bluuebunny/crossref_metadata_2025 huggingface dataset:
The limitations of extending nature’s color palette in correlated, disordered systems
Authors: Jacucci Gianni , Vignolini Silvia , Schertel Lukas
Published: September 2020

Significance

Scattering from 2D correlated disordered structures is often at the core of matte color appearances in nature. However, the hues related to this mechanism are restricted to UV radiation and the blue part of the visible spectrum. Here we present a numerical study on short-range correlated materials—photonic glasses—without the restriction to a specific light transport regime. We demonstrate that with these materials, saturated angle-independent structural colors cannot be reached in the long-wavelength region of the visible spectrum. In this context, we discuss promising approaches toward 3D isotropic structural colored materials.
SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification
Authors: Rabe Brian A. , Cepko Constance
Published: September 2020

Significance

This work describes the optimization of a sample preparation and detection pipeline for a SARS-CoV-2 diagnostic test that is rapid and does not require specialized equipment. This pipeline consists of viral inactivation, rendering samples safer to work with, followed by a sensitive 30-min isothermal detection reaction with a color-based red to yellow readout. Sensitivity can be further improved using a simple and inexpensive purification protocol. This pipeline can help address the shortage of testing capacity and can be run in a variety of settings.
Dynamic changes in DICER levels in adipose tissue control metabolic adaptations to exercise
Authors: Brandão Bruna B. , Madsen Søren , Rabiee Atefeh , Oliverio Matteo , Ruiz Gabriel P. , Ferrucci Danilo L. , Branquinho Jéssica L. , Razolli Daniela , Pinto Silas , Nielsen Thomas S. , Festuccia William T. , Martins Adriano S. , Guerra Beatriz A. , Knittel Thiago L. , Søgaard Ditte , Larsen Steen , Helge Jørn W. , Brandauer Josef , Velloso Lício A. , Emanuelli Brice , Kornfeld Jan-Wilhelm , Kahn C. Ronald , Vienberg Sara G. , Zierath Juleen R. , Treebak Jonas T. , Mori Marcelo A.
Published: September 2020

Significance

Aerobic exercise elicits an integrated metabolic response that involves multiple tissues and confers beneficial effects to metabolic health. Here we found that this integrative response involves energy-sensing pathways in muscle and fat and circulating factors that lead to the upregulation of the type III endoribonuclease DICER in adipose tissue and the consequent increase of microRNAs. Upon upregulation, DICER and the microRNA-203-3p inhibit glucose utilization by fat cells and favor oxidative metabolism. In turn, this supports the exercised muscle with adequate substrate availability. When this pathway is disrupted, whole-body metabolism is affected, and exercise performance is impaired. Thus, adipose tissue DICER integrates signals from the exercising muscle to allow a proper metabolic response to exercise training.
Internet memes we live by (and die by)
Authors: Xie Chaoqun
Published: September 2020

In the internet age, memes are at once products and driving forces of social practices. A meme contains a memetic message and a meme output, and boasts, if guided by a pragmatic way of thinking, several features, including but not limited to salience, frequency, adaptability, argumentativity, sociality, embeddedness, embodiedness, locality, relativity, emotionality and dynamicity. The current global COVID-19 pandemic serves as a fitting and timely touchstone to testify how human beings are surrounded by numerous good and evil memes in the online world, and how internet memes, as can be seen from the illustration of two specific memes, namely, the ‘stay home, stay safe’ meme and the ‘wear a mask’ meme, are impacting human life-worlds, online and offline, with their transformative power, be it constructive or destructive. Moreover, researching how memes plays a decisive part in internet-mediated interaction provides a lens of insight through which ‘deep states’ of human nature of both self and others can be uncovered and through which what Nietzsche called “a revaluation of values” is possible.
Second language immersion impacts native language lexical production and comprehension
Authors: Botezatu Mona Roxana , Kroll Judith F. , Trachsel Morgan I. , Guo Taomei
Published: September 2020

We investigated whether the features of the second language (L2) matter when we consider the consequence of short-term L2
immersion on performance in the native language (L1). We compared L1 performance in English-speaking learners of a typologically-dissimilar
L2-Chinese immersed in Chinese while living in Beijing, China and learners of a typologically-similar L2 (Spanish or French) exposed to the
L2 in a classroom setting only. The groups were matched on cognitive abilities. Each group performed a battery of language tasks in English
that assessed the ability to produce and recognize spoken words, as well as to name written words and pseudo-words in the native language.
Immersed learners produced fewer words in their native language, made more semantic errors, and benefited more from higher lexical frequency
when retrieving L1 words relative to classroom learners. Immersed learners also revealed reduced competition from dense phonological
neighborhoods when listening to English words presented in noise, but no difference in English word reading and phonemic decoding
performance compared to classroom learners. Results are consistent with the view that L2 immersion reduces access to the native language,
but suggest that the consequences of L2 immersion on the L1 may be dependent upon the form of cross-language differences.
Mapping terminological variation and ideology in data protection laws
Authors: Pei Jiamin , Cheng Le
Published: September 2020

This study aims to deal with the relationship between terminological variation and ideology by examining the system of
terminology and the defined individual terms in data protection legislation. With two self-compiled corpora incorporating data protection
laws in the United States and the European Union respectively, we adopt a corpus-assisted approach as an effective toolkit to generate a
general profile of the system of legal terminology on the one hand and identify the defined legal terms in the two corpora on the other.
This study, based on Van Dijk’s (1998) multidisciplinary approach to ideology, seeks to unravel
the underlying ideological configurations behind the variation of legal terminology. The findings show that one plausible – though certainly
not definitive – interpretation of the variation in legal terminology in the data protection domain lies in the distinct ideological stances
imposed by such discourse communities as lawmakers, judges as well as the president and the party in power. The ideological investigation of
terminology is a significant aspect of the study of variation phenomena. It is argued that the ideologically variable slants and historical
experiences, as the contextual constraints on the ideological beliefs, may contribute to accounting for the spatial and temporal variation
of legal terminology.
How do supranational terms transfer into national legal systems?
Authors: Biel Łucja , Doczekalska Agnieszka
Published: September 2020

The objective of this paper is to analyse how European Union (EU) supranational terms related to consumer protection
transfer into domestic legal systems of three English-language jurisdictions (the UK, Ireland and Malta) during the transposition of EU
directives. Transposition is a process of incorporating EU directives into national law and capturing supranational terms during their entry
into national legal systems. We adopt a mixed-method approach of corpus linguistics and legal analysis of terms, working with a corpus of
five directives and their UK, Irish and Maltese transposing acts. Distinguishing between a term and a concept level, we propose a
categorisation of transfer techniques arranged along a cline from foreignization to domestication. They involve imports, modifications
(non-denominative and denominative variants), localisations and zero transfer both at the term level and the concept level.
Data driven regularization by projection
Authors: Aspri Andrea , Korolev Yury , Scherzer Otmar
Published: September 2020

We study linear inverse problems under the premise that the forward operator is not at hand but given indirectly through some input-output training pairs. We demonstrate that regularization by projection and variational regularization can be formulated by using the training data only and without making use of the forward operator. We study convergence and stability of the regularized solutions in view of Seidman (1980 J. Optim. Theory Appl.
30 535), who showed that regularization by projection is not convergent in general, by giving some insight on the generality of Seidman’s nonconvergence example. Moreover, we show, analytically and numerically, that regularization by projection is indeed capable of learning linear operators, such as the Radon transform.
Exterior Steklov eigenvalues and modified exterior Steklov eigenvalues in inverse scattering
Authors: Li Yuan
Published: September 2020

The inverse scattering problem for anisotropic media with data measured inside a cavity is considered. We aim to introduce the exterior Steklov eigenvalues (ESEs) and the modified exterior Steklov eigenvalues (MESEs) to detect changes in the material properties of the medium from a knowledge of a modified near field operator each. First, a connection between a modified near field operator and the exterior Steklov eigenvalue problem is established. Then the ESEs are proved to be discrete and lie in the lower half-plane. Since the existence of the ESEs is unknown due to non-self-adjointness, we propose the modified exterior Steklov eigenvalue problem for which infinitely many eigenvalues exist. Based on the factorizations of both the modified near field operator and the auxiliary near field operator, a nonsymmetric version of generalized linear sampling method (GLSM) is employed to compute the ESEs. This method also allows for the computation of the MESEs by adjusting the definitions of some associated operators. Numerical examples are presented to demonstrate the viability of this method and show the potential use of these eigenvalues as new classes of target signatures in nondestructive testing.
Size reduction of boron particles by high-power ultrasound for optimization of bulk MgB2
Authors: Arvapalli Sai Srikanth , Miryala Muralidhar , Jirsa Milos , Murakami Masato
Published: September 2020

Critical current density, J
c, in superconductors is strongly connected with size of defects in the material. Frequently, the smaller defects, the higher J
c. In this work, we tried to reduce the size of cheap commercial boron precursor powder using high energy ultra-sonication in ethanol media. The resulting powder was then utilized in synthesizing bulk MgB2 via sintering at 775 °C. Effect of boron powder ultra-sonication on superconducting properties of the bulk MgB2 was studied and discussed. SEM of ultra-sonicated boron showed fine particles with sharp edges (high-energy surfaces), irregular shapes and clustering of fine particles occurred for longer ultra-sonication durations. XRD proved a high quality of MgB2 with only small traces of MgO. Around 36% improvement in Jc
at 20 K and Tc
close to 39 K were observed in MgB2 bulk prepared with boron ultra-sonicated for 15 min. Microstructure studies showed numerous nanometre sized MgB2 grains in the bulk. Other bulks (made of boron ultra-sonicated longer, for 30, 45, and 60 min) have larger grains. It resulted in slightly lower J
c, anyway, still by 22% higher than in reference bulk. The present results demonstrate that the high performance bulk MgB2 can be achieved without reduction in T
c via employing a cheap boron, reduced in size by high-energy ultra-sonication.
Chondrobags: A high throughput alginate-fibronectin micromass platform for in vitro human cartilage formation
Authors: Witte Kimia , de Andrés María C , Wells Julia , Dalby Matthew J , Salmeron-Sanchez Manuel , Oreffo Richard O C
Published: September 2020

The maintenance and expansion of the cells required for formation of tissue-engineered cartilage has, to date, proven difficult. This is, in part, due to the initial solid phase extracellular matrix demanded by the cells inhabiting this avascular tissue. Herein, we engineer an innovative alginate-fibronectin microfluidic-based carrier construct (termed a chondrobag) equipped with solid phase presentation of growth factors that support skeletal stem cell chondrogenic differentiation while preserving human articular chondrocyte phenotype. Results demonstrate biocompatibility, cell viability, proliferation and tissue-specific differentiation for chondrogenic markers SOX9, COL2A1 and ACAN. Modulation of chondrogenic cell hypertrophy, following culture within chondrobags loaded with TGF-β1, was confirmed by down-regulation of hypertrophic genes COL10A1 and MMP13. MicroRNAs involved in the chondrogenesis process, including miR-140, miR-146b and miR-138 were observed. Results demonstrate the generation of a novel high-throughput, microfluidic-based, scalable carrier that supports human chondrogenesis with significant implications therein for cartilage repair-based therapies.
Limitations of paraxial approximation to model elec-tron acceleration by a laser pulse in vacuum in the presence of an axial magnetic field
Authors: Singh Kunwar Pal , Malik Anil K
Published: September 2020

We model electron acceleration using paraxial approximation (PA) and seventh order correction description (O7) of a laser field in vacuum in the presence of an axial magnetic field. The effect of initial momentum, laser intensity, spot size, and initial position of electron on optimum value of magnetic field and electron energy for linearly and circularly polarized laser pulse has been investigated. We show that PA fails to obtain correct values of optimum magnetic field and electron energy. The amplitude of oscillations of the electron increases with time in the presence of axial magnetic field and PA fails to correctly take into account focusing and defocusing of laser and obtain correct results.
Seasonal coordination of leaf hydraulics and gas exchange in a wintergreen fern
Authors: Prats Kyra A , Brodersen Craig R
Published: September 2020

Wintergreen fern Polystichum acrostichoides has fronds that are photosynthetically active year-round, despite diurnal and seasonal changes in soil moisture, air temperature and light availability. This species can fix much of its annual carbon during periods when the deciduous canopy is open. Yet, remaining photosynthetically active year-round requires the maintenance of photosynthetic and hydraulic systems that are vulnerable to freeze–thaw cycles. We aimed to determine the anatomical and physiological strategies P. acrostichoides uses to maintain positive carbon gain, and the coordination between the hydraulic and photosynthetic systems. We found that the first night below 0 °C led to 25 % loss of conductivity (PLC) in stipes, suggesting that winter-induced embolism occurred. Maximum photosynthetic rate and chlorophyll fluorescence declined during winter but recovered by spring, despite PLC remaining high; the remaining hydraulic capacity was sufficient to supply the leaves with water. The onset of colder temperatures coincided with the development of a necrotic hinge zone at the stipe base, allowing fronds to overwinter lying prostrate and maintain a favourable leaf temperature. Our conductivity data show that the hinge zone did not affect leaf hydraulics because of the flexibility of the vasculature. Collectively, these strategies help P. acrostichoides to survive in northeastern forests.
Built to change: dominance strategy changes with life stage in a primitively eusocial bee
Authors: Orlova Margarita , Treanore Erin , Amsalem Etya
Published: September 2020

Access to reproduction is determined by an individual’s dominance rank in many species and is achieved through aggression and/or dominance signaling. In eusocial insects, one or several dominant females (queens) monopolize reproduction but to what extent queens rely on aggression and signaling remains obscure. Aggression is costly and its efficiency depends on the group size, whereas signaling may reduce the risks and costs of aggression. Both strategies are used to regulate reproduction in social taxa, with aggression being more common in small social groups, compared to signaling in larger societies. Here, we examine the use of aggression and chemical signaling in a social species (Bombus impatiens) where the dominant queen interacts with increasing numbers of workers as she ages. We found that the queen’s strategy to monopolize reproduction changes with life stage, shifting from overt aggression to chemical signaling as the queen gets older. Particularly, old queens exhibited a higher ratio of short to long cuticular hydrocarbons compared to young queens, an endogenous shift that was attributed to age, as all egg-laying queens were fecund and kept with the same number of workers. Our findings contribute to the understanding of reproductive dominance in the context of an individual’s life history.
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation
Authors: Saha Chayan Kumar , Sanches Pires Rodrigo , Brolin Harald , Delannoy Maxence , Atkinson Gemma Catherine
Published: September 2020

Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin–antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.

Availability and implementation

FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.

Supplementary information

Supplementary data are available at Bioinformatics online.
SCHNEL: scalable clustering of high dimensional single-cell data
Authors: Abdelaal Tamim , de Raadt Paul , Lelieveldt Boudewijn P F , Reinders Marcel J T , Mahfouz Ahmed
Published: September 2020

Motivation

Single cell data measures multiple cellular markers at the single-cell level for thousands to millions of cells. Identification of distinct cell populations is a key step for further biological understanding, usually performed by clustering this data. Dimensionality reduction based clustering tools are either not scalable to large datasets containing millions of cells, or not fully automated requiring an initial manual estimation of the number of clusters. Graph clustering tools provide automated and reliable clustering for single cell data, but suffer heavily from scalability to large datasets.

Results

We developed SCHNEL, a scalable, reliable and automated clustering tool for high-dimensional single-cell data. SCHNEL transforms large high-dimensional data to a hierarchy of datasets containing subsets of data points following the original data manifold. The novel approach of SCHNEL combines this hierarchical representation of the data with graph clustering, making graph clustering scalable to millions of cells. Using seven different cytometry datasets, SCHNEL outperformed three popular clustering tools for cytometry data, and was able to produce meaningful clustering results for datasets of 3.5 and 17.2 million cells within workable time frames. In addition, we show that SCHNEL is a general clustering tool by applying it to single-cell RNA sequencing data, as well as a popular machine learning benchmark dataset MNIST.

Availability and implementation

Implementation is available on GitHub (https://github.com/biovault/SCHNELpy). All datasets used in this study are publicly available.

Supplementary information

Supplementary data are available at Bioinformatics online.
The effect of kinship in re-identification attacks against genomic data sharing beacons
Authors: Ayoz Kerem , Aysen Miray , Ayday Erman , Cicek A Ercument
Published: September 2020

Motivation

Big data era in genomics promises a breakthrough in medicine, but sharing data in a private manner limit the pace of field. Widely accepted ‘genomic data sharing beacon’ protocol provides a standardized and secure interface for querying the genomic datasets. The data are only shared if the desired information (e.g. a certain variant) exists in the dataset. Various studies showed that beacons are vulnerable to re-identification (or membership inference) attacks. As beacons are generally associated with sensitive phenotype information, re-identification creates a significant risk for the participants. Unfortunately, proposed countermeasures against such attacks have failed to be effective, as they do not consider the utility of beacon protocol.

Results

In this study, for the first time, we analyze the mitigation effect of the kinship relationships among beacon participants against re-identification attacks. We argue that having multiple family members in a beacon can garble the information for attacks since a substantial number of variants are shared among kin-related people. Using family genomes from HapMap and synthetically generated datasets, we show that having one of the parents of a victim in the beacon causes (i) significant decrease in the power of attacks and (ii) substantial increase in the number of queries needed to confirm an individual’s beacon membership. We also show how the protection effect attenuates when more distant relatives, such as grandparents are included alongside the victim. Furthermore, we quantify the utility loss due adding relatives and show that it is smaller compared with flipping based techniques.
MMAP: a cloud computing platform for mining the maximum accuracy of predicting phenotypes from genotypes
Authors: Huang Wei , Zheng Ping , Cui Zhenhai , Li Zhuo , Gao Yifeng , Yu Helong , Tang You , Yuan Xiaohui , Zhang Zhiwu
Published: September 2020

Accurately predicting phenotypes from genotypes holds great promise to improve health management in humans and animals, and breeding efficiency in animals and plants. Although many prediction methods have been developed, the optimal method differs across datasets due to multiple factors, including species, environments, populations and traits of interest. Studies have demonstrated that the number of genes underlying a trait and its heritability are the two key factors that determine which method fits the trait the best. In many cases, however, these two factors are unknown for the traits of interest. We developed a cloud computing platform for Mining the Maximum Accuracy of Predicting phenotypes from genotypes (MMAP) using unsupervised learning on publicly available real data and simulated data. MMAP provides a user interface to upload input data, manage projects and analyses and download the output results. The platform is free for the public to conduct computations for predicting phenotypes and genetic merit using the best prediction method optimized from many available ones, including Ridge Regression, gBLUP, compressed BLUP, Bayesian LASSO, Bayes A, B, Cpi and many more. Users can also use the platform to conduct data analyses with any methods of their choice. It is expected that extensive usage of MMAP would enrich the training data, which in turn results in continual improvement of the identification of the best method for use with particular traits.

Availability and implementation

The MMAP user manual, tutorials and example datasets are available at http://zzlab.net/MMAP.

Supplementary information

Supplementary data are available at Bioinformatics online.
Spectral Power in Marmoset Frontal Motor Cortex during Natural Locomotor Behavior
Authors: Tia Banty , Takemi Mitsuaki , Kosugi Akito , Castagnola Elisa , Ricci Davide , Ushiba Junichi , Fadiga Luciano , Iriki Atsushi
Published: September 2020

During primate arboreal locomotion, substrate orientation modifies body axis orientation and biomechanical contribution of fore- and hindlimbs. To characterize the role of cortical oscillations in integrating these locomotor demands, we recorded electrocorticographic activity from left dorsal premotor, primary motor, and supplementary motor cortices of three common marmosets moving across a branch-like small-diameter pole, fixed horizontally or vertically. Animals displayed behavioral adjustments to the task, namely, the horizontal condition mainly induced quadrupedal walk with pronated/neutral forelimb postures, whereas the vertical condition induced walk and bound gaits with supinated/neutral postures. Examination of cortical activity suggests that β (16–35 Hz) and γ (75–100 Hz) oscillations could reflect different processes in locomotor adjustments. During task, modulation of γ ERS by substrate orientation (horizontal/vertical) and epoch (preparation/execution) suggests close tuning to movement dynamics and biomechanical demands. β ERD was essentially modulated by gait (walk/bound), which could illustrate contribution to movement sequence and coordination. At rest, modulation of β power by substrate orientation underlines its role in sensorimotor processes for postural maintenance.
Risk factors for severity of COVID-19 in chronic dialysis patients from a multicentre French cohort
Authors: Lano Guillaume , Braconnier Antoine , Bataille Stanislas , Cavaille Guilhem , Moussi-Frances Julie , Gondouin Bertrand , Bindi Pascal , Nakhla Magued , Mansour Janette , Halin Pascale , Levy Bénédicte , Canivet Eric , Gaha Khaled , Kazes Isabelle , Noel Natacha , Wynckel Alain , Debrumetz Alexandre , Jourde-Chiche Noemie , Moal Valerie , Vial Romain , Scarfoglière Violaine , Bobot Mickael , Gully Marion , Legris Tristan , Pelletier Marion , Sallee Marion , Burtey Stephane , Brunet Philippe , Robert Thomas , Rieu Philippe
Published: September 2020

Background

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease, related to severe acute respiratory syndrome coronavirus 2 infection. Few data are available in patients with end-stage renal disease (ESRD).

Methods

We conducted an observational cohort study of COVID-19 patients at 11 dialysis centres in two distinct districts of France to examine the epidemiological and clinical characteristics of COVID-19 in this population, and to determine risk factors of disease severity (defined as a composite outcome including intensive care unit admission or death) and mortality.

Results

Among the 2336 patients enrolled, 5.5% had confirmed COVID-19 diagnosis. Of the 122 patients with a follow-up superior to 28 days, 37% reached the composite outcome and 28% died. Multivariate analysis showed that oxygen therapy on diagnosis and a decrease in lymphocyte count were independent risk factors associated with disease severity and with mortality. Chronic use of angiotensin II receptor blockers (ARBs) (18% of patients) was associated with a protective effect on mortality. Treatment with azithromycin and hydroxychloroquine (AZT/HCQ) (46% of patients) were not associated with the composite outcome and with death in univariate and multivariate analyses.

Conclusions

COVID-19 is a severe disease with poor prognosis in patients with ESRD. Usual treatment with ARBs seems to be protective of critical evolution and mortality. There is no evidence of clinical benefit with the combination of AZT/HCQ.
Safety and feasibility of minimally invasive esophagectomy for elderly esophageal cancer patients
Authors: Sugita Y , Nakamura T , Sawada R , Takiguchi G , Urakawa N , Hasegawa H , Yamamoto M , Kanaji S , Matsuda Y , Yamashita K , Matsuda T , Oshikiri T , Suzuki S , Kakeji Y
Published: September 2020

The number of elderly patients with esophageal cancer has increased in recent years. The use of thoracoscopic esophagectomy has also increased, and its minimal invasiveness is believed to contribute to postoperative outcomes. However, the short- and long-term outcomes in elderly patients remain unclear. This study aimed to elucidate the safety and feasibility of minimally invasive esophagectomy in elderly patients. This retrospective study included 207 patients who underwent radical thoracoscopic esophagectomy for thoracic esophageal squamous cell carcinoma at Kobe University Hospital between 2005 and 2014. Patients were divided into non-elderly (<75 years) and elderly (≥75 years) groups. A propensity score matching analysis was performed for sex and clinical T and N stage, with a total of 29 matched pairs. General preoperative data, surgical procedures, intraoperative data, postoperative complications, in-hospital death, cancer-specific survival, and overall survival were compared between groups. The elderly group was characterized by lower preoperative serum albumin levels and higher American Society of Anesthesiologists grade. Intraoperative data and postoperative complications did not differ between the groups. The in-hospital death rate was 4% in the elderly group, which did not significantly differ from the non-elderly group. Cancer-specific survival was similar between the two groups. Although overall survival tended to be poor in the elderly group, it was not significantly worse than that of the non-elderly group. In conclusion, the short- and long-term outcomes of minimally invasive esophagectomy in elderly versus non-elderly patients were acceptable. Minimally invasive esophagectomy is a safe and feasible modality for elderly patients with appropriate indications.
Predictors of left ventricular reverse remodelling after coarctation of aorta intervention
Authors: Egbe Alexander C , Miranda William R , Connolly Heidi M
Published: September 2020

Aims

Several coarctation of aorta (COA) severity indices are used for timing of COA intervention, and to define severity of residual coarctation post-intervention. However, it is unclear how many of these COA indices are required in order to recommend intervention, and what degree of residual coarctation results in suboptimal recovery of the left ventricle (LV). Our aim was to assess the correlation between different COA indices and effects of chronic LV pressure overload (LV hypertrophy, diastolic, and systolic dysfunction), and to determine the effect of residual coarctation on LV reverse remodelling after COA intervention.

Methods and results

COA severity indices were defined as Doppler COA gradient, systolic blood pressure (SBP, upper-to-lower-extremity SBP gradient, aortic isthmus ratio. LV remodelling indices were defined as LV mass index (LVMI), LV global longitudinal strain (LVGLS), e′ and E/e′. LV reverse remodelling was defined as the difference between indices obtained pre-intervention and 5-year post-intervention (delta LVMI, e′, E/e′, LVGLS).

Of the COA indices analysed in 546 adult COA patients, aortic isthmus ratio had the strongest correlation with LVMI (β ± standard error −28.3 ± 14.1, P < 0.001), LVGLS (1.51 ± 0.42, P = 0.005), e′ (3.11 ± 1.10, P = 0.014), and E/e′ (−13.4 ± 6.67, P = 0.008). Residual aortic isthmus ratio also had the strongest correlation with LV reverse remodelling, and residual aortic isthmus ratio <0.7 was predictive of suboptimal LV reverse remodelling post-intervention.

Conclusion

Considering the known prognostic implications of LV remodelling and reverse remodelling in response to pressure overload, these results support the use of aortic isthmus ratio for timing of COA intervention, and for prognostication post-intervention.
The role of HIF-1α in nicotine-induced root and bone resorption during orthodontic tooth movement
Authors: Ullrich Niklas , Schröder Agnes , Bauer Maria , Spanier Gerrit , Jantsch Jonathan , Deschner James , Proff Peter , Kirschneck Christian
Published: September 2020

Background

In orthodontic tooth movement (OTM), pseudo-inflammatory processes occur that are similar to those of nicotine-induced periodontitis. Previous studies have shown that nicotine accelerates OTM, but induces periodontal bone loss and dental root resorption via synergistically increased osteoclastogenesis. This study aimed to investigate the role of hypoxia-inducible factor 1 alpha (HIF-1α) in nicotine-induced osteoclastogenesis during OTM.

Materials/Methods

Male Fischer-344 rats were treated with l-Nicotine (1.89 mg/kg/day s.c., N = 10) or NaCl solution (N = 10). After a week of premedication, a NiTi spring was inserted to mesialize the first upper left molar. The extent of dental root resorption, osteoclastogenesis, and HIF-1α protein expression was determined by (immuno)histology, as well as bone volume (BV/TV) and trabecular thickness (TbTh) using µCT. Receptor activator of nuclear factor of activated B-cells ligand (RANK-L), osteoprotegerin (OPG), and HIF-1α expression were examined at the protein level in periodontal ligament fibroblasts (PDLF) exposed to pressure, nicotine and/or hypoxia, as well as PDLF-induced osteoclastogenesis in co-culture experiments with osteoclast progenitor cells.

Results

Nicotine favoured dental root resorptions and osteoclastogenesis during OTM, while BV/TV and TbTh were only influenced by force. This nicotine-induced increase does not appear to be mediated by HIF-1α, since HIF-1α was stabilized by force application and hypoxia, but not by nicotine. The in vitro data showed that the hypoxia-induced increase in RANK-L/OPG expression ratio and PDLF-mediated osteoclastogenesis was less pronounced than the nicotine-induced increase.

Conclusions

Study results indicate that the nicotine-induced increase in osteoclastogenesis and periodontal bone resorption during OTM may not be mediated by hypoxic effects or HIF-1α stabilization in the context of nicotine-induced vasoconstriction, but rather by an alternative mechanism.
Reconstructing the Invasion Route of the P-Element inDrosophila melanogasterUsing Extant Population Samples
Authors: Weilguny Lukas , Vlachos Christos , Selvaraju Divya , Kofler Robert
Published: September 2020

The P-element, one of the best understood eukaryotic transposable elements, spread in natural Drosophila melanogaster populations in the last century. It invaded American populations first and later spread to the Old World. Inferring this invasion route was made possible by a unique resource available in D. melanogaster: Many strains sampled from different locations over the course of the last century. Here, we test the hypothesis that the invasion route of the P-element may be reconstructed from extant population samples using internal deletions (IDs) as markers. These IDs arise at a high rate when DNA transposons, such as the P-element, are active. We suggest that inferring invasion routes is possible as: 1) the fraction of IDs increases in successively invaded populations, which also explains the striking differences in the ID content between American and European populations, and 2) successively invaded populations end up with similar sets of IDs. This approach allowed us to reconstruct the invasion route of the P-element with reasonable accuracy. Our approach also sheds light on the unknown timing of the invasion in African populations: We suggest that African populations were invaded after American but before European populations. Simulations of TE invasions in spatially distributed populations confirm that IDs may allow us to infer invasion routes. Our approach might be applicable to other DNA transposons in different host species.
Seismic discontinuities in the lithospheric mantle at the Dead Sea Transform
Authors: Mohsen Ayman , Kind Rainer , Yuan Xiaohui
Published: September 2020

The Dead Sea Transform (DST) was formed in the mid-Cenozoic, about 18 Myr ago, as a result of the breakaway of the Arabian plate from the African plate. Higher resolution information about the sub-Moho structure is still sparse in this region. Here, we study seismic discontinuities in the mantle lithosphere in the region of the DST using a modified version of the P- and S-receiver function methods. We use open data from permanent and temporary seismic stations. The results are displayed in a number of depth profiles through the study area. The Moho is observed on both sides of the transform at nearly 40 km depth by S-to-p and in P-to-s converted signals. The lithosphere–asthenosphere boundary (LAB) on the eastern side of the DST is observed near 180–200 km depth, which is according to our knowledge the first LAB observation at that depth in this region. This observation could lead to the conclusion that the thickness of the Arabian lithosphere east of the DST is likely cratonic. In addition, we observe in the entire area a negative velocity gradient at 60–80 km depth, which was previously interpreted as LAB.
Staff recognition and its importance for surgical service delivery: a qualitative study in Freetown, Sierra Leone
Authors: Willott Chris , Boyd Nick , Wurie Haja , Smalle Isaac , Kamara T B , Davies Justine I , Leather Andrew J M
Published: September 2020

We examined the views of providers and users of the surgical system in Freetown, Sierra Leone on processes of care, job and service satisfaction and barriers to achieving quality and accessible care, focusing particularly on the main public tertiary hospital in Freetown and two secondary and six primary sites from which patients are referred to it. We conducted interviews with health care providers (N = 66), service users (n = 24) and people with a surgical condition who had chosen not to use the public surgical system (N = 13), plus two focus groups with health providers in primary care (N = 10 and N = 10). The overall purpose of the study was to understand perceptions on processes of and barriers to care from a variety of perspectives, to recommend interventions to improve access and quality of care as part of a larger study. Our research suggests that providers perceive their relationships with patients to be positive, while the majority of patients see the opposite: that many health workers are unapproachable and uncaring, particularly towards poorer patients who are unable or unwilling to pay staff extra in the form of informal payments for their care. Many health care providers note the importance of lack of recognition shown to them by their superiors and the health system in general. We suggest that this lack of recognition underlies poor morale, leading to poor care. Any intervention to improve the system should therefore consider staff–patient relations as a key element in its design and implementation, and ideally be led and supported by frontline healthcare workers.
Adoption of evidence-based global policies at the national level: intermittent preventive treatment for malaria in pregnancy and first trimester treatment in Kenya, Malawi, Mali and The Gambia
Authors: Webster Jayne , Hoyt Jenna , Diarra Samba , Manda-Taylor Lucinda , Okoth George , Achan Jane , Ghilardi Ludovica , D’Alessandro Umberto , Madanista Mwayi , Kariuki Simon , Kayentao Kassoum , Hill Jenny
Published: September 2020

In 2012, the World Health Organization (WHO) updated its policy on intermittent preventive treatment in pregnancy with sulphadoxine–pyrimethamine (IPTp-SP). A global recommendation to revise the WHO policy on the treatment of malaria in the first trimester is under review. We conducted a retrospective study of the national policy adoption process for revised IPTp-SP dosing in four sub-Saharan African countries. Alongside this retrospective study, we conducted a prospective policy adoption study of treatment of first trimester malaria with artemisinin combination therapies (ACTs). A document review informed development and interpretation of stakeholder interviews. An analytical framework was used to analyse data exploring stakeholder perceptions of the policies from 47 in-depth interviews with a purposively selected range of national level stakeholders. National policy adoption processes were categorized into four stages: (1) identify policy need; (2) review the evidence; (3) consult stakeholders and (4) endorse and draft policy. Actors at each stage were identified with the roles of evidence generation; technical advice; consultative and statutory endorsement. Adoption of the revised IPTp-SP policy was perceived to be based on strong evidence, support from WHO, consensus from stakeholders; and followed these stages. Poor tolerability of quinine was highlighted as a strong reason for a potential change in treatment policy. However, the evidence on safety of ACTs in the first trimester was considered weak. For some, trust in WHO was such that the anticipated announcement on the change in policy would allay these fears. For others, local evidence would first need to be generated to support a change in treatment policy. A national policy change from quinine to ACTs for the treatment of first trimester malaria will be less straightforward than experienced with increasing the IPTp dosing regimen despite following the same policy processes. Strong leadership will be needed for consultation and consensus building at national level.
Revealing antibiotic cross-resistance patterns in hospitalized patients through Bayesian network modelling
Authors: Cherny Stacey S , Nevo Daniel , Baraz Avi , Baruch Shoham , Lewin-Epstein Ohad , Stein Gideon Y , Obolski Uri
Published: September 2020

Objectives

Microbial resistance exhibits dependency patterns between different antibiotics, termed cross-resistance and collateral sensitivity. These patterns differ between experimental and clinical settings. It is unclear whether the differences result from biological reasons or from confounding, biasing results found in clinical settings. We set out to elucidate the underlying dependency patterns between resistance to different antibiotics from clinical data, while accounting for patient characteristics and previous antibiotic usage.

Methods

Additive Bayesian network modelling was employed to simultaneously estimate relationships between variables in a dataset of bacterial cultures derived from hospitalized patients and tested for resistance to multiple antibiotics. Data contained resistance results, patient demographics and previous antibiotic usage, for five bacterial species: Escherichia coli (n = 1054), Klebsiella pneumoniae (n = 664), Pseudomonas aeruginosa (n = 571), CoNS (n = 495) and Proteus mirabilis (n = 415).

Results

All links between resistance to the various antibiotics were positive. Multiple direct links between resistance of antibiotics from different classes were observed across bacterial species. For example, resistance to gentamicin in E. coli was directly linked with resistance to ciprofloxacin (OR = 8.39, 95% credible interval 5.58–13.30) and sulfamethoxazole/trimethoprim (OR = 2.95, 95% credible interval 1.97–4.51). In addition, resistance to various antibiotics was directly linked with previous antibiotic usage.

Conclusions

Robust relationships among resistance to antibiotics belonging to different classes, as well as resistance being linked to having taken antibiotics of a different class, exist even when taking into account multiple covariate dependencies. These relationships could help inform choices of antibiotic treatment in clinical settings.
Large pseudoaneurysm arising from the deep femoral artery after hip fracture fixation
Authors: Bowden Sylvie , Jaberi Arash , Roche-Nagle Graham
Published: September 2020

Hip fracture is a common condition of increasing global concern. Vascular injury as a complication after hip fracture repair is rare. A 90-year-old woman developed swelling and pain to her proximal thigh 1 month after uneventful hip fracture fixation. Ultrasound revealed a large pseudoaneurysm of the deep femoral artery, which was successfully treated with transcatheter embolization. Pseudoaneurysms have numerous etiologies. In this case, vascular injury is suspected to be a consequence of proximal migration of the lesser trochanteric fragment. Unfortunately, pseudoaneurysms are often not appreciated due to the nonspecific nature of the presenting symptoms. Diagnosis should be confirmed radiologically and management depends on the location and size of the pseudoaneurysm, as well as patient comorbidities. Pseudoaneurysm after hip fracture fixation is a rare but serious complication. Diagnosis is challenging due to nonspecific symptoms. A high index of suspicion is imperative to prevent life-threatening rupture.
Recent Work in African Philosophy: Its Relevance beyond the Continent
Authors: Metz Thaddeus
Published: September 2020

In this article I critically discuss some recent English language books in African philosophy. Specifically, I expound and evaluate key claims from books published by sub-Saharan thinkers since 2017 that address epistemology, metaphysics, and value theory and that do so in ways of interest to an audience of at least Anglo-American-Australasian analytic philosophers. My aim is not to establish a definitive conclusion about these claims, but rather to facilitate cross-cultural engagement by highlighting their relevance, at least to many western philosophers, and by presenting challenges to these claims that such philosophers would be likely to mount.
A simple relationship for the spectro-temporal structure of bursts from FRB 121102
Authors: Rajabi Fereshteh , Chamma Mohammed A , Wyenberg Christopher M , Mathews Abhilash , Houde Martin
Published: September 2020

We consider a simple dynamical and relativistic model to explain the spectro-temporal structure often displayed by repeating fast radio bursts (FRBs). We show how this model can account for the downward frequency drift in a sequence of sub-bursts of increasing arrival time (the ‘sad trombone’ effect) and their tendency for exhibiting a reduced pulse width with increasing frequency of observation. Most importantly, this model also predicts a systematic inverse relationship between the (steeper) slope of the frequency drift observed within a single sub-burst and its temporal duration. Using already published data for FRB 121102, we find and verify the relationship predicted by this model. We therefore argue that the overall behaviour observed for this object as a function of frequency is consistent with an underlying narrow-band emission process, where the wide-band nature of the measured FRB spectrum is due to relativistic motions. Although this scenario and the simple dynamics we consider could be applied to other theories, they are well suited for a model based upon Dicke’s superradiance as the physical process responsible for FRB radiation in this and similar sources.