data is challenging because it is difficult to model their correlation structure using explicit statistical models.

Results
To address the challenge of simulating realistic microbiome data, we designed a novel simulation framework termed MB-GAN, by using a generative adversarial network (GAN) and utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from them. In practice, MB-GAN showed the following advantages. First, MB-GAN avoids explicit statistical modeling assumptions, and it only requires real datasets as inputs. Second, unlike the traditional GANs, MB-GAN is easily applicable and can converge efficiently.

Conclusions
By applying MB-GAN to a case-control gut microbiome study of 396 samples, we demonstrated that the simulated data and the original data had similar first-order and second-order properties, including sparsity, diversities, and taxa-taxa correlations. These advantages are suitable for further microbiome methodology development where high-fidelity microbiome data are needed.
Food havens not swamps: a strength-based approach to sustainable food environments
Authors: Tonumaipe’a Daysha , Cammock Radilaite , Conn Cath 
Published: February 2021

Abstract
The current paper provides a critical review of food environments’ literature, with a focus on the metaphoric typology that has been developed over recent decades. This has tended to focus understandably on harmful food environments using well-known metaphors: that of food deserts, food swamps and food mirages. The purpose of the review was to consider the current typology in relation to what constitutes healthy food environments, and the implications for population groups in low socioeconomic environments who are often disadvantaged by current food systems and unhealthy food environments. The paper posits a new term, alongside the notion of the food oasis, that of food havens. Oasis indicates a small place of plenty in a setting of scarcity. Haven extends the boundaries of plenty in society by positing places and settings of refuge and safety, even sanctuary from which health and well-being can be attained and supported. We argue for focusing on creating such sustainable food environments so as to proliferate and promote examples of what needs to be done urgently in the fight to transform global food environments for the health of people particularly those that are vulnerable and the planet. Elements of the food haven as proposed in this paper have been drawn from indigenous perspectives—these include Māori and Pacific worldviews. Future research should consider what food environments might look like in different contexts and how we might move away from food swamps and deserts to food oases and havens; and utilize these positive motifs to go further in creating whole sustainable food environments encompassing all of society.
Outcome of Reverse Switching From CT-P13 to Originator Infliximab in Patients With Inflammatory Bowel Disease
Authors: Mahmmod Shaden , Schultheiss Johannes P D , van Bodegraven Ad A , Dijkstra Gerard , Gilissen Lennard P L , Hoentjen Frank , Lutgens Maurice W M D , Mahmmod Nofel , van der Meulen–de Jong Andrea E , Smits Lisa J T , Tan Adriaan C I T L , Oldenburg Bas , Fidder Herma H 
Published: February 2021

Abstract

Background
Patients suffering from inflammatory bowel diseases (IBD) and treated with originator infliximab are increasingly being switched to biosimilars. Some patients, however, are “reverse switched” to treatment with the originator. Here we assess the prevalence of reverse switching, including its indication and outcomes.

Methods
In this retrospective multicenter cohort study, data on patients with IBD from 9 hospitals in the Netherlands were collected. All adult patients with IBD were included if they previously had been switched from originator infliximab to the biosimilar CT-P13 and had a follow-up time of at least 52 weeks after the initial switch. The reasons for reverse switching were categorized into worsening gastrointestinal symptoms, adverse effects, or loss of response to CT-P13. Drug persistence was analyzed through survival analyses.

Results
A total of 758 patients with IBD were identified. Reverse switching was observed in 75 patients (9.9%). Patients with reverse switching were predominantly female (70.7%). Gastrointestinal symptoms (25.5%) and dermatological symptoms (21.8%) were the most commonly reported reasons for reverse switching. In 9 patients (12.0%), loss of response to CT-P13 was the reason for reverse switching. Improvement of reported symptoms was seen in 73.3% of patients after reverse switching and 7 out of 9 patients (77.8%) with loss of response regained response. Infliximab persistence was equal between patients who were reverse-switched and those who were maintained on CT-P13.

Conclusions
Reverse switching occurred in 9.9% of patients, predominantly for biosimilar-attributed adverse effects. Switching back to originator infliximab seems effective in patients who experience adverse effects, worsening gastrointestinal symptoms, or loss of response after switching from originator infliximab to CT-P13.
Fisher or fisheries scientist?
Authors: Bjordal Åsmund 
Published: February 2021

AbstractI have the pleasure to invite you on my trip—or rather voyage, from childhood to retirement as a fisheries scientist. We will go fishing, do fishing gear and aquaculture research, provide scientific management advice, and cooperate with developing countries along the way. My advice to young scientists is to build trust, have passion for your work, and make it relevant for sustainable development.
Using Blueprints to promote interorganizational knowledge transfer in digital health initiatives—a qualitative exploration of a national change program in English hospitals
Authors: Williams Robin , Sheikh Aziz , Franklin Bryony Dean , Krasuska Marta , Nguyen Hung The , Hinder Susan , Lane Wendy , Mozaffar Hajar , Mason Kathy , Eason Sally , Potts Henry W W , Cresswell Kathrin 
Published: February 2021

Abstract

Objective
The Global Digital Exemplar (GDE) Program is a national attempt to accelerate digital maturity in healthcare providers through promoting knowledge transfer across the English National Health Service (NHS). “Blueprints”—documents capturing implementation experience—were intended to facilitate this knowledge transfer. Here we explore how Blueprints have been conceptualized, produced, and used to promote interorganizational knowledge transfer across the NHS.

Materials and Methods
We undertook an independent national qualitative evaluation of the GDE Program. This involved collecting data using semistructured interviews with implementation staff and clinical leaders in provider organizations, nonparticipant observation of meetings, and key documents. We also attended a range of national meetings and conferences, interviewed national program managers, and analyzed a range of policy documents. Our analysis drew on sociotechnical principles, combining deductive and inductive methods.

Results
Data comprised 508 interviews, 163 observed meetings, and analysis of 325 documents. We found little evidence of Blueprints being adopted in the manner originally conceived by national program managers. However, they proved effective in different ways to those planned. As well as providing a helpful initial guide to a topic, we found that Blueprints served as a method of identifying relevant expertise that paved the way for subsequent discussions and richer knowledge transfers amongst provider organizations. The primary value of Blueprinting, therefore, seemed to be its role as a networking tool. Members of different organizations came together in developing, applying, and sustaining Blueprints through bilateral conversations—in some circumstances also fostering informal communities of practice.

Conclusions
Blueprints may be effective in facilitating knowledge transfer among healthcare organizations, but need to be accompanied by other evolving methods, such as site visits and other networking activities, to iteratively transfer knowledge and experience.
DNA barcoding enhances large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico and adjacent waters
Authors: Varela Carlos , Golightly Charles , Timm Laura E , Wilkins Blake , Frank Tamara , Fenolio Danté , Collins Stormie B , Bracken-Grissom Heather D 
Published: February 2021

AbstractThe application of DNA barcoding represents a complementary and efficient approach to identifying specimens at all stages of their life cycle when used in combination with traditional morphological methods. Due to difficulties obtaining samples from the deep sea (&gt; 200 m), these methods have been less frequently applied to deep-water taxa. We used DNA-barcoding techniques to enhance large-scale biodiversity initiatives for deep-pelagic crustaceans within the Gulf of Mexico, a region that has recently been identified as one of the world’s four most hyperdiverse ocean ecosystems. This study was conceptualized in direct response to the Deepwater Horizon Oil Spill in 2010, which identified major knowledge gaps in our understanding of deep-sea biodiversity. We employed traditional Sanger sequencing and a genomic skimming approach to target the mitochondrial ribosomal large subunit 16S and the protein-coding cytochrome oxidase subunit 1 (COI). Alongside these molecular approaches, traditional taxonomic investigations allowed for advancements in biodiversity, evolutionary relationships, cryptic species complexes, and distributional records across four abundant and common deep-pelagic orders (Amphipoda, Euphausiacea, Lophogastrida, and Decapoda). DNA barcodes were successfully obtained from 82 species for a total of 158 and 169 new 16S and COI sequences, respectively. Evidence of cryptic diversity has been found in the genera EucopiaDana, 1852 (Lophogastrida) and Allosergestes Judkins & Kensley, 2008 (Decapoda). New records for the Gulf of Mexico of species of LanceolaSay, 1818 (Amphipoda), Eupasiphae Wood-Mason in Wood-Mason & Alcock, 1893, PasiphaeaSavigny, 1816, and MeningodoraSmith, 1882 (Caridea) are presented. Preliminary results allow us to reconsider the current classification and evolutionary relationships of several lineages. The urgency to document biodiversity in the deep-pelagic is pressing against a backdrop of future threats including oil spills and deep-sea drilling.
Banks’ Sovereign Exposures: In Search of New Rules
Authors: Baglioni Angelo , Cefalà Francesco 
Published: February 2021

ABSTRACT
In this article, we examine the reform of the prudential treatment of banks’ sovereign exposures with the purpose of introducing risk-sensitive capital charges and limiting home bias. We consider six different options and measure their impact on the common equity Tier 1 (CET1) ratio of 82 banks fom 10 euro-area countries, participating in the 2019 European Banking Authority EU-wide transparency exercise and subject to European Central Bank supervision. Our evidence shows that the proposal put forward by the Basel Committee on Banking Supervision in 2017 is the proposal which leads to the most evenly distributed impact across countries, in terms of CET1 ratio decline. That proposal targets the goals of risk sensitivity and diversification, with two independent instruments: rating-based risk weights and concentration add-ons. As a consequence, it is the only proposal which introduces an incentive for banks located in all countries, whether low rated or high rated, to reduce their home bias. Some proposals focus on one objective only: either risk sensitivity or diversification. Others introduce heavy penalization for banks located in low-rated countries, without addressing the home bias of banks located in high-rated countries. Several options are prone to pro-cyclicality, and we measure this effect by simulating the impact of a two-notch downgrading of high debt countries on the CET1 ratio of banks. Some relevant cross-country effects emerge from our analysis, due to the large cross-country exposures of a few intermediaries.
‘Ordinary’, ‘insignificant’ and ‘useless’ artefacts from Rome and Athens
Authors: Mannoni Chiara 
Published: February 2021

Abstract
The edicts relating to the protection of antiquities and works of art published in the Papal States and in Greece in the nineteenth century were the first inclusive regulations in the world on the management and supervision of cultural heritage. Their aim was to control and reduce the massive exportation of artefacts that had despoiled both countries. However, the continuing stream of exports that followed the issuing of these regulations shows that their impact was limited. Questions of taste and aesthetics were introduced that allowed the disposal of the ‘insignificant’, ‘useless’, ‘multiple’ and ‘ordinary’ pieces considered unworthy of protection. Analysis of several such cases approved for export from Rome and Athens identifies a number of legal loopholes and artistic formulae that were adduced in order to circumvent the edicts, and contributes to an understanding of the impact of new approaches to art history scholarship on both the law and the nineteenth-century art market.
The ALOHA trial: (intra-articular local anaesthetic in hip arthroscopy)—a three-arm randomized trial comparing pre-emptive, high- and low-dose intra-articular local anaesthetic in hip arthroscopy
Authors: Tan Chong O , Tran Phong , Chong Yew Ming , Howard William , Weinberg Laurence 
Published: February 2021

Abstract
Pain after hip arthroscopy is variable and can be severe despite multimodal analgesia. Intra-articular local anaesthetic (IALA) may reduce acute postoperative pain after hip arthroscopy. However, neither its optimum dose nor timing of administration have been systematically evaluated. In 132 patients, a double-blinded, three-arm randomized controlled trial comparing IALA used during hip arthroscopy was conducted comparing 100 mg ropivacaine given at the end of the procedure (Group L, lose dose), 200 mg ropivacaine at the end of the procedure (Group H, high dose) and 100 mg of ropivacaine given at the beginning and end of the procedure (Group P, pre-emptive). There were no statistically significant differences between the three groups for Numerical Rating Scale-11 pain scores in the recovery room [mean (standard deviation): Group L—2.2 (1.9); Group H—2.3 (2.1); Group P—2.7 (2.5); lowest P = 0.6], or post-recovery room Visual Analogue Scale pain scores at 2, 4 and 6 h. There were also no significant differences in antiemetic usage and requirement for rescue fascia iliaca blockade between the three groups. Compared to a single 100 mg dose of ropivacaine at the end of the procedure, we were unable to demonstrate any advantage of either a higher dose IALA or a pre-emptive dose IALA when multimodal analgesia is used.
Transmission Potential of Zika Virus by Aedes aegypti (Diptera: Culicidae) and Ae. mediovittatus (Diptera: Culicidae) Populations From Puerto Rico
Authors: Zimler Rebecca A , Yee Donald A , Alto Barry W 
Published: February 2021

Abstract
Recurrence of local transmission of Zika virus in Puerto Rico is a major public health risk to the United States, where mosquitoes Aedes aegypti (Linnaeus) and Aedes mediovittatus (Coquillett) are abundant. To determine the extent to which Ae. mediovittatus are capable of transmitting Zika virus and the influence of viremia, we evaluated infection and transmission in Ae. mediovittatus and Ae. aegypti from Puerto Rico using serial dilutions of infectious blood. Higher doses of infectious blood resulted in greater infection rates in both mosquitoes. Aedes aegypti females were up to twice as susceptible to infection than Ae. mediovittatus, indicating a more effective midgut infection barrier in the latter mosquito species. Aedes aegypti exhibited higher disseminated infection (40–95%) than Ae. mediovittatus (&lt;5%), suggesting a substantial midgut escape barrier in Ae. mediovittatus. For Ae. aegypti, transmission rates were low over a range of doses of Zika virus ingested, suggesting substantial salivary gland barriers.
Characterization of New Molecular Markers of Three Botflies Parasitizing Cervid Hosts
Authors: de la Fuente Ana M , Caparrós Noelia , Mora-Rodríguez José M , Molina María , Aleix-Mata Gaël , Velarde Roser , Fidalgo Luis E , López-Beceiro Ana M , Lorite Pedro , Boos Mathieu , Faure Eva , Pérez Jesús M , Sánchez Antonio 
Published: February 2021

AbstractSpecific identification of oestrid larvae is usually problematic not only when using morphobiometric features, but also when applying molecular criteria, since very few molecular markers have been described for this group of flies. New molecular markers for oestrid are needed for more reliable species identification, diagnostic purposes, and epidemiological surveys; moreover, they can help in phylogenetic reconstruction. Here, we report the characterization of COI, 28S rDNA, ITS1, and ITS2 in Cephenemyia stimulator from roe deer and in Cephenemyia auribarbis and Pharyngomyia picta from red deer. The COI and 28S rDNA are very uniform in length, while the ITSs sequences are highly variable at both intraspecific and interspecific levels. The described ITSs sequences were longer than those described for other dipteran species by the presence of simple repeats and tandem repeat sequences. In C. auribarbis both ITS1 and ITS2 appeared as two variants, one short and the other long. In general, the analyzed markers present low intraspecific genetic variation and high interspecific variation. ITSs showed the greatest amount of intraspecific and interspecific variation. Phylogenetic analysis demonstrated that the characterized sequences differentiate the species and genera of Oestridae.
Nutrient resorption and stoichiometric responses of poplar (Populus deltoids) plantations to N addition in a coastal region of eastern China
Authors: Jiang Dalong , Li Qian , Geng Qinghong , Zhang Menghua , Xu Chonghua , Hu Guoqing , Shen Caiqin , Ruan Honghua , Xu Xia 
Published: February 2021

Abstract

Aims
Leaf nutrient resorption is sensitive to changes in soil nutrients. However, the effects of N deposition on nutrient resorption efficiency (NuRE) in plant macro-nutrients remain unclear. Poplar (Populus deltoids) is one of the most extensively cultivated hardwood species worldwide. We explored general patterns and dominant drivers of NuRE and stoichiometry of poplar plantations in response to N addition.

Methods
We conducted a 4-year N-addition experiment to explore NuRE and stoichiometric responses to N addition in two poplar (P. deltoids) plantations (8- and 12-year-old stands) in a coastal region of eastern China. We measured soil and foliar (green and senesced leaves) concentrations of nitrogen (N), phosphorus (P), potassium (K), calcium (Ca) and magnesium (Mg) for a series of N addition treatments including N0 (0 kg N ha−1 yr−1), N1 (50 kg N ha−1 yr−1), N2 (100 kg N ha−1 yr−1), N3 (150 kg N ha−1 yr−1) and N4 (300 kg N ha−1 yr−1).

Important Findings
Consistent for (both) 8- and 12-year-old stands, N addition did not affect the NuRE and stoichiometry (with the exception of CaRE and CaRE:MgRE ratio). N resorption efficiency–P resorption efficiency (NRE–PRE) scaling slopes were consistently less than 1.0 under N addition. These results suggest that NRE generally decouples from PRE within each N treatment. Moreover, these results point to robust control of green leaf nutritional status on nutrient resorption processes as indicated by the positive relationships between NuRE and green leaf nutrient concentrations. Our findings provided a direct evidence that growth in 12-year-old poplar plantations was N-limited in the coastal region of eastern China.