bluuebunny/crossref_metadata_2025 huggingface dataset:
Inducing upwards band bending by surface stripping ZnO nanowires with argon bombardment
Authors: Barnett Chris J , Navarro-Torres Jorge , McGettrick James D , Maffeis Thierry G G , Barron Andrew R
Published: September 2020

Metal oxide semiconductors such as ZnO have attracted much scientific attention due their material and electrical properties and their ability to form nanostructures that can be used in numerous devices. However, ZnO is naturally n-type and tailoring its electrical properties towards intrinsic or p-type in order to optimise device operation have proved difficult. Here, we present an x-ray photon-electron spectroscopy and photoluminescence study of ZnO nanowires that have been treated with different argon bombardment treatments including with monoatomic beams and cluster beams of 500 atoms and 2000 atoms with acceleration volte of 0.5 keV–20 keV. We observed that argon bombardment can remove surface contamination which will improve contact resistance and consistency. We also observed that using higher intensity argon bombardment stripped the surface for nanowires causing a reduction in defects and surface OH– groups both of which are possible causes of the n-type nature and observed a shift in the valance band edge suggest a shift to a more p-type nature. These results indicate a simple method for tailoring the electrical characteristic of ZnO.
Direct electron attachment to fast hydrogen in 10−9 contrast 1018 W cm−2 intense laser solid target interaction
Authors: Tata Sheroy , Mondal Angana , Sarkar Soubhik , Lad Amit D , Colgan James , Pasley John , Krishnamurthy M
Published: September 2020

The interaction of an ultra-short (<30 fs), high-contrast (<10−9), high-intensity (>1018 W cm−2) laser pulse with a solid target is not generally known to produce and accelerate negative ions. The transient accelerating electrostatic-fields are so strong that they ionize any atom or negative ion at the target surface. In spite of what may appear to be unfavourable conditions, here it is reported that H− ions extending up to 80 keV are measured from such an interaction. The H− ion flux is about 0.1% that of the H+ ions at 20 keV. These measurements employ a recently developed temporally-gated Thomson parabola ion spectrometry diagnostic which significantly improves signal-to-noise ratios. Electrons that co-propagate with the fast protons cause a two-step charge-reduction reaction. The gas phase three-body attachment of electrons to fast neutral hydrogen atoms accounts for the measured H− yield. It is intriguing that such a fundamental gas-phase reaction, involving the attachment of an electron to a hydrogen atom, has not been observed in laboratory experiments previously. Laser-produced plasma offers an alternative environment to the conventional charged particle beam experiments, in which such atomic physics processes can be investigated.
A review of shaped colloidal particles in fluids: anisotropy and chirality
Authors: Witten Thomas A , Diamant Haim
Published: September 2020

This review treats asymmetric colloidal particles moving through their host fluid under the action of some form of propulsion. The propulsion can come from an external body force or from external shear flow. It may also come from externally-induced stresses at the surface, arising from imposed chemical, thermal or electrical gradients. The resulting motion arises jointly from the driven particle and the displaced fluid. If the objects are asymmetric, every aspect of their motion and interaction depends on the orientation of the objects. This orientation in turn changes in response to the driving. The objects’ shape can thus lead to a range of emergent anisotropic and chiral motion not possible with isotropic spherical particles. We first consider what aspects of a body’s asymmetry can affect its drift through a fluid, especially chiral motion. We next discuss driving by injecting external force or torque into the particles. Then we consider driving without injecting force or torque. This includes driving by shear flow and driving by surface stresses, such as electrophoresis. We consider how time-dependent driving can induce collective orientational order and coherent motion. We show how a given particle shape can be represented using an assembly of point forces called a Stokeslet object. We next consider the interactions between anisotropic propelled particles, the symmetries governing the interactions, and the possibility of bound pairs of particles. Finally we show how the collective hydrodynamics of a suspension can be qualitatively altered by the particles’ shapes. The asymmetric responses discussed here are broadly relevant also for swimming propulsion of active micron-scale objects such as microorganisms.
What happens to an acellular scar matrix after implantation in vivo? A histological and related molecular biology study
Authors: Lai Chenzhi , Song Guodong , Pan Bo , Zhao Bo , Wang Hongquan , Tian Dan , Zhao Jingyi , Du Le , Guo Xiaoshuang , Jin Xiaolei , Zong Xianlei
Published: September 2020

It has been established that scar acellular matrices (AMs), which allow cell proliferation, have similar characteristics. The aim of this study was to investigate the repair effect of scar AMs on animals, thus providing a reference for clinical application. Selected mature and immature scar AMs were implanted into animals, and then a negative control group was set for comparison. The effect of scar AMs on wound healing was observed through tissue staining, RT-qPCR, and immunohistochemistry. The materials showed milder inflammation and faster extracellular matrix (ECM) deposition than the negative control group. The ECM deposition and new vessels increased over time. However, the arrangement of ECM in mature scar AM was more regular than in immature scar AM and the negative control group, and more new vessels grew in the mature scar AM group than in the immature scar AM group and negative control group over the same period. The transforming growth factor-β level was elevated at one month, two months, and six months. COLA1 and vimentin levels all peaked at six months. Matrix metalloproteinase and TIMP1 were also elevated at different months. Collectively, scar AMs can effectively promote wound healing and vascularization. Mature scar AMs have a better regeneration effect.
Hydrothermal oxidation method to synthesize nitrogen containing carbon dots from compost humic acid as selective Fe(III) sensor
Authors: Zhu Yan , Bao Ying , Wang Liping , Bi Jingtao , Liu Yong , Xie Chuang
Published: September 2020

Residual sludge which is generated as a by-product during wastewater treatment needs efficient and environmentally friendly disposal. In this work, nitrogen containing carbon dots (N-CDs) was synthesized via one-step hydrothermal oxidation of humic acid for the first time, which was alkalinely extracted from the compost of sludge. The successful doping of the functional groups (hydroxyl, carboxyl and amino) on the surface of N-CDs were characterized by x-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FT-IR). The optical properties of the synthetic N-CDs were obtained from Ultraviolet-visible spectroscopy and Photoluminescence spectra. The N-CDs had an average diameter at 1.88 nm and exhibited a well-defined spherical shape. The aqueous solution of N-CDs with excitation-dependent properties showed a strong blue emission with 8.8% quantum yield (QY) under an excitation wavelength of 340 nm, which indicate the synthesized N-CDs a promising sensing probes for iron ions in aquatic system. Moreover, the mechanism of the N-CDs sensing technique was investigated in detail, which can be explained by the fluorescence static quenching effect and a ground-state complex formed in this process. This research demonstrates an extremely sensitive method for detecting heavy metal Fe3+ at a lower 1.9 nM level by using N-CDs as fluorescent probes without a complicated procedure.
The sequential effects of a multifactorial detergent based decellularization process on bovine pericardium
Authors: Laker L , Dohmen P M , Smit F E
Published: September 2020

Decellularization is a promising method for obtaining extracellular matrix scaffolds (ECM) to be used as replacement material in reconstructive procedures. The effectiveness of decellularization and the alterations to the ECM vary, depending on several factors, including the tissue source, composition and density. With an optimized decellularization process, decellularized scaffolds can preserve the spatial and temporal ECM microenvironment, which play an integral role in modulating cell migration, proliferation and differentiation. The exploration of a variety of decellularization protocols has led to mixed outcomes and comparisons between decellularization protocols could not attribute these differences to any single step in a multiple-step process. This study aimed to characterize the effects of each step of a multifactorial decellularization method on the scaffold structure and mechanical integrity of bovine pericardium. Each step of the decellularization process and the effect on the tissue was assessed using hematoxylin and eosin staining, electron microscopy, total protein, ECM protein and triglyceride quantification. The biomechanical properties were assessed using uniaxial tensile strength testing. Cell lysis occurred mainly during the detergent and alcohol steps. Collagen structural damage occurred during the detergent and alcohol steps, with no significant decreased in collagen concentration. No significant damage to elastin could be shown throughout the process, however glycosaminoglycans were significantly removed by detergent treatment. Triglycerides were removed mostly by the alcohol treatment. The strength of the pericardium decreased somewhat after each step of the protocol. It is important to characterize each decellularization protocol with regards to the decellularization efficiency and the effect on the ECM proteins structure and function to accurately evaluate in vivo outcomes.
Femtosecond laser shockwave peening ablation in liquids for hierarchical micro/nanostructuring of brittle silicon and its biological application
Authors: Zhang Dongshi , Wu Liang-Chun , Ueki Masashi , Ito Yoshihiro , Sugioka Koji
Published: September 2020

This paper presents a new technique, termed femtosecond laser shock peening ablation in liquids (fs-LSPAL), which can realize simultaneous crack micro/nanomanufacturing and hierarchical micro/nanolaser ablation, giving rise to the formation of diverse multiscale hierarchical structures, such as macroporous ratcheted structures and en échelon microfringes decorated with parabolic nanoripples. Through analysis of surface morphologies, many phenomena have been confirmed to take place during fs-LSPAL, including en échelon cracks, nanostriation, ripple densification, crack branching, and selective formation of high spatial frequency laser-induced periodic surface structures of 100–200 nm in period. At a high laser power of 700 mW, fs-LSPAL at scanning speeds of 0.2 mm s−1 and 1 mm s−1 enables the generation of height-fluctuated and height-homogeneous hierarchical structures, respectively. The height-fluctuated structures can be used to induce ‘colony’ aggregates of embryonic EB3 stem cells. At 200 mW, fs-LSPAL at 1 mm s−1 is capable of producing homogeneous tilt macroporous structures with cracked structures interleaved among them, which are the synergistic effects of bubble-induced light refraction/reflection ablation and cracks. As shown in this paper, the conventional laser ablation technique integrated with its self-driven unconventional cracking under extreme conditions expands the horizons of extreme manufacturing and offers more opportunities for complex surface structuring, which can potentially be used for biological applications.
Predation risk increases intraspecific heterogeneity in white-tailed deer diel activity patterns
Authors: Crawford Daniel A , Conner L Mike , Morris Gail , Cherry Michael J
Published: September 2020

Prey species often mitigate predation risk through alteration of spatiotemporal diel activity patterns whereby prey access high-quality resources in risky areas during predator downtimes. However, dominance hierarchies exist in some prey species, and temporal partitioning is a mechanism thought to reduce aggressive intraspecific interactions. How demographic-specific responses to predation risk influence intraspecific temporal partitioning in prey are largely unknown and could be key to understanding the effects of predators on intraspecific interactions in prey. To assess the effects of predation risk on intraspecific interactions in white-tailed deer (Odocoileus virginianus), we monitored deer diel activity during the fawning season in four pairs of predator exclusion and control plots (~40 ha) from 2015 to 2018 using 16 camera traps. We examined the effect of predation risk on diel activity of males, females, and nursery groups by comparing the within-group coefficient of activity overlap (d̂) across predator exclusion and control plots. We then examined within-treatment activity overlap between groups in the predator exclosure and control plots. All groups maintained different diel activity patterns in safe and risky areas. Unconstrained by predation risk, all groups behaved more similarly, and interspecific group overlap was greater in the predator exclusion plots than control plots. Male-nursery group overlap exhibited the strongest treatment effect, increasing 24% in predator exclusion plots (d̂ = 0.91, confidence interval [CI]: 0.87–0.95) relative to control plots (d̂ = 0.67, CI: 0.57–0.76). Our results suggest predators increase heterogeneity in prey behavior and may be important drivers of behavioral processes, such as temporal partitioning, that minimize antagonistic intraspecific interactions of prey.
Joint epitope selection and spacer design for string-of-beads vaccines
Authors: Dorigatti Emilio , Schubert Benjamin
Published: September 2020

Motivation

Conceptually, epitope-based vaccine design poses two distinct problems: (i) selecting the best epitopes to elicit the strongest possible immune response and (ii) arranging and linking them through short spacer sequences to string-of-beads vaccines, so that their recovery likelihood during antigen processing is maximized. Current state-of-the-art approaches solve this design problem sequentially. Consequently, such approaches are unable to capture the inter-dependencies between the two design steps, usually emphasizing theoretical immunogenicity over correct vaccine processing, thus resulting in vaccines with less effective immunogenicity in vivo.

Results

In this work, we present a computational approach based on linear programming, called JessEV, that solves both design steps simultaneously, allowing to weigh the selection of a set of epitopes that have great immunogenic potential against their assembly into a string-of-beads construct that provides a high chance of recovery. We conducted Monte Carlo cleavage simulations to show that a fixed set of epitopes often cannot be assembled adequately, whereas selecting epitopes to accommodate proper cleavage requirements substantially improves their recovery probability and thus the effective immunogenicity, pathogen and population coverage of the resulting vaccines by at least 2-fold.

Availability and implementation

The software and the data analyzed are available at https://github.com/SchubertLab/JessEV.

Supplementary information

Supplementary data are available at Bioinformatics online.
CLPred: a sequence-based protein crystallization predictor using BLSTM neural network
Authors: Xuan Wenjing , Liu Ning , Huang Neng , Li Yaohang , Wang Jianxin
Published: September 2020

Motivation

Determining the structures of proteins is a critical step to understand their biological functions. Crystallography-based X-ray diffraction technique is the main method for experimental protein structure determination. However, the underlying crystallization process, which needs multiple time-consuming and costly experimental steps, has a high attrition rate. To overcome this issue, a series of in silico methods have been developed with the primary aim of selecting the protein sequences that are promising to be crystallized. However, the predictive performance of the current methods is modest.

Results

We propose a deep learning model, so-called CLPred, which uses a bidirectional recurrent neural network with long short-term memory (BLSTM) to capture the long-range interaction patterns between k-mers amino acids to predict protein crystallizability. Using sequence only information, CLPred outperforms the existing deep-learning predictors and a vast majority of sequence-based diffraction-quality crystals predictors on three independent test sets. The results highlight the effectiveness of BLSTM in capturing non-local, long-range inter-peptide interaction patterns to distinguish proteins that can result in diffraction-quality crystals from those that cannot. CLPred has been steadily improved over the previous window-based neural networks, which is able to predict crystallization propensity with high accuracy. CLPred can also be improved significantly if it incorporates additional features from pre-extracted evolutional, structural and physicochemical characteristics. The correctness of CLPred predictions is further validated by the case studies of Sox transcription factor family member proteins and Zika virus non-structural proteins.

Availability and implementation

https://github.com/xuanwenjing/CLPred.
RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials
Authors: Ubels Joske , Schaefers Tilman , Punt Cornelis , Guchelaar Henk-Jan , de Ridder Jeroen
Published: September 2020

Motivation

When phase III clinical drug trials fail their endpoint, enormous resources are wasted. Moreover, even if a clinical trial demonstrates a significant benefit, the observed effects are often small and may not outweigh the side effects of the drug. Therefore, there is a great clinical need for methods to identify genetic markers that can identify subgroups of patients which are likely to benefit from treatment as this may (i) rescue failed clinical trials and/or (ii) identify subgroups of patients which benefit more than the population as a whole. When single genetic biomarkers cannot be found, machine learning approaches that find multivariate signatures are required. For single nucleotide polymorphism (SNP) profiles, this is extremely challenging owing to the high dimensionality of the data. Here, we introduce RAINFOREST (tReAtment benefIt prediction using raNdom FOREST), which can predict treatment benefit from patient SNP profiles obtained in a clinical trial setting.

Results

We demonstrate the performance of RAINFOREST on the CAIRO2 dataset, a phase III clinical trial which tested the addition of cetuximab treatment for metastatic colorectal cancer and concluded there was no benefit. However, we find that RAINFOREST is able to identify a subgroup comprising 27.7% of the patients that do benefit, with a hazard ratio of 0.69 (P = 0.04) in favor of cetuximab. The method is not specific to colorectal cancer and could aid in reanalysis of clinical trial data and provide a more personalized approach to cancer treatment, also when there is no clear link between a single variant and treatment benefit.

Availability and implementation

The R code used to produce the results in this paper can be found at github.com/jubels/RAINFOREST. A more configurable, user-friendly Python implementation of RAINFOREST is also provided. Due to restrictions based on privacy regulations and informed consent of participants, phenotype and genotype data of the CAIRO2 trial cannot be made freely available in a public repository. Data from this study can be obtained upon request. Requests should be directed toward Prof. Dr. H.J. Guchelaar (h.j.guchelaar@lumc.nl).

Supplementary information

Supplementary data are available at Bioinformatics online.
CoLiDe: Combinatorial Library Design tool for probing protein sequence space
Authors: Tretyachenko Vyacheslav , Voráček Václav , Souček Radko , Fujishima Kosuke , Hlouchová Klára
Published: September 2020

Motivation

Current techniques of protein engineering focus mostly on re-designing small targeted regions or defined structural scaffolds rather than constructing combinatorial libraries of versatile compositions and lengths. This is a missed opportunity because combinatorial libraries are emerging as a vital source of novel functional proteins and are of interest in diverse research areas.

Results

Here, we present a computational tool for Combinatorial Library Design (CoLiDe) offering precise control over protein sequence composition, length and diversity. The algorithm uses evolutionary approach to provide solutions to combinatorial libraries of degenerate DNA templates. We demonstrate its performance and precision using four different input alphabet distribution on different sequence lengths. In addition, a model design and experimental pipeline for protein library expression and purification is presented, providing a proof-of-concept that our protocol can be used to prepare purified protein library samples of up to 1011–1012 unique sequences. CoLiDe presents a composition-centric approach to protein design towards different functional phenomena.

Availabilityand implementation

CoLiDe is implemented in Python and freely available at https://github.com/voracva1/CoLiDe.

Supplementary information

Supplementary data are available at Bioinformatics online.
Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated
Authors: Barba-Montoya Jose , Tao Qiqing , Kumar Sudhir
Published: September 2020

Motivation

As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates.

Results

We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations.

Availability and implementation

All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.
Politics as Social Work: A Qualitative Study of Emplaced Empathy and Risk Work by British Members of Parliament
Authors: Warner Jo
Published: September 2020

The constituency work of British Members of Parliament (MPs) has long been referred to in political circles as a form of social work. This article reports on a qualitative study using semi-structured interviews with thirteen MPs. The aim of the research was to find out what characterises their constituency work to understand why it apparently bears comparison with social work. The article draws on the concepts of proximity and place from the mobilities paradigm to articulate the idea of ‘politics as social work’. MPs in the study engaged in face-to-face emotional labour in which they formed and sustained empathic relationships with people and places to represent them. They practised judgement under uncertainty and risk work, and they were embedded in local organisational networks of risk and trust with local authorities and other agencies. The article argues that this analysis of politics as social work provides a deeper understanding of the politics of social work. In the era of the COVID-19 pandemic and its severe socio-economic impact, the importance for social work of the concept of emplaced empathy and the need for our reorientation to place is thrown into particularly sharp focus.
Non-invasive measurement of fasciculation frequency demonstrates diagnostic accuracy in amyotrophic lateral sclerosis
Authors: Tamborska Arina , Bashford James , Wickham Aidan , Iniesta Raquel , Masood Urooba , Cabassi Cristina , Planinc Domen , Hodson-Tole Emma , Drakakis Emmanuel , Boutelle Martyn , Mills Kerry , Shaw Chris
Published: September 2020

Delayed diagnosis of amyotrophic lateral sclerosis prevents early entry into clinical trials at a time when neuroprotective therapies would be most effective. Fasciculations are an early hallmark of amyotrophic lateral sclerosis, preceding muscle weakness and atrophy. To assess the potential diagnostic utility of fasciculations measured by high-density surface electromyography, we carried out 30-min biceps brachii recordings in 39 patients with amyotrophic lateral sclerosis, 7 patients with benign fasciculation syndrome, 1 patient with multifocal motor neuropathy and 17 healthy individuals. We employed the surface potential quantification engine to compute fasciculation frequency, fasciculation amplitude and inter-fasciculation interval. Inter-group comparison was assessed by Welch’s analysis of variance. Logistic regression, receiver operating characteristic curves and decision trees discerned the diagnostic performance of these measures. Fasciculation frequency, median fasciculation amplitude and proportion of inter-fasciculation intervals <100 ms showed significant differences between the groups. In the best-fit regression model, increasing fasciculation frequency and median fasciculation amplitude were independently associated with the diagnosis of amyotrophic lateral sclerosis. Fasciculation frequency was the single best measure predictive of the disease, with an area under the curve of 0.89 (95% confidence interval 0.81–0.98). The cut-off of more than 14 fasciculation potentials per minute achieved 80% sensitivity (95% confidence interval 63–90%) and 96% specificity (95% confidence interval 78–100%). In conclusion, non-invasive measurement of fasciculation frequency at a single time-point reliably distinguished amyotrophic lateral sclerosis from its mimicking conditions and healthy individuals, warranting further research into its diagnostic applications.
Jiehebuor suburb? Towards a translational turn in urban studies
Authors: Zhao Yimin
Published: September 2020

Engaging with reflections on improper urban vocabularies, this article proposes a translational turn to foreground dialogues—rather than equivalences—between languages. Drawing on the philosophies of language and hermeneutics, I adopt ‘the fusion of horizons’ as an alternative perspective to redefine translation where different languages encounter each other. To better capture global urban experiences, we should recognise the role of translation that exposes us to strangeness and alterity. This point is elaborated with heterogeneous names of the urban frontier, which inform us how and how far appropriating gaps/distances can initiate creative and unexpected dialogues for more global urban studies.
Impact of the coronavirus disease 2019 (COVID-19) pandemic on the Italian congenital cardiac surgery system: a national survey
Authors: Giamberti Alessandro , Varrica Alessandro , Agati Salvatore , Gargiulo Gaetano , Luciani Giovanni Battista , Marianeschi Stefano Maria , Pace Napoleone Carlo , Oppido Guido , Brunelli Federico , Palma Gaetano , Pak Vitali , Arcieri Luigi , Scalzo Gabriele , Padalino Massimo , Galletti Lorenzo ,   the Congenital Domain of the Italian Society of Cardiac Surgery
Published: September 2020

OBJECTIVES

Italy has been one of the countries most severely affected by the coronavirus disease 2019 (COVID-19). The Italian government was forced to introduce quarantine measures quickly, and all elective health services were stopped or postponed. This emergency has dramatically changed the management of paediatric and adult patients with congenital heart disease. We analysed data from 14 Italian congenital cardiac surgery centres during lockdown, focusing on the impact of the pandemic on surgical activity, patients and healthcare providers and resource allocation.

METHODS

Fourteen centres participated in this study. The period analysed was from 9 March to 4 May. We collected data on the involvement of the hospitals in the treatment of patients with COVID-19 and on limitations on regular activity and on the contagion among patients and healthcare providers.

RESULTS

Four hospitals (29%) remained COVID-19 free, whereas 10 had a 39% reduction in the number of beds for surgical patients, especially in the northern area. Two hundred sixty-three surgical procedures were performed: 20% elective, 62% urgent, 10% emergency and 3% life-saving. Hospital mortality was 0.4%. Compared to 2019, the reduction in surgical activity was 52%. No patients operated on had positive test results before surgery for severe acute respiratory syndrome coronavirus 2, the virus responsible for COVID-19. Three patients were infected during the postoperative period. Twenty-nine nurses and 12 doctors were infected. Overall, 80% of our infected healthcare providers were in northern centres.

CONCLUSIONS

Our study shows that the pandemic had a different impact on the various Italian congenital cardiac surgery centres based on the different patterns of spread of the virus across the country. During the lockdown, the system was able to satisfy all emergency clinical needs with excellent results.
Clinical features and prognostic impact of coexisting autoimmune disease other than myasthenia gravis in resected thymomas: analysis of a Japanese multi-institutional retrospective database
Authors: Hishida Tomoyuki , Asamura Hisao , Yoshida Kazuo , Tsuboi Masahiro , Yokoi Kohei , Toyooka Shinichi , Matsumura Akihide , Tagawa Tetsuzo , Okumura Meinoshin
Published: September 2020

OBJECTIVES

The purpose of this study was to clarify the prevalence, clinical features and survival of patients with thymoma and non-myasthenia gravis autoimmune disease (NMAD) using a nationwide cohort.

METHODS

The Japanese Association for Research on the Thymus nationwide database, which includes data from 32 institutions, was examined to clarify the prevalence and characteristics of NMAD associated with thymomas and elucidate the prognostic impact of NMAD for thymoma patients.

RESULTS

Among the 2423 patients with thymomas who were surgically treated between 1991 and 2010, 114 (4.7%) were identified with NMAD. The most frequently observed NMAD was pure red cell aplasia (PRCA) in 44 (1.8%), followed by hypogammaglobulinaemia (0.5%) and rheumatic arthritis (0.5%). Twenty-eight percent of patients with NMAD had concomitant myasthenia gravis. The presence of NMAD was not an independent prognostic factor for overall survival (OS) irrespective of the type of NMAD [PRCA+: hazard ratio (HR) 1.99, 95% confidence interval 0.74–4.47; PRCA− NMAD: HR 1.28, 0.30–3.56]; however, there were more cases with advanced age and disease of the thymoma amongst PRCA+ patients and these showed a worse OS than patients with PRCA− NMAD (P < 0.001), who had an OS similar to those without NMAD (P = 0.489). The 10-year OS rates in PRCA+, PRCA− NMAD and NMAD− groups were 45.5%, 97.4% and 89.5%, respectively. The main causes of death in PRCA+ patients were the progression of thymoma and other diseases including pneumonia.

CONCLUSIONS

Although the presence of NMAD itself did not significantly affect survival after surgery for thymoma, the type of NMAD was associated with different clinical features and prognosis. The NMAD+ thymomas should be separately categorized according to the presence or absence of PRCA.
Moving between Politics and Aesthetics in Zadie Smith’s Shorter Forms
Authors: Eagleton Mary
Published: September 2020

Zadie Smith’s shorter forms – the short story and the essay – have received much less critical attention than her five novels. As an approach to these shorter forms and, specifically, to Smith’s interest in politics and aesthetics, I consider, in various ways, the notion of ‘moving between’. In the introductory section, I discuss Smith’s comments on the characteristics of the two forms, namely the association of the short story with feeling and the essay with the intellectual or analytic, and Smith’s repeated claim that she fails in both forms. In each of the following two sections, a short story and an essay are paired. The context is the period from 2016 to 2018 in the USA and the UK. In the first pairing, the essay, ‘Getting In and Out’ (2017), and the story, ‘Now More Than Ever’ (2018), the focus is the fevered debate around identity politics and political correctness, and a punitive use of social media. The second pairing, ‘Fences: A Brexit Diary (2016) and the story, ‘The Lazy River’, is, self-evidently, about Brexit. In these texts, we see how a sense of aesthetic possibility and intellectual freedom confronts a prescriptive politics; how Smith draws the reader’s attention to problems of political divisiveness in her use of pronouns, figures of speech, and catchphrases; and how, sometimes, her aesthetic response can sit awkwardly alongside her political principles. In the range, interest, and provocativeness of Smith’s short stories and essays, the reader is led to question her claims of incompetence.
1970–2020: 50 years of research on the long QT syndrome—from almost zero knowledge to precision medicine
Authors: Schwartz Peter J
Published: September 2020

To those of us involved in clinical research it seldom happens to begin working on a rather obscure disease, still largely unexplored, and to follow its ripening into a medical entity of large interest to clinicians and basic scientists alike, and moreover to do so for exactly 50 years. This is what has been my privilege in the relentless pursuit of the intriguing disease known as the long QT syndrome (LQTS). This essay begins with the encounter with my first patient affected by LQTS when just a handful of cardiologists had seen similar cases and continues with the series of efforts, some sound some amateurish, which eventually led—together with many brilliant partners and associates—to describe and understand the natural history of the disease and the most effective therapies. It then touches on how our International Registry for LQTS, with its well-documented family trees, constituted the necessary springboard for the major genetic discoveries of the 1990s. From the explosion of genetic data, my own interest focused first on the intriguing genotype–phenotype correlation and then on ‘modifier genes’, in the attempt of understanding why family members with the same disease-causing mutation could have an opposite clinical history. And from there on to iPS-derived cardiomyocytes, used to unravelling the specific mechanisms of action of modifier genes and to exploring novel therapeutic strategies. This long, and highly rewarding, journey continues because the fascination and the attraction of the unknown are irresistible.
A retrospective cohort study examining STI testing and perinatal records demonstrates reproductive health burden of chlamydia and gonorrhea
Authors: Callan Torrington , Debattista Joseph , Berry Brooke , Brown James , Woodcock Stephen , Hocking Jane S , Huston Wilhelmina M
Published: September 2020

Adverse reproductive health outcomes, such as pelvic inflammatory disease, ectopic pregnancy and tubal factor infertility, have been associated with Chlamydia trachomatis and Neisseria gonorrhoea infections. These reproductive health outcomes could be complemented by measuring subsequent pregnancies to assess impact on fertility. The study design was a cohort study of women in Queensland (QLD), Australia, using data linkage methods to link chlamydia and/or gonorrhea testing records (including an unexposed group undergoing full blood count tests; 2000 and 2005) with the QLD Perinatal Registry (2000–2013). The cohort included 132 962 women, with 69 533 records of pregnancies. Women in the exposed group, with no prior pregnancy, had a reduced odds of a pregnancy during the follow up of the study (20-year-old (at 2005) aOR 0.91 95% CI 0.87–0.95, and 25-year-old aOR 0.71 95% CI 0.68–0.75). Women in the exposed group with a prior pregnancy had increased odds of pregnancy during the follow up of the study (20-year-old (at 2005) aOR 1.72 95% CI 1.59–1.86, and 25-year-old aOR 1.35 95% CI 1.26–1.45). Our data provides further evidence at a population level of the significant impact on reproductive outcomes associated with chlamydia and gonorrhea.
Telomere Length in Healthy Adults Is Positively Associated With Polyunsaturated Fatty Acids, Including Arachidonic Acid, and Negatively With Saturated Fatty Acids
Authors: Dhillon Varinderpal S , Deo Permal , Chua Ann , Thomas Phil , Fenech Michael
Published: September 2020

Lymphocyte telomere length (LTL) is a biomarker of aging that may be modified by dietary factors including fat. Red blood cell fatty acid status is a well-validated indicator of long-term dietary intake of fat from various sources. Recent findings from epidemiological studies of LTL in relation to fatty acids in red blood cells are not conclusive. The present study was carried out to investigate if red blood cell fatty acid status in 174 healthy older South Australians is associated with LTL. Lymphocyte telomere length was measured by real-time qPCR and fatty acid content in red blood cells was measured by gas chromatography. Our results indicate that the majority of saturated fatty acids and monounsaturated fatty acids are negatively associated with LTL, whereas polyunsaturated fatty acids are positively associated with LTL. Multiple regression analysis revealed that arachidonic acid (C20:4n-6) is significantly, independently, positively correlated with LTL (β = 0.262; p = .000). The significant association of fatty acids, particularly C20:4n-6, with telomere length warrants further research.
Association Between Variation in Red Cell Size and Multiple Aging-Related Outcomes
Authors: Kim Kyoung Min , Lui Li-Yung , Browner Warren S , Cauley Jane A , Ensrud Kristine E , Kado Deborah M , Orwoll Eric S , Schousboe John T , Cummings Steven R
Published: September 2020

Background

We tested whether greater variation in red blood cell size, measured by red cell distribution width (RDW), may predict aging-related degenerative conditions and therefore, serve as a marker of biological aging.

Methods

Three thousand six hundred and thirty-five community-dwelling older men were enrolled in the prospective Osteoporotic Fractures in Men Study. RDW was categorized into 4 groups (≤13.0%, 13.1%–14.0%, 14.1%–15.0%, and ≥15.1%). Functional limitations, frailty, strength, physical performance, and cognitive function were measured at baseline and 7.4 years later. Falls were recorded in the year after baseline; hospitalizations were obtained for 2 years after baseline. Mortality was assessed during a mean of 8.3 years of follow-up.

Results

Participants with greater variability in red cell size were weaker, walked more slowly, and had a worse cognitive function. They were more likely to have functional limitations (35.2% in the highest RDW category vs 16.0% in the lowest, p < .001) and frailty (30.3% vs 11.3%, p < .001). Those with greater variability in red cell size were more likely to develop new functional limitations and to become frail. The risk of having 2 or more falls was also greater (highest 19.2% vs lowest 10.3%, p < .001). The risk of hospitalization was higher in those with the highest variability (odds ratio [95% confidence interval], 1.8 [1.3–2.5]) compared with the lowest. Variability in red cell size was related to total and cause-specific mortality.

Conclusion

Greater variability in red cell size is associated with diverse aging-related outcomes, suggesting that it may have potential value as a marker for biological aging.
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads
Authors: Xu Mengyang , Guo Lidong , Gu Shengqiang , Wang Ou , Zhang Rui , Peters Brock A , Fan Guangyi , Liu Xin , Xu Xun , Deng Li , Zhang Yongwei
Published: September 2020

Background

Analyses that use genome assemblies are critically affected by the contiguity, completeness, and accuracy of those assemblies. In recent years single-molecule sequencing techniques generating long-read information have become available and enabled substantial improvement in contig length and genome completeness, especially for large genomes (>100 Mb), although bioinformatic tools for these applications are still limited.

Findings

We developed a software tool to close sequence gaps in genome assemblies, TGS-GapCloser, that uses low-depth (~10×) long single-molecule reads. The algorithm extracts reads that bridge gap regions between 2 contigs within a scaffold, error corrects only the candidate reads, and assigns the best sequence data to each gap. As a demonstration, we used TGS-GapCloser to improve the scaftig NG50 value of 3 human genome assemblies by 24-fold on average with only ~10× coverage of Oxford Nanopore or Pacific Biosciences reads, covering with sequence data up to 94.8% gaps with 97.7% positive predictive value. These improved assemblies achieve 99.998% (Q46) single-base accuracy with final inserted sequences having 99.97% (Q35) accuracy, despite the high raw error rate of single-molecule reads, enabling high-quality downstream analyses, including up to a 31-fold increase in the scaftig NGA50 and up to 13.1% more complete BUSCO genes. Additionally, we show that even in ultra-large genome assemblies, such as the ginkgo (~12 Gb), TGS-GapCloser can cover 71.6% of gaps with sequence data.

Conclusions

TGS-GapCloser can close gaps in large genome assemblies using raw long reads quickly and cost-effectively. The final assemblies generated by TGS-GapCloser have improved contiguity and completeness while maintaining high accuracy. The software is available at https://github.com/BGI-Qingdao/TGS-GapCloser.
Slowness vector estimation over large-aperture sparse arrays with the Continuous Wavelet Transform (CWT): application to Ocean Bottom Seismometers
Authors: Cabieces Roberto , Krüger Frank , Garcia-Yeguas Araceli , Villaseñor Antonio , Buforn Elisa , Pazos Antonio , Olivar-Castaño Andrés , Barco Jaime
Published: September 2020

This work presents a new methodology designed to estimate the slowness vector in large-aperture sparse Ocean Bottom Seismometer (OBS) arrays. The Continuous Wavelet Transform (CWT) is used to convert the original incoherent traces that span a large array, into coherent impulse functions adapted to the array aperture. Subsequently, these impulse functions are beamformed in the frequency domain to estimate the slowness vector. We compare the performance of this new method with that of an alternative solution, based on the Short-/Long-Term Average algorithm and with a method based on the trace envelope, with the ability to derive a very fast detection and slowness vector estimation of seismic signal arrivals. The new array methodology has been applied to data from an OBS deployment with an aperture of 80 km and an interstation distance of about 40 km, in the vicinity of Cape Saint Vincent (SW Iberia). A set of 17 regional earthquakes with magnitudes 2 < mbLg < 5, has been selected to test the capabilities of detecting and locating regional seismic events with the Cape Saint Vincent OBS Array. We have found that there is a good agreement between the epicentral locations obtained previously by direct search methods and those calculated using the slowness vector estimations resulting from application of the CWT technique. We show that the proposed CWT method can detect seismic signals and estimate the slowness vector from regional earthquakes with high accuracy and robustness under low signal-to-noise ratio conditions. Differences in epicentral distances applying direct search methods and the CWT technique are between 1 and 21 km with an average value of 12 km. The backazimuth differences range from 1° to 7° with an average of 1.5° for the Pwave and ranging from 1° to 10° with an average of 3° for the Swave.
Is COVID-19 the end of US hegemony? Public bads, leadership failures and monetary hegemony
Authors: Norrlöf Carla
Published: September 2020

COVID-19 is the most invasive global crisis in the postwar era, jeopardizing all dimensions of human activity. By theorizing COVID-19 as a public bad, I shed light on one of the great debates of the twentieth and twenty-first centuries regarding the relationship between the United States and liberal international order (LIO). Conceptualizing the pandemic as a public bad, I analyze its consequences for US hegemony. Unlike other international public bads and many of the most important public goods that make up the LIO, the COVID-19 public bad not only has some degree of rivalry but can be made partially excludable, transforming it into more of a club good. Domestically, I demonstrate how the failure to effectively manage the COVID-19 public bad has compromised America's ability to secure the health of its citizens and the domestic economy, the very foundations for its international leadership. These failures jeopardize US provision of other global public goods. Internationally, I show how the US has already used the crisis strategically to reinforce its opposition to free international movement while abandoning the primary international institution tasked with fighting the public bad, the World Health Organization (WHO). While the only area where the United States has exercised leadership is in the monetary sphere, I argue this feat is more consequential for maintaining hegemony. However, even monetary hegemony could be at risk if the pandemic continues to be mismanaged.
Why the COVID-19 response needs International Relations
Authors: Davies Sara E , Wenham Clare
Published: September 2020

The COVID-19 pandemic affects all countries, but how governments respond is dictated by politics. Amid this, the World Health Organization (WHO) has tried to coordinate advice to states and offer ongoing management of the outbreak. Given the political drivers of COVID-19, we argue this is an important moment to advance International Relations knowledge as a necessary and distinctive method for inclusion in the WHO repertoire of knowledge inputs for epidemic control. Historical efforts to assert technical expertise over politics is redundant and outdated: the WHO has always been politicized by member states. We suggest WHO needs to embrace the politics and engage foreign policy and diplomatic expertise. We suggest practical examples of the entry points where International Relations methods can inform public health decision-making and technical policy coordination. We write this as a primer for those working in response to COVID-19 in WHO, multilateral organizations, donor financing departments, governments and international non-governmental organizations, to embrace political analysis rather than shy away from it. Coordinated political cooperation is vital to overcome COVID-19.