bluuebunny/crossref_metadata_2025 huggingface dataset:
An application of Systematic Anomalous Case Analysis to improve models predicting contraceptive use in the Philippines
Authors: Narasimhan Subasri , Gipson Jessica D.
Published: April 2021

Amidst persistently high unintended pregnancy rates and lags in contraceptive use, novel methodological approaches may prove useful in investigating sexual and reproductive health outcomes in the Philippines. Systematic Anomalous Case Analysis (SACA) – a mixed-methods technique – was employed to examine predictors of women’s lifetime contraceptive use. First, multivariable, longitudinal Poisson regression models predicted fertility and sexual debut using the 1998–2009 Cebu Longitudinal Health and Nutrition Surveys (CLHNS), then regression outliers and normative cases were used to identify 48 participants for in-depth interviews (2013–2014) for further examination. Qualitative findings from 24 women highlighted ‘control over life circumstances’ was critical, prompting the addition of two items to the original quantitative models predicting any contraceptive use (n=532). Each of the items, ‘what happens to [them] is their own doing’ and ‘[I] do not [have] enough control over direction life is taking [me]’, significantly and independently predicted any contraceptive use (aOR: 2.37 (CI: 1.24–4.55) and aOR: 0.46 (CI: 0.28–0.77), respectively). The findings demonstrate the utility of SACA to improve the understanding and measurement of sexual and reproductive health outcomes and underscore the importance of integrating psychosocial constructs into existing models of fertility and reproductive behaviour in the Philippines to improve sexual and reproductive health outcomes.
Description of a new species ofAuriculostoma(Digenea: Allocreadiidae) fromCharacidium heirmostigmata(Characiformes: Crenuchidae) from Argentina, using morphological and molecular data
Authors: Montes M.M. , Barneche J. , Croci Y. , Balcazar D. , Almirón A. , Martorelli S. , Pérez-Ponce de León G.
Published: April 2021

During a parasitological survey of fishes at Iguazu National Park, Argentina, specimens belonging to the allocreadiid genusAuriculostomawere collected from the intestine ofCharacidium heirmostigmata. The erection of the new species is based on a unique combination of morphological traits as well as on phylogenetic analysis.Auriculostoma guacurariin. sp. resembles four congeneric species –Auriculostoma diagonale,Auriculostoma platense,Auriculostoma ticaandAuriculostoma totonacapanensis– in having smooth and oblique testes, but can be distinguished by a combination of several morphological features, hosts association and geographic distribution. Morphologically, the new species can be distinguished from bothA. diagonaleandA. platenseby the egg size (bigger in the first and smaller in the last); fromA. ticaby a shorter body length, the genital pore position and the extension of the caeca; and fromA. totonacapanensisby the size of the oral and ventral sucker and the post-testicular space. Additionally, one specimen ofAuriculostomacf.stenopterifrom the characidCharax stenopterus(Characiformes) from La Plata River, Argentina, was sampled and the partial 28S rRNA gene was sequenced. The phylogenetic analysis revealed thatA. guacurariin. sp. clustered withA. ticaand these two as sister taxa toA.cf.stenopteri. The new species described herein is the tenth species in the genus and the first one parasitizing a member of the family Crenuchidae.
Comment on “Stepped pressure profile equilibria in cylindrical plasmas via partial Taylor relaxation” [J. Plasma Physics (2006), vol. 72, part 6, pp. 1167–1171]
Authors: Wang Yuanfan , Malhotra Dhairya , Cerfon Antoine J.
Published: April 2021

In an early study of the properties and capabilities of the multiregion, relaxed magnetohydrodynamic model, Hole, Hudson & Dewar claim that they are able to construct a multiregion stepped pressure cylindrical equilibrium which does not require the existence of surface currents. We present a brief argument showing that this claim is incorrect, and clarify the meaning of their statement. Furthermore, even with the statement clarified, we demonstrate that it is not possible to find solutions to reproduce the equilibrium corresponding to the parameters given in the article. We invite the authors to provide a corrigendum with the correct values of the equilibrium they constructed.
Does genetic variation on the shy–bold continuum influence carnivore attacks on people? Evidence from the brown bear
Authors: Blanco Juan C. , Palomero Guillermo , López-Bao José V. , Ballesteros Fernando
Published: April 2021

Little is known about the heritable behavioural traits of attacks by large carnivores on people. During the last 30 years attacks by brown bears Ursus arctos on people in the Cantabrian Mountains of Spain have been disproportionately concentrated in the eastern subpopulation. Excluding factors such as the existence of a single unusually bold bear, a higher human population density, particular human activities promoting encounters, or clear habitat differences in the area of this subpopulation, we propose that a plausible explanation for the unbalanced geographical attack pattern is that this subpopulation, separated a century earlier from the western subpopulation, may harbour a higher proportion of bolder bears. In the absence of genetic analyses this explanation remains speculative, but supports the hypothesis that genetic variation on the shy–bold continuum may influence attacks of large carnivores on people.
“Ibizagate”: Capturing a Political Field in Flux
Authors: Karner Christian
Published: April 2021

The “Ibiza affair,” a succession of scandals triggered by undercover recordings of the FPÖ's former head, Heinz-Christian Strache, in compromising discussions with a purported Russian oligarch's niece has profoundly altered Austria's political landscape and public debates. This article offers a historically contextualized analysis of the multiple voices and competing truth claims articulated by diverse actors in the course of the scandal's fallout. Empirically, this discussion offers a systematic analysis of political and media discourses focused on “Ibiza” between May 2019 and June 2020. Conceptually, the argument builds on Michel Foucault's approach outlined in I, Pierre Rivière and its subsequent applications within nationalism studies. This analysis thus examines data through the questions as to who speaks about the event in question, how they do so, what is being claimed and disputed, and which political strategies and trajectories this enables. The competing, partly shifting positions revealed are the following: Strache's initial regret that soon turned to a self-ascribed “victim-cum-martyr” status; the FPÖ's distancing and eventual rupture from its long-standing Bundesparteiobmann; the Kronen Zeitung's attempted ideological repositioning; the ÖVP's need and opportunity to shift its positions vis-à-vis its political competitors; and critical voices calling for far-reaching structural changes. With the full facts behind the scandal still to be established, the (post-Foucauldian) approach applied here captures the contestations, (new) fault lines, and (shifting) political boundaries constitutive of a discursive field in a crisis context.
PHILOSOPHERS’ PATH OR CULT ROAD? THE PERIPATOS ON THE SLOPES OF THE AKROPOLIS AND LYKOURGOS’ POLICY OF RENEWAL
Authors: Rubel Alexander
Published: April 2021

The Peripatos, the pathway that encircles the slopes of the Athenian Akropolis, was renovated in the late fourth centurybcunder Lykourgos. The crucial question concerning this somewhat neglected but important path is whether it was simply a walkway, perhaps built for philosophers of the school of Aristotle, who taught their lessons while walking, or whether this pathway had a specific cultic function. This paper gathers arguments for a cultic interpretation of the Peripatos. On this view, the pathway and its renovation were important because only the Peripatos offered access to several minor sanctuaries on the slopes of the Akropolis as well as the Aglaureion, the sanctuary where the ephebes swore their oath, a crucial institution for Lykourgos’ reforms.
COVID-19 research priorities for non-pharmaceutical public health and social measures
Authors: Semenza Jan C. , Adlhoch Cornelia , Baka Agoritsa , Broberg Eeva , Cenciarelli Orlando , De Angelis Stefania , Einoder-Moreno Margot , Dalmau Irina Jovel Quinonez , Kinross Pete , Kinsman John , Leitmeyer Katrin , Melidou Angeliki , Needham Howard , Plachouras Diamantis , Robesyn Emmanuel , Rosales-Klintz Senia , Suk Jonathan E. , Suetens Carl , Weist Klaus , Würz Andrea , Penttinen Pasi
Published: April 2021

Europe is in the midst of a COVID-19 epidemic and a number of non-pharmaceutical public health and social measures have been implemented, in order to contain the transmission of severe acute respiratory syndrome coronavirus 2. These measures are fundamental elements of the public health approach to controlling transmission but have proven not to be sufficiently effective. Therefore, the European Centre for Disease Prevention and Control has conducted an assessment of research gaps that can help inform policy decisions regarding the COVID-19 response. We have identified research gaps in the area of non-pharmaceutical measures, physical distancing, contact tracing, transmission, communication, mental health, seasonality and environment/climate, surveillance and behavioural aspects of COVID-19. This prioritisation exercise is a step towards the global efforts of developing a coherent research road map in coping with the current epidemic but also developing preparedness measures for the next unexpected epidemic.
The politics of everyday life: urban materialities, modernity and conflictual interactions on two Danish mass housing estates in the 1970s
Authors: Høghøj Mikkel
Published: April 2021

This article explores the relations between everyday life, materiality and urban modernity on two Danish mass housing estates, the Gellerup Plan and Vollsmose, in the 1970s. Specifically, the article examines a series of conflicts concerning the residents’ use and misuse of seemingly mundane material devices, including shopping trolleys, waste disposal and laundry facilities. In doing so, the article argues that the residents’ daily engagements with everyday materialities and technologies constitute a privileged, yet overlooked, point of entry into the shifting relations between modernity, materiality and agency in the Danish welfare city in the 1970s.
A new discovered gene mutation in a child with dilated cardiomyopathy
Authors: Chen Xiaolong , Xie Yewei , Li Xiaobing , Gong Jin , Shen Li , Zhang Rufang
Published: April 2021

Dilated cardiomyopathy is characterised by dilatation and impaired contraction of the left ventricle or both ventricles, which is the most common childhood cardiomyopathy. In recent years, it has been recognised that many sorts of genetic mutations may contribute to dilated cardiomyopathy. We now report a rare association of dilated cardiomyopathy with site mutation of BMPR2 gene. We did not find such an association reported in the medical literature.
Prehospital Intubations Are Associated with Elevated Endotracheal Tube Cuff Pressures: A Cross-Sectional Study Characterizing ETT Cuff Pressures at a Tertiary Care Emergency Department
Authors: Chen Ruo S. , O’Connor Laurel , Rebesco Matthew R. , LaBarge Kara L. , Remotti Edgar J. , Tennyson Joseph C.
Published: April 2021

Introduction:

Emergency Medical Services (EMS) providers are trained to place endotracheal tubes (ETTs) in the prehospital setting when indicated. Endotracheal tube cuffs are traditionally inflated with 10cc of air to provide adequate seal against the tracheal lumen. There is literature suggesting that many ETTs are inflated well beyond the accepted safe pressures of 20-30cmH2O, leading to potential complications including ischemia, necrosis, scarring, and stenosis of the tracheal wall. Currently, EMS providers do not routinely check ETT cuff pressures. It was hypothesized that the average ETT cuff pressure of patients arriving at the study site who were intubated by EMS exceeds the safe pressure range of 20-30cmH2O.

Objectives:

While ETT cuff inflation is necessary to close the respiratory system, thus preventing air leaks and aspiration, there is evidence to suggest that over-inflated ETT cuffs can cause long-term complications. The purpose of this study is to characterize the cuff pressures of ETTs placed by EMS providers.

Methods:

This project was a single center, prospective observational study. Endotracheal tube cuff pressures were measured and recorded for adult patients intubated by EMS providers prior to arrival at a large, urban, tertiary care center over a nine-month period. All data were collected by respiratory therapists utilizing a cuff pressure measurement device which had a detectable range of 0-100cmH2O and was designed as a syringe. Results including basic patient demographics, cuff pressure, tube size, and EMS service were recorded.

Results:

In total, 45 measurements from six EMS services were included with ETT sizes ranging from 6.5-8.0mm. Mean patient age was 52.2 years (67.7% male). Mean cuff pressure was 81.8cmH2O with a range of 15 to 100 and a median of 100. The mode was 100cmH2O; 40 out of 45 (88.9%) cuff pressures were above 30cmH2O. Linear regression showed no correlation between age and ETT cuff pressure or between ETT size and cuff pressure. Two-tailed T tests did not show a significant difference in the mean cuff pressure between female versus male patients.

Conclusion:

An overwhelming majority of prehospital intubations are associated with elevated cuff pressures, and cuff pressure monitoring education is indicated to address this phenomenon.
Near-term impact of climate variability on yam rot incidence over a humid tropical region: projections in CORDEX-Africa scenarios
Authors: Okoro Ugochukwu K. , Akalazu Jacinta N. , Nwulu Nobert C.
Published: April 2021

The global population is projected to be enormous by the mid-21st century, whereas, most essential crops being sustained by the rain-fed agriculture are threatened by climate change. Therefore, the study investigated the projected near-future effect of rainfall variability on rot incidence and yam production in humid tropical Nigeria. Production data from the Food and Agriculture Organization and the Nigeria National Bureau of Statistics showed the significant increasing trend in the annual yam output. The field survey conducted in 2018 showed that the maximum percentage of rot incidence occurred in July. Climate Research Unit observational rainfall data from 1979 to 2018 showed the nonsignificant trend in the interannual rainfall variability; however, it showed low variability and a significant decreasing trend in the July rainfall. A pathogenicity test on yam samples confirmed rot by fungi, bacteria and nematodes as virulent pathogens, whereas, the nutritional qualities of the rotted yams were indicated. Monthly rainfall and rot incidence showed positive correlation (r = 0.84, significant at 99% from t-test). The positive characteristic impact values indicated that increase (decrease) in the monthly rainfall corresponds to increase (decrease) in the magnitude of monthly percentage rot incidence. Thus, the significantly decreasing rainfall reduced the quantity of rot incidence and consequently increased the annual yam production for the period. Selected CoOrdinated Regional Downscaling EXperiment-Africa models and the ensemble mean showed a good measure of agreement with observational rainfall in the historical experiments. The efficiencies of the bias-corrected outputs in the representative concentration pathway (RCP) 4.5 and 8.5 indicated improved ‘reasonable’ performances. Bias-corrected projections of the July rainfall showed an increasing trend in both the RCPs, which indicate a potential increase in rot incidence and the consequent decline in annual yam production. The findings are imperative in sustaining the global food supply.
The ‘last mile’ for climate data supporting local adaptation
Authors: Celliers Louis , Costa María Máñez , Williams David Samuel , Rosendo Sergio
Published: April 2021

Non-technical summary

The ‘last mile’ is a transportation planning term that describes the movement of people and goods from a transportation hub to a final destination; a local place such as a home or a shop. This is the final step of the logistics process that unites the product with its new owner. We present and explain challenges of science-guided adaptation at the local level, and how this is an equivalent ‘last mile’ challenge for climate adaptation.

Technical summary

The ‘last mile’ issue, a term used in transportation planning, describes the movement of people and goods from a transportation hub to a final destination, a local place such as a home or a shop. This is the critical final step of the logistics process that unites the product with its new owner, and the point of the value chain. This analogy aptly describes the last steps between presenting scientific evidence of climate change to decision-makers for use in local adaptation and planning. Climate change data (observational and model simulation data e.g. climate change projections and predictions) remain under-utilised, especially by local institutions and actors for which adaptation is a priority. The assumptions and assertions of the classical data–information–knowledge–wisdom are challenged, and a derivative form of the information hierarchy is proposed. Elements of the classical information hierarchy are offset by four balancing elements of access (to data); usability (of information); governance (of knowledge) and politics (of wisdom). These balancing elements and their relatedness coincide with newer models of innovation relating to the interaction between different stakeholders across the different levels of governance, the inclusion of stakeholder expectations, transparency and accountability.

Social media summary

Climate data to wise decision-making in the ‘last mile’: a novel perspective on science-guided local adaptation.
Interference of wild oat (Avena fatua) and sterile oat (Avena sterilis ssp. ludoviciana) in wheat
Authors: Mahajan Gulshan , Chauhan Bhagirath Singh
Published: April 2021

Prevalence of wild oat (Avena fatua L.) and sterile oat [Avena sterilis ssp. ludoviciana (Durieu) Gillet & Magne; referred to as A. sterilis hereafter], winter-season weeds, is increasing in the eastern grain region of Australia. Biological attributes of these weeds enable them to survive in a wide range of environments and under different weed infestation levels. The interference of A. fatua and A. sterilis in a wheat (Triticum aestivum L.) crop was examined in southeast Queensland, Australia, through field studies in 2019 and 2020. Different infestation levels (0, 3, 6, 12, 24, and 48 plants m−2) of A. fatua and A. sterilis were evaluated for their potential to cause yield losses in wheat. Based on a three-parameter logarithmic model, the A. fatua and A. sterilis infestation levels corresponding to 50% wheat yield loss were 15 and 16 plants m−2, respectively. The yield reduction was due to a reduced spike number per unit area because of an increased weed infestation level. At the highest weed infestation level (48 plants m−2), A. fatua and A. sterilis produced a maximum of 4,800 and 3,970 seeds m−2, respectively. Avena fatua exhibited lower seed retention (17% to 39%) than A. sterilis (64% to 80%) at wheat harvest, as most of the seeds of A. fatua had shattered at crop maturity. Our results implied that there is a good opportunity for harvest weed seed control if the paddock is infested with A. sterilis. This study suggests that in the absence of an integrated weed management strategy (using both chemical and nonchemical options), a high infestation of these weeds could cause a severe crop yield loss, increase weed seed production, and replenish the weed seedbank in the soil.
DFENS: Diffusion Chronometry Using Finite Elements and Nested Sampling
Authors: Mutch Euan J. F. , Maclennan John , Shorttle Oliver , Rudge John F. , Neave David A.
Published: April 2021

In order to reconcile petrological and geophysical observations of magmatic processes in the temporal domain, the uncertainties in diffusion timescales need to be rigorously assessed. Here, we present a new diffusion chronometry method: Diffusion chronometry using Finite Elements and Nested Sampling (DFENS). This method combines a finite element numerical model with a nested sampling Bayesian inversion, meaning that uncertainties in the parameters contributing to diffusion timescale estimates can be obtained and that observations from multiple elements can be used to better constrain individual timescales. Uncertainties associated with diffusion timescales can be reduced by accounting for covariance in the uncertainty structure of diffusion parameters rather than assuming that they are independent of each other. We applied the DFENS method to the products of the Skuggafjöll eruption from the Bárðarbunga volcanic system in Iceland, which contains zoned macrocrysts of olivine and plagioclase that record a shared magmatic history. Olivine and plagioclase provide consistent pre‐eruptive mixing and mush disaggregation timescales of less than 1 year. The DFENS method goes some way toward improving our ability to rigorously address the uncertainties of diffusion timescales, but efforts still need to be made to understand other systematic sources of uncertainty such as crystal morphology, appropriate choice of diffusion coefficients, initial conditions, crystal growth, and the petrological context of diffusion timescales.
Global Lightning Quanta
Authors: Füllekrug Martin
Published: April 2021

The World Meteorological Organization recently declared lightning an essential climate variable which makes the global lightning flash rate density a key quantity, currently assessed by geostationary satellites and ground‐based lightning location networks. Yet, no theory has been put forward to explain the physical relationships between the thermodynamic temperature of the Earth’s atmosphere T, the global lightning flash occurrence frequency fg, and its radiant energy E of resonant electromagnetic waves within the Earth ionosphere cavity. These three parameters are combined here by adapting the rigorous framework of quantum physics. The minimum amount of radiant energy produced by the lightning flash occurrence frequency is the global lightning quantum E = hfg, h being Planck’s constant. The superposition of numerous global lightning quanta distributes its radiant energy around the world as Earth ionosphere cavity resonances. The novel theory is in agreement with measurements using a radiometer at Arrival Heights, Antarctica, as part of the Stanford ELF/VLF Radio Noise Survey. It is found that the measurements agree with the theory within ∼30%. The operation of the theory is illustrated with an interpretation of the measurements for an exemplary thermodynamic energy. In this case, the measurements correspond to a radiant temperature ∼−30°C akin to the mixed phase region of thunderclouds where lightning discharges are initiated. The theory can help to assess the mutual impact of climate change and global lightning on each other as proposed by the World Meteorological Organization.
Evaluation of High Mountain Asia‐Land Data Assimilation System (Version 1) From 2003 to 2016, Part I: A Hyper‐Resolution Terrestrial Modeling System
Authors: Xue Yuan , Houser Paul R. , Maggioni Viviana , Mei Yiwen , Kumar Sujay V. , Yoon Yeosang
Published: April 2021

This first paper of the two‐part series focuses on demonstrating the accuracy of a hyper‐resolution, offline terrestrial modeling system used for the High Mountain Asia (HMA) region. To this end, this study systematically evaluates four sets of model simulations at point scale, basin scale, and domain scale obtained from different spatial resolutions including 0.01° (∼1‐km) and 0.25° (∼25‐km). The assessment is conducted via comparisons against ground‐based observations and satellite‐derived reference products. The key variables of interest include surface net shortwave radiation, surface net longwave radiation, skin temperature, near‐surface soil temperature, snow depth, snow water equivalent, and total runoff. In the evaluation against ground‐based measurements, the superiority of the 0.01° estimates are mostly demonstrated across relatively complex terrain. Specifically, hyper‐resolution modeling improves the skill in meteorological forcing estimates (except precipitation) by 9% relative to coarse‐resolution estimates. The model forced by downscaled forcings in its entirety yields the highest skill in model output states as well as precipitation, which improves the skill obtained by coarse‐resolution estimates by 7%. These findings, on one hand, corroborate the importance of employing the hyper‐resolution versus coarse‐resolution modeling in areas characterized by complex terrain. On the other hand, by evaluating four sets of model simulations forced with different precipitation products, this study emphasizes the importance of accurate hyper‐resolution precipitation products to drive model simulations.
Impact of the 2016 Southeastern US Wildfires on the Vertical Distribution of Ozone and Aerosol at Huntsville, Alabama
Authors: Wang Bo , Kuang Shi , Pfister Gabriele G. , Pour‐Biazar Arastoo , Buchholz Rebecca R. , Langford Andrew O. , Newchurch Michael J.
Published: April 2021

We present an integrated analysis of measurements from ozonesonde, ozone (O3) Differential Absorption Lidar (DIAL), ceilometer, surface monitors, and space‐borne observations in conjunction with the regional chemical transport model Weather Research and Forecast Model with Chemistry (WRF‐Chem) to investigate the effect of biomass burning emissions on the vertical distribution of ozone and aerosols during an episode of the 2016 Southeastern United States wildfires. The ceilometer and DIAL measurements capture the vertical extent of the smoke plumes affecting the surface and upper air over Huntsville, AL. The model evaluation results suggest a scaling factor of 3–4 for the wildfire aerosol emissions in order to better match observed aerosol optical depth, fine particulate matter (PM2.5), and DIAL aerosol extinction. We use the scaled emissions together with WRF‐Chem tendency diagnostics to quantify the fire impacts and characterize the processes affecting the vertical ozone budget downstream of the wildfires. During the daytime at Huntsville on November 12 and 13, we estimate that fire emissions contribute 12–32 μg/m3 (44%–70%) to hourly surface PM2.5 and 7–8 ppb/10 h (30%–37%) to the surface ozone increase (ΔO3), respectively. Net chemical ozone production (PO3) is the main contributor to upper‐air ozone, which reaches 17–19 ppb/10 h with an estimated 14%–25% contribution from fire sources. Vertical mixing and advection are the major drivers of changes in surface ozone. Model analysis indicates that advection dominates ΔO3 due to fire emissions below 1 km on November 12, while local photochemistry dominates on November 13. These results quantify the different mechanisms through which fires can influence the vertical ozone budget and point out uncertainties in fire inventories that need to be addressed in light of the increasing role of wildfires on air quality.
Insulin-positive ductal cells do not migrate into preexisting islets during pregnancy
Authors: Liu Qun , Jiang Yinan , Zhu Lingyan , Qian Jieqi , Wang Chaoban , Yang Tianlun , Prasadan Krishna , Gittes George K. , Xiao Xiangwei
Published: April 2021

The adult pancreatic ductal system was suggested to harbor facultative beta-cell progenitors similar to the embryonic pancreas, and the appearance of insulin-positive duct cells has been used as evidence for natural duct-to-beta-cell reprogramming. Nevertheless, the phenotype and fate of these insulin-positive cells in ducts have not been determined. Here, we used a cell-tagging dye, CFDA-SE, to permanently label pancreatic duct cells through an intraductal infusion technique. Representing a time when significant increases in beta-cell mass occur, pregnancy was later induced in these CFDA-SE-treated mice to assess the phenotype and fate of the insulin-positive cells in ducts. We found that a small portion of CFDA-SE-labeled duct cells became insulin-positive, but they were not fully functional beta-cells based on the in vitro glucose response and the expression levels of key beta-cell genes. Moreover, these insulin-positive cells in ducts expressed significantly lower levels of genes associated with extracellular matrix degradation and cell migration, which may thus prevent their budding and migration into preexisting islets. A similar conclusion was reached through analysis of the Gene Expression Omnibus database for both mice and humans. Together, our data suggest that the contribution of duct cells to normal beta-cells in adult islets is minimal at best.
Salmonella nomenclature in the genomic era: a time for change
Authors: Chattaway Marie A. , Langridge Gemma C. , Wain John
Published: April 2021

Salmonella enterica nomenclature has evolved over the past one hundred years into a highly sophisticated naming convention based on the recognition of antigens by specific antibodies. This serotyping scheme has led to the definition of over 2500 serovars which are well understood, have standing in nomenclature and, for the majority, biological relevance. Therefore, it is highly desirable for any change in naming convention to maintain backwards compatibility with the information linked to these serovars. The routine use of whole genome sequencing and the well-established link between sequence types and serovars presents an opportunity to update the scheme by incorporating the phylogenetically relevant sequence data whilst preserving the best of serotyping nomenclature. Advantages include: overcoming the variability in antibody preparations; removing the need to use laboratory animals and implementing a truly universal system. However, the issue of trying to reproduce the phenotyping gold standard needs to be relaxed if we are to fully embrace the genomic era. We have used whole genome sequence data from over 46,000 isolates of Salmonella enterica subspecies enterica to define clusters in two stages: Multi Locus Sequence Typing followed by antigen prediction. Sequence type—serotype discrepancies were resolved using core SNP clustering to determine the phylogenetic groups and this was confirmed by overlaying the antigenic prediction onto the core SNP clusters and testing the separation of clusters using cgMLST Hierarchical Clustering. This allowed us to define any major antigenic clusters within an ST—here called the MAC type and written as ST-serovar. Using this method, 99.96% of Salmonella isolates reported in the UK were assigned a MAC type and linked to a serovar name taken from the Kauffmann and White scheme. We propose a change for reporting of Salmonella enterica sub-types using the ST followed by serovar.
Prediction of PCR amplification from primer and template sequences using recurrent neural network
Authors: Kayama Kotetsu , Kanno Miyuki , Chisaki Naoto , Tanaka Misaki , Yao Reika , Hanazono Kiwamu , Camer Gerry Amor , Endoh Daiji
Published: April 2021

We have developed a novel method to predict the success of PCR amplification for a specific primer set and DNA template based on the relationship between the primer sequence and the template. To perform the prediction using a recurrent neural network, the usual double-stranded formation between the primer and template nucleotide sequences was herein expressed as a five-lettered word. The set of words (pseudo-sentences) was placed to indicate the success or failure of PCR targeted to learn recurrent neural network (RNN). After learning pseudo-sentences, RNN predicted PCR results from pseudo-sentences which were created by primer and template sequences with 70% accuracy. These results suggest that PCR results could be predicted using learned RNN and the trained RNN could be used as a replacement for preliminary PCR experimentation. This is the first report which utilized the application of neural network for primer design and prediction of PCR results.
Plasma biomarkers for prediction of early tumor recurrence after resection of pancreatic ductal adenocarcinoma
Authors: Rittmann Marie-Claire , Hussung Saskia , Braun Lukas M. , Klar Rhena F. U. , Biesel Esther A. , Fichtner-Feigl Stefan , Fritsch Ralph , Wittel Uwe A. , Ruess Dietrich A.
Published: April 2021

Pancreatic ductal adenocarcinoma (PDAC) is a disease with a very unfavorable prognosis. Surgical resection represents the only potentially curative treatment option, but recurrence after complete resection is almost certain. In an exploratory attempt we here aimed at identifying preoperative plasma protein biomarkers with the potential to predict early recurrence after resection of PDAC. Peripheral blood samples from 14 PDAC patients divided into three groups according to their time to tumor recurrence after curatively intended resection (early: < 6 months, medium: 6–12 months, late: > 12 months) underwent targeted proteome analysis. Proteins most strongly discriminating early and late recurrence were then examined in a number of established PDAC cell lines and their culture supernatants. Finally, PDAC organoid lines from primary tumors of patients with early and late recurrence were analyzed for confirmation and validation of results. In total, 23 proteins showed differential abundance in perioperative plasma from PDAC patients with early recurrence when compared to patients with late recurrence. Following confirmation of expression on a transcriptional and translational level in PDAC cell lines we further focused on three upregulated (MAEA, NT5E, AZU1) and two downregulated proteins (ATP6AP2, MICA). Increased expression of NT5E was confirmed in a subset of PDAC organoid cultures from tumors with early recurrence. MICA expression was heterogeneous and ATP6AP2 levels were very similar in both organoids from early and late recurrent tumors. Most strikingly, we observed high MAEA expression in all tested PDAC (n = 7) compared to a non-cancer ductal organoid line. MAEA also demonstrated potential to discriminate early recurrence from late recurrence PDAC organoids. Our study suggests that identification of plasma protein biomarkers released by tumor cells may be feasible and of value to predict the clinical course of patients. Prediction of recurrence dynamics would help to stratify up-front resectable PDAC patients for neoadjuvant chemotherapy approaches in an individualized fashion. Here, MAEA and NT5E were the most promising candidates for further evaluation.
Common genetic variants and pathways in diabetes and associated complications and vulnerability of populations with different ethnic origins
Authors: Shoily Sabrina Samad , Ahsan Tamim , Fatema Kaniz , Sajib Abu Ashfaqur
Published: April 2021

Diabetes mellitus is a complex and heterogeneous metabolic disorder which is often pre- or post-existent with complications such as cardiovascular disease, hypertension, inflammation, chronic kidney disease, diabetic retino- and nephropathies. However, the frequencies of these co-morbidities vary among individuals and across populations. It is, therefore, not unlikely that certain genetic variants might commonly contribute to these conditions. Here, we identified four single nucleotide polymorphisms (rs5186, rs1800795, rs1799983 and rs1800629 in AGTR1, IL6, NOS3 and TNFA genes, respectively) to be commonly associated with each of these conditions. We explored their possible interplay in diabetes and associated complications. The variant allele and haplotype frequencies at these polymorphic loci vary among different super-populations (African, European, admixed Americans, South and East Asians). The variant alleles are particularly highly prevalent in different European and admixed American populations. Differential distribution of these variants in different ethnic groups suggests that certain drugs might be more effective in selective populations rather than all. Therefore, population specific genetic architectures should be considered before considering a drug for these conditions.
The role of mechanical control of biofilm in the salivary pH after sucrose exposure in children with early childhood caries
Authors: Lima-Holanda Aline Tavares , de Sousa Emerson Tavares , Nobre-dos-Santos Marinês , Steiner-Oliveira Carolina
Published: April 2021

This quasi-experimental study sought to investigate if the mechanical control of biofilm (3-times-a-day) modifies the saliva’s ability to buffer the oral environment after 20% sucrose rinse (SR20%) in children with early childhood caries (ECC). Here, SR20% reduced the saliva’s pH in both groups and the mechanical control of biofilm had a greater effect on this parameter after SR20% in CF children. The mechanical control of biofilm evidenced a higher buffering capacity in CF children before SR20%, which was not observed after SR20%. Otherwise, the absence of mechanical control of biofilm showed that buffering capacity was comparable in the two groups before SR20%, whereas after SR20% the saliva’s buffering capacity of CF children was higher than ECC children. When biofilm was mechanically controlled, carbonic anhydrase VI activity did not change after SR20% whereas the absence of mechanical control of biofilm reduced this enzyme activity after SR20%. In conclusion, the mechanical control of biofilm did not change saliva’s ability to buffer the oral environment after SR20% in children with ECC. On the other hand, CF children appeared to regulate more effectively the saliva’s pH than ECC children while the absence of mechanical control of biofilm mediated their pH-modifying ability after SR20%.
Deep anomaly detection of seizures with paired stereoelectroencephalography and video recordings
Authors: Martini Michael L. , Valliani Aly A. , Sun Claire , Costa Anthony B. , Zhao Shan , Panov Fedor , Ghatan Saadi , Rajan Kanaka , Oermann Eric Karl
Published: April 2021

Real-time seizure detection is a resource intensive process as it requires continuous monitoring of patients on stereoelectroencephalography. This study improves real-time seizure detection in drug resistant epilepsy (DRE) patients by developing patient-specific deep learning models that utilize a novel self-supervised dynamic thresholding approach. Deep neural networks were constructed on over 2000 h of high-resolution, multichannel SEEG and video recordings from 14 DRE patients. Consensus labels from a panel of epileptologists were used to evaluate model efficacy. Self-supervised dynamic thresholding exhibited improvements in positive predictive value (PPV; difference: 39.0%; 95% CI 4.5–73.5%; Wilcoxon–Mann–Whitney test; N = 14; p = 0.03) with similar sensitivity (difference: 14.3%; 95% CI − 21.7 to 50.3%; Wilcoxon–Mann–Whitney test; N = 14; p = 0.42) compared to static thresholds. In some models, training on as little as 10 min of SEEG data yielded robust detection. Cross-testing experiments reduced PPV (difference: 56.5%; 95% CI 25.8–87.3%; Wilcoxon–Mann–Whitney test; N = 14; p = 0.002), while multimodal detection significantly improved sensitivity (difference: 25.0%; 95% CI 0.2–49.9%; Wilcoxon–Mann–Whitney test; N = 14; p < 0.05). Self-supervised dynamic thresholding improved the efficacy of real-time seizure predictions. Multimodal models demonstrated potential to improve detection. These findings are promising for future deployment in epilepsy monitoring units to enable real-time seizure detection without annotated data and only minimal training time in individual patients.
Diminished growth and vitality in juvenile Hydractinia echinata under anticipated future temperature and variable nutrient conditions
Authors: Tschink Daniel , Gerlach Gabriele , Winklhofer Michael , Kohlmeier Cora , Blasius Bernd , Eickelmann Laura , Schadewell Yvonne , Strahl Julia
Published: April 2021

In a warming climate, rising seawater temperatures and declining primary and secondary production will drastically affect growth and fitness of marine invertebrates in the northern Atlantic Ocean. To study the ecological performance of juvenile hydroids Hydractinia echinata we exposed them to current and predicted water temperatures which reflect the conditions in the inter- and subtidal in combination with changing food availability (high and low) in laboratory experiments. Here we show, that the interplay between temperature stress and diminished nutrition affected growth and vitality of juvenile hydroids more than either factor alone, while high food availability mitigated their stress responses. Our numerical growth model indicated that the growth of juvenile hydroids at temperatures beyond their optimum is a saturation function of energy availability. We demonstrated that the combined effects of environmental stressors should be taken into consideration when evaluating consequences of climate change. Interactive effects of ocean warming, decreasing resource availability and increasing organismal energy demand may have major impacts on biodiversity and ecosystem function.
Effect of polyaniline content and protonating dopants on electroconductive composites
Authors: Bednarczyk Katarzyna , Matysiak Wiktor , Tański Tomasz , Janeczek Henryk , Schab-Balcerzak Ewa , Libera Marcin
Published: April 2021

Elastic constructive elements prepared by electrospinning using polyacrylonitrile/polyaniline (PAN/PANI) electroconductive composites were prepared and investigated in terms of their thermal and mechanical properties. This study was focused on the impact of the type of counterion of polyaniline and the PANI content in composites on the thermal, conductive and morphological properties of electrospun fibers. In this study, composites obtained from PANI doped with sulfuric acid showed the highest conductivity, and composites obtained from PANI doped with hydrochloric acid showed the highest thermal stability. All obtained composites exhibited good thermal stability, with T5values in the range of 230–268 °C that increased with increasing PANI content. The prepared composites exhibited comparable PAN Tgvalues, which indicates their suitability for processing. Instrumental analysis of polymers and composites was carried out using UV–visible spectroscopy, thermogravimetric analysis, differential scanning calorimetry, dynamic mechanical thermal analysis and scanning electron microscopy.
Critical role of SMG7 in activation of the ATR-CHK1 axis in response to genotoxic stress
Authors: Ho Kathleen , Luo Hongwei , Zhu Wei , Tang Yi
Published: April 2021

CHK1 is a crucial DNA damage checkpoint kinase and its activation, which requires ATR and RAD17, leads to inhibition of DNA replication and cell cycle progression. Recently, we reported that SMG7 stabilizes and activates p53 to induce G1 arrest upon DNA damage; here we show that SMG7 plays a critical role in the activation of the ATR-CHK1 axis. Following genotoxic stress, SMG7-null cells exhibit deficient ATR signaling, indicated by the attenuated phosphorylation of CHK1 and RPA32, and importantly, unhindered DNA replication and fork progression. Through its 14-3-3 domain, SMG7 interacts directly with the Ser635-phosphorylated RAD17 and promotes chromatin retention of the 9-1-1 complex by the RAD17-RFC, an essential step to CHK1 activation. Furthermore, through maintenance of CHK1 activity, SMG7 controls G2-M transition and facilitates orderly cell cycle progression during recovery from replication stress. Taken together, our data reveals SMG7 as an indispensable signaling component in the ATR-CHK1 pathway during genotoxic stress response.
Knockout of zebrafish desmin genes does not cause skeletal muscle degeneration but alters calcium flux
Authors: Kayman Kürekçi Gülsüm , Kural Mangit Ecem , Koyunlar Cansu , Unsal Seyda , Saglam Berk , Ergin Bora , Gizer Merve , Uyanik Ismail , Boustanabadimaralan Düz Niloufar , Korkusuz Petek , Talim Beril , Purali Nuhan , Hughes Simon M. , Dincer Pervin R.
Published: April 2021

Desmin is a muscle-specific intermediate filament protein that has fundamental role in muscle structure and force transmission. Whereas human desmin protein is encoded by a single gene, two desmin paralogs (desma and desmb) exist in zebrafish. Desma and desmb show differential spatiotemporal expression during zebrafish embryonic and larval development, being similarly expressed in skeletal muscle until hatching, after which expression of desmb shifts to gut smooth muscle. We generated knockout (KO) mutant lines carrying loss-of-function mutations for each gene by using CRISPR/Cas9. Mutants are viable and fertile, and lack obvious skeletal muscle, heart or intestinal defects. In contrast to morphants, knockout of each gene did not cause any overt muscular phenotype, but did alter calcium flux in myofibres. These results point to a possible compensation mechanism in these mutant lines generated by targeting nonsense mutations to the first coding exon.
Muscle activation time and free-throw effectiveness in basketball
Authors: Pakosz Paweł , Domaszewski Przemysław , Konieczny Mariusz , Bączkowicz Dawid
Published: April 2021

This study attempts to analyze the relationship between free-throw efficiency and the time of arm muscle activation in players from 3 basketball teams with different levels of experience was investigated. During the experiment each player made 20 free throws during which the activation time of his right and left biceps and triceps brachii muscles were measured with the use of surface electromyography and high-speed cameras. Significant differences in muscle activation time (t) during a free throw were found between the groups of basketball players (p = 0.038) (novices: t = 0.664 ± 0.225 s, intermediate-level players: t = 1.15 ± 0.146 s, experts: t = 1.01 ± 0.388 s). In the right triceps brachii muscle in expert basketball players the coefficient of variation (CV) amounted to 44.60% at 81% efficiency, and in novices to 27.12% at 53% efficiency. The time of arm muscle activation during a free throw and its fluctuations vary along with the training experience of basketball players. In all studied groups of players, the variability of muscle activation time in accurate free throws is greater than in inaccurate free throws. Free-throw speed is irrelevant for free-throw efficiency.
Macular neovascularization in eyes with pachydrusen
Authors: Teo Kelvin Yi Chong , Cheong Kai Xiong , Ong Ricardo , Hamzah Haslina , Yanagi Yasuo , Wong Tien Yin , Chakravarthy Usha , Cheung Chui Ming Gemmy
Published: April 2021

The natural history and clinical significance of pachydrusen is unclear. This study aims to compare the longitudinal changes of eyes with pachydrusen and soft drusen and progression to exudative macular neovascularisation (MNV). Patients with a diagnosis of MNV in one eye only and the fellow eye was selected as the study eye. Study eyes were required to have pachydrusen or soft drusen on fundus photographs and follow up of at least 2 years or until exudative MNV occurred. Systematic grading was performed at baseline and change in drusen area and onset of exudative MNV recorded over the period of follow up. A total of 75 eyes from 75 patients (29 with pachydrusen and 46 with soft drusen) were included. There was no difference in the rate of progression to exudative MNV in the soft and pachydrusen groups (13.3% versus 24.1%, p = 0.38). Pachydrusen, as compared to soft drusen, was associated with polypoidal choroidal vasculopathy subtype (85.7% versus 16.7%, p < 0.01) and the location of exudation was co-localised with soft drusen but not with pachydrusen. There was a higher rate of increase in soft drusen area compared to pachydrusen area (27.7 ± 31.9%/year versus 8.7 ± 12.4%/year respectively, p < 0.01). We found no difference in the proportion of eyes that developed exudative MNV in this study however characterisation of drusen evolution patterns revealed a strong association with exudative MNV subtype.