bluuebunny/crossref_metadata_2025 huggingface dataset:
Residual stress determination using full-field optical methods
Authors: Nelson Drew V
Published: August 2021

Residual stresses are created in engineering components during fabrication and processing. Such stresses can strongly influence structural behavior. They are generally found by experimental means. A widely used way of finding residual stresses is removal of a small volume of material containing stresses and measurement of the strains that develop in surrounding material as a result of stresses being released. The strains can then be used to compute residual stresses. Drilling a small shallow hole is the most common way of implementing this approach, with strains measured by nearby strain gages adhered to the surface. This paper provides an overview of how full-field optical methods can be used instead of strain gages with hole drilling, overcoming limitations associated with gages and expanding capabilities of the hole drilling approach. The methods considered are holographic and electronic speckle pattern interferometry, Moire interferometry and digital image correlation. Advantages of using optical methods to find residual stresses are shown. A variety of applications is presented, ranging from determination of stresses in underground piping to stresses in microscale specimens. In addition, optical approaches employing different ways of material removal for stress release are reviewed, as well as several non-destructive optical methods for determining residual stresses.
Edge to quantum: hybrid quantum-spiking neural network image classifier
Authors: Ajayan A , James A P
Published: August 2021

The extreme parallelism property warrant convergence of neural networks with that of quantum computing. As the size of the network grows, the classical implementation of neural networks becomes computationally expensive and not feasible. In this paper, we propose a hybrid image classifier model using spiking neural networks (SNN) and quantum circuits that combines dynamic behaviour of SNN with the extreme parallelism offered by quantum computing. The proposed model outperforms models in comparison with spiking neural network in classical computing, and hybrid convolution neural network-quantum circuit models in terms of various performance parameters. The proposed hybrid SNN-QC model achieves an accuracy of 99.9% in comparison with CNN-QC model accuracy of 96.3%, and SNN model of accuracy 91.2% in MNIST classification task. The tests on KMNIST and CIFAR-1O also showed improvements.
Doxycycline inducible overexpression systems: how to induce your gene of interest without inducing misinterpretations
Authors: De Boeck Jolan , Verfaillie Catherine
Published: August 2021

The doxycycline inducible overexpression system is a highly flexible and widely used tool for both in vitro and in vivo studies. However, during the past decade, a handful of reports have explicitly called for caution when using this system. The raised concerns are based on the notion that doxycycline can impair mitochondrial function of mammalian cells and can alter properties such as cell proliferation. As such, experimental outcomes can be confounded with the side effects of doxycycline and valid interpretation can be seriously threatened. Today, no consensus seems to exist about how these problems should be prevented. Moreover, some of the strategies that have been used to cope with these difficulties can actually introduce additional problems that are related to genomic instability and genetic modification of the cells. Here, we elaborate on the above statements and clarify them by some basic examples taken from our personal wet-lab experience. As such, we provide a nuanced overview of the doxycycline inducible overexpression system, some of its limitations and how to deal with them.
Determination of Wolbachia Diversity in 23 Cricket Species (Gryllidae) From China
Authors: Li Yue-Yuan , Zeng Yang , Zhu Dao-Hong
Published: August 2021

Wolbachia (Hertig) (Rickettsiales: Anaplasmataceae) are maternally inherited endosymbiotic bacteria that are widely present in nematodes and arthropods. These endosymbiont bacteria receive significant research attention because they can have important effects on the biology of their hosts. Here, we present the first detailed analyses of Wolbachia in crickets from China, with screening of 23 species from eight genera. In total, 21 species from the eight genera were positive for Wolbachia. Significant diversity was observed among Wolbachia strains from the crickets based on five multilocus sequence typing (MLST) genes, with 15 different sequence types (STs), of which 12 STs were new to the MLST database. Five species were infected with Wolbachia of supergroup A, 11 species were infected with Wolbachia of supergroup B, and seven species were infected with Wolbachia of supergroup F. Some of the same host species harbored distinctly different Wolbachia strains, suggesting multiple infections of crickets by Wolbachia. Different cricket hosts also harbored closely related Wolbachia strains, and there were three gene recombinations. Horizontal transmission and gene recombination may allow crickets to acquire new Wolbachia strains and have increased the genetic diversity of Wolbachia.
Healthcare for older people in Asia
Authors: Woo Jean
Published: August 2021

Populations in Asian developed economies are rapidly ageing, such that, currently, Hong Kong and Japan have the longest life expectancy at birth for both men and women. However, extended lifespan is not necessarily accompanied by prolongation of health span, such that there is increasing prevalence of frailty and dependency, which translates into increase in complex health and social needs as well as increase in absolute numbers of older adults that require such needs. Consideration of social determinants of healthy ageing would be important in the design of equitable health and social care systems. There is a trend towards development of integrated medical social care in the community in Asian countries. Long-term care insurance and also philanthropic support play a role in the financing of such care models.
A Cyst-ematic Analysis of the Adrenal Gland: A Compilation of Primary Cystic Lesions From Our Institution and Review of the Literature
Authors: Gubbiotti Maria A , LiVolsi Virginia , Montone Kathleen , Baloch Zubair
Published: August 2021

Objectives

Although primary adrenal lesions and metastases are most commonly encountered, de novo cysts of the adrenal gland can occasionally occur.

Methods

We analyzed the pathology archives at the Hospital of the University of Pennsylvania for diagnoses of cystic lesions of the adrenal gland between 1998 and 2020. Patient demographics and clinical information were extracted, and pathology slides and stains, as appropriate, were analyzed. The literature between 1998 and 2020 was also searched for large case series involving cystic adrenal lesions.

Results

We found 18 cystic lesions of the adrenal gland in our archives, categorized as pseudocysts (7), endothelial cysts (5), mesothelial cysts (2), mature teratoma (1), cystic adrenal cortical adenoma (1), cystic pheochromocytoma (1), and cystic metastasis (1). The mean age at time of diagnosis was 52.3 years, and the mean size of the cysts was 6.0 cm. There was a slight female predilection, and cysts were more likely to be found on the left side. All lesions were incidental findings. The cystic metastasis was clear cell renal cell carcinoma. Our findings were also compared with those found in the literature published within the same timeframe.

Conclusions

Adrenal cysts are rare entities. Our findings are concordant with other large studies and provide additional cases to the existing literature. In addition, our literature search expands the possible differential diagnoses for cystic lesions arising in the adrenal gland.
Identification of Predictive Factors for Patient-Reported Outcomes in the Prospective Australian Breast Device Registry
Authors: Hansen Jessy , Ahern Susannah , Gartoulla Pragya , Khu Ying , Elder Elisabeth , Moore Colin , Farrell Gillian , Hopper Ingrid , Earnest Arul
Published: August 2021

Background

Patient-reported outcome measures (PROMs) are an important tool for evaluating outcomes following breast device procedures and are used by breast device registries. PROMs can assist with device monitoring through benchmarked outcomes but need to account for demographic and clinical factors that may affect PROM responses.

Objectives

This study aimed to develop appropriate risk-adjustment models for the benchmarking of PROM data to accurately track device outcomes and identify outliers in an equitable manner.

Methods

Data for this study were obtained from the Australian Breast Device Registry, which consists of a large prospective cohort of patients with primary breast implants. The 5-question BREAST-Q implant surveillance module was used to assess PROMs at 1 year following implant insertion. Logistic regression models were used to evaluate associations between demographic and clinical characteristics and PROMs separately by implant indication. Final multivariate risk-adjustment models were built sequentially, assessing the independent significant association of these variables.

Results

In total, 2221 reconstructive and 12,045 aesthetic primary breast implants with complete 1-year follow-up PROMs were included in the study. Indication for operation (post-cancer, risk reduction, or developmental deformity) was included in the final model for all reconstructive implant PROMs. Site type (private or public hospital) was included in the final breast reconstruction model for look, rippling, and tightness. Age at operation was included in the reconstruction models for rippling and tightness and in the aesthetic models for look, rippling, pain, and tightness.

Conclusions

These multivariate models will be useful for equitable benchmarking of breast devices by PROMs to help track device performance.

Level of Evidence: 2
Drug–target interaction predication via multi-channel graph neural networks
Authors: Li Yang , Qiao Guanyu , Wang Keqi , Wang Guohua
Published: August 2021

Drug–target interaction (DTI) is an important step in drug discovery. Although there are many methods for predicting drug targets, these methods have limitations in using discrete or manual feature representations. In recent years, deep learning methods have been used to predict DTIs to improve these defects. However, most of the existing deep learning methods lack the fusion of topological structure and semantic information in DPP representation learning process. Besides, when learning the DPP node representation in the DPP network, the different influences between neighboring nodes are ignored. In this paper, a new model DTI-MGNN based on multi-channel graph convolutional network and graph attention is proposed for DTI prediction. We use two independent graph attention networks to learn the different interactions between nodes for the topology graph and feature graph with different strengths. At the same time, we use a graph convolutional network with shared weight matrices to learn the common information of the two graphs. The DTI-MGNN model combines topological structure and semantic features to improve the representation learning ability of DPPs, and obtain the state-of-the-art results on public datasets. Specifically, DTI-MGNN has achieved a high accuracy in identifying DTIs (the area under the receiver operating characteristic curve is 0.9665).
DAMA: a method for computing multiple alignments of protein structures using local structure descriptors
Authors: Daniluk Paweł , Oleniecki Tymoteusz , Lesyng Bogdan
Published: August 2021

Motivation

The well-known fact that protein structures are more conserved than their sequences forms the basis of several areas of computational structural biology. Methods based on the structure analysis provide more complete information on residue conservation in evolutionary processes. This is crucial for the determination of evolutionary relationships between proteins and for the identification of recurrent structural patterns present in biomolecules involved in similar functions. However, algorithmic structural alignment is much more difficult than multiple sequence alignment. This study is devoted to the development and applications of DAMA—a novel effective environment capable to compute and analyze multiple structure alignments.

Results

DAMA is based on local structural similarities, using local 3D structure descriptors and thus accounts for nearest-neighbor molecular environments of aligned residues. It is constrained neither by protein topology nor by its global structure. DAMA is an extension of our previous study (DEDAL) which demonstrated the applicability of local descriptors to pairwise alignment problems. Since the multiple alignment problem is NP-complete, an effective heuristic approach has been developed without imposing any artificial constraints. The alignment algorithm searches for the largest, consistent ensemble of similar descriptors. The new method is capable to capture most of the biologically significant similarities present in canonical test sets and is discriminatory enough to prevent the emergence of larger, but meaningless, solutions. Tests performed on the test sets, including protein kinases, demonstrate DAMA’s capability of identifying equivalent residues, which should be very useful in discovering the biological nature of proteins similarity. Performance profiles show the advantage of DAMA over other methods, in particular when using a strict similarity measure QC, which is the ratio of correctly aligned columns, and when applying the methods to more difficult cases.

Availability and implementation

DAMA is available online at http://dworkowa.imdik.pan.pl/EP/DAMA. Linux binaries of the software are available upon request.

Supplementary information

Supplementary data are available at Bioinformatics online.
Inhibition of METTL3/m6A/miR126 promotes the migration and invasion of endometrial stromal cells in endometriosis
Authors: Li Xiaoou , Xiong Wenqian , Long Xuefeng , Dai Xin , Peng Yuan , Xu Ying , Zhang Zhibing , Zhang Ling , Liu Yi
Published: August 2021

N 6-methyladenosine (m6A), one of the most abundant RNA modifications, is involved in the progression of many diseases, but its role and related molecular mechanisms in endometriosis remain unknown. To address these issues, we detected m6A levels in normal, eutopic, and ectopic endometrium and found the m6A levels decreased in eutopic and ectopic endometrium compared with normal endometrium. In addition, we proved that methyltransferase-like 3 (METTL3) downregulation accounted for m6A reduction in endometriosis. Furthermore, we observed that METTL3 knockdown facilitated the migration and invasion of human endometrial stromal cells (HESCs), whereas METTL3 overexpression exerted opposite effects, suggesting that METTL3 downregulation might contribute to endometriosis development by enhancing cellular migration and invasion. Mechanistically, METTL3-dependent m6A was involved in the DGCR8-mediated maturation of primary microRNA126 (miR126 and pri-miR126). Moreover, miR126 inhibitor significantly enhanced the migration and invasion of METTL3-overexpressing HESCs, whereas miR126 mimics attenuated the migration and invasion of METTL3-silenced HESCs. Our study revealed the METTL3/m6A/miR126 pathway, whose inhibition might contribute to endometriosis development by enhancing cellular migration and invasion. It also showed that METTL3 might be a novel diagnostic biomarker and therapeutic target for endometriosis.
A New Approach to Evaluate and Reduce Uncertainty of Model-Based Biodiversity Projections for Conservation Policy Formulation
Authors: Myers Bonnie J E , Weiskopf Sarah R , Shiklomanov Alexey N , Ferrier Simon , Weng Ensheng , Casey Kimberly A , Harfoot Mike , Jackson Stephen T , Leidner Allison K , Lenton Timothy M , Luikart Gordon , Matsuda Hiroyuki , Pettorelli Nathalie , Rosa Isabel M D , Ruane Alex C , Senay Gabriel B , Serbin Shawn P , Tittensor Derek P , Beard T Douglas
Published: August 2021

Biodiversity projections with uncertainty estimates under different climate, land-use, and policy scenarios are essential to setting and achieving international targets to mitigate biodiversity loss. Evaluating and improving biodiversity predictions to better inform policy decisions remains a central conservation goal and challenge. A comprehensive strategy to evaluate and reduce uncertainty of model outputs against observed measurements and multiple models would help to produce more robust biodiversity predictions. We propose an approach that integrates biodiversity models and emerging remote sensing and in-situ data streams to evaluate and reduce uncertainty with the goal of improving policy-relevant biodiversity predictions. In this article, we describe a multivariate approach to directly and indirectly evaluate and constrain model uncertainty, demonstrate a proof of concept of this approach, embed the concept within the broader context of model evaluation and scenario analysis for conservation policy, and highlight lessons from other modeling communities.
Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae
Authors: Estrada Bonilla Boris , Costa Ana Rita , van den Berg Daan F , van Rossum Teunke , Hagedoorn Stefan , Walinga Hielke , Xiao Minfeng , Song Wenchen , Haas Pieter-Jan , Nobrega Franklin L , Brouns Stan J J
Published: August 2021

Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.
Renal function and outcome of patients with non-valvular atrial fibrillation
Authors: Barashi Rami , Hornik-Lurie Tzipi , Gabay Hagit , Haskiah Feras , Minha Saar , Shuvy Mony , Assali Abid , Pereg David
Published: August 2021

Aims

Atrial fibrillation and renal dysfunction are associated with increased cardiovascular risk. We examined the association between renal function and incident ischaemic stroke or myocardial infarction in patients with atrial fibrillation treated with direct oral anticoagulants (DOACs).

Methods and results

This study was conducted using a large health record database. Included were 19 713 patients with first time diagnosis of non-valvular atrial fibrillation treated with DOACs between 2010 and 2018. Patients were categorized into four groups according to the estimated glomerular filtration rate (eGFR) (<30, 30–59, 60–89, and ≥90 mL/min/1.73 m2). Ischaemic stroke and acute myocardial infarction rates were compared between the groups. During 55 086 person-years of follow-up, there were 2295 (11.6%) cases of ischaemic stroke and 1158 (5.9%) cases of acute myocardial infarction. There was a significant inverse association between eGFR and the risk of myocardial infarction. A multivariate analysis using the group with eGFR ≥90 mL/min/1.73 m2 as a reference demonstrated an increased risk of myocardial infarction with lower eGFR [hazard ratio (HR) = 1.2 95% confidence interval (CI) 0.9–1.4, HR = 1.4, 95% CI 1.2–1.7, and HR = 2.5, 95% CI 1.8–3.4 for patients with eGFR 60–89, 30–59, and <30 mL/min/1.73 m2, respectively, P < 0.001]. Each 10 mL decrease in eGFR was associated with an 8% increase in the risk of myocardial infarction. There was no association between eGFR and the risk of ischaemic stroke (HR = 0.9 95% CI 0.8–1.1, HR = 0.93, 95% CI 0.8–1.1, and HR = 1.1, 95% CI 0.8–1.4 for patients with eGFR 60–89, 30–59, and <30 mL/min/1.73 m2, respectively, P = 0.325).

Conclusions

Renal dysfunction is associated with an increased risk of myocardial infarction but not of ischaemic stroke among patients with atrial fibrillation treated with DOACs.
Acute cardiac manifestations under immune checkpoint inhibitors—beware of the obvious: a case report
Authors: Arangalage Dimitri , Pavon Anna Giulia , Özdemir Berna C , Michielin Olivier , Schwitter Jurg , Monney Pierre
Published: August 2021

Background

Immune checkpoint inhibitors (ICI) have revolutionized the management of many cancer types by drastically improving the median survival rate of patients. However, this efficiency comes at the cost of a high rate of immune-related adverse events, including lethal cardiac manifestations. Rapidly fatal cases of ICI-induced myocarditis have been reported and drawn considerable attention over the past years. However, it is essential to bear in mind that not all cardiac events occurring under ICI therapy are necessarily myocarditis.

Case summary

A 61-year-old female treated with pembrolizumab for a stage IV melanoma was admitted for chest pain leading to the diagnosis of ICI-related myocarditis based on the description of a discrete left ventricular subepicardial late gadolinium enhancement (LGE) on cardiac magnetic resonance (CMR) imaging. ICI were suspended and intravenous methylprednisolone initiated. A second line anti-MEK therapy was initiated. After a month of treatment, similar chest pain occurred. CMR revealed a midventricular stress cardiomyopathy and no LGE was detected. A posteriori interrogation revealed emotional stressors preceding both episodes. Review of the first CMR, performed 2 weeks after symptom onset, indicated a pattern compatible with the recovery phase of a stress cardiomyopathy and the presence of LGE was questioned. ICI were reintroduced without recurrence of cardiac events.

Discussion

Not all cardiac manifestations occurring under ICI therapy are drug-related adverse events, therefore differential diagnoses must systematically be considered as the contraindication of ICI may have a major impact on patient prognosis. Cardiac imaging should be performed early and plays a key role in the management strategy.
Intracoronary acetylcholine testing among 746 consecutive Japanese patients with angina-like chest pain and unobstructed coronary artery disease
Authors: Sueda Shozo , Sakaue Tomoki
Published: August 2021

Aims 

Intracoronary acetylcholine (ACh) testing is useful for the detection of epicardial spasm (ES) and coronary microvascular spasm (CMS). We retrospectively analysed the incidence of ES and CMS in consecutive Japanese patients with unobstructed coronary artery disease.

Methods and results

From January 1991 to February 2019, we performed intracoronary ACh testing of 1864 patients. Among these patients, a total of 746 consecutive patients (254 women, mean age 64 ± 11 years) who underwent first diagnostic angiography for suspected myocardial ischaemia and had unobstructed coronary arteries (<50%) were enrolled. Epicardial spasm was defined as ≥90% stenosis and usual chest symptoms and ischaemic ECG changes, while CMS was defined as <75% stenosis and usual chest symptoms and ischaemic ECG changes. We performed intracoronary ACh testing on both coronary arteries in 96% (716/746) of all subjects. Overall, ES was found in 329 patients (44%), whereas CMS was revealed in 40 patients (5%) including 4 patients with coexisting ES. In patients with ES, women made up 22%, and approximately three-quarters of the patients had resting chest pain. In contrast, women composed 65% (26/40) of those with CMS, and 15 patients with CMS had another chest symptom. Coronary microvascular spasm was frequently observed in the left coronary artery (LCA) but not the right coronary artery. Electrical cardioversion was necessary for two patients.

Conclusions 

Coronary microvascular spasm was recognized in only 5% of consecutive Japanese patients with unobstructed coronary artery disease, whereas ES was revealed in 44% of those patients. Coronary microvascular spasm was often observed in women and in the LCA.
Association of clinical trial participation after myocardial infarction with socioeconomic status, clinical characteristics, and outcomes
Authors: Ohm Joel , Jernberg Tomas , Johansson David , Warnqvist Anna , Leosdottir Margrét , Hambraeus Kristina , Svensson Per
Published: August 2021

Aims

To investigate whether participants in clinical trials after myocardial infarction (MI) are representable for the post-MI population concerning characteristics, secondary prevention, and prognosis.

Methods and results

Cohort study on 31 792 attendants to 1-year revisits after MI throughout Sweden (n = 2941 clinical trial participants) between 2008 and 2013 identified in the Swedish Web-System for Enhancement and Development of Evidence-Based Care in Heart Disease Evaluated According to Recommended Therapies (SWEDEHEART). Individual-level data on socioeconomic status (SES) (disposable income, educational level, and marital status) and outcomes (first recurrent non-fatal MI, coronary heart disease death, fatal or non-fatal stroke until study end 2018) were linked from other national registries. Trial participants were more likely to be men [risk ratio 1.09; 95% confidence interval (CI) 1.07–1.11], and married (1.07; 1.04–1.10), have a highest-quintile income (1.42; 1.36–1.48), and post-secondary education (1.25; 1.18–1.33), while less likely to have a history of MI (0.88; 0.80–0.97), be persistent smokers (0.83; 0.75–0.92) and have left ventricular dysfunction (0.59; 0.44–0.79) compared to non-participants. During a mean 6.7-year follow-up, 5206 outcome events occurred. Risk was lower in trial participants (hazard ratio 0.80; 95% CI 0.72–0.89), also after adjusting for clinical characteristics and post-MI therapies (0.85; 0.77–0.94) and additionally for SES (0.88; 0.79–0.97).

Conclusions

Clinical trial participants post-MI are more often male, have higher SES, a more advantageous risk profile, and better prognosis. Additional unmeasured participation bias was implied. Questionable external validity of post-MI trials highlights the importance of complementary studies using real-world data.
Routine early postoperative computed tomography angiography after coronary artery bypass surgery: clinical value and management implications
Authors: Károlyi Mihály , Eberhard Matthias , Gloor Tobias , Polacin Malgorzata , Manka Robert , Savic Vedran , Plass André R , Vogt Paul Robert , Alkadhi Hatem , Schmiady Martin O
Published: August 2021

OBJECTIVES

Computed tomography angiography (CTA) is broadly used for long-term follow-up of graft patency after coronary artery bypass graft surgery (CABG). However, its clinical value in the early postoperative setting has not been established yet. We evaluated the benefit of adding CTA to the routine clinical work-up after CABG on patient management.

METHODS

A total of 305 consecutive patients (269 males, median age 68 years) underwent CABG and postoperative CTA with a median of 6 days after surgery. Graft patency and additional imaging findings were assessed and their influence on diagnosis and clinical management was evaluated.

RESULTS

Graft occlusion or high-grade stenosis was found in 15% of the patients. Additional findings were reported in 44% of the patients, including pericardial (2%) and pleural effusion (27%), large pneumothorax (11%), pulmonary infection (4%), cardiac or vascular thrombus (2%), pulmonary embolism (2%), sternal dehiscence (1%) and additional incidental findings requiring follow-up (6%). CT findings initiated new diagnostic and/or therapeutic measures in 15% of the patients, 47% of those with diseased grafts and 19% of patients with non-graft-related findings. No adverse events related to CTA were documented.

CONCLUSIONS

Early routine postoperative assessment of CABG with CTA reveals both cardiac and non-cardiac findings with a high frequency, affecting clinical management in a substantial proportion of patients.
A need for null models in understanding disease transmission: the example ofMycobacterium ulcerans(Buruli ulcer disease)
Authors: Receveur Joseph P , Bauer Alexandra , Pechal Jennifer L , Picq Sophie , Dogbe Magdalene , Jordan Heather R , Rakestraw Alex W , Fast Kayla , Sandel Michael , Chevillon Christine , Guégan Jean-François , Wallace John R , Benbow M Eric
Published: August 2021

Understanding the interactions of ecosystems, humans and pathogens is important for disease risk estimation. This is particularly true for neglected and newly emerging diseases where modes and efficiencies of transmission leading to epidemics are not well understood. Using a model for other emerging diseases, the neglected tropical skin disease Buruli ulcer (BU), we systematically review the literature on transmission of the etiologic agent, Mycobacterium ulcerans (MU), within a One Health/EcoHealth framework and against Hill's nine criteria and Koch's postulates for making strong inference in disease systems. Using this strong inference approach, we advocate a null hypothesis for MU transmission and other understudied disease systems. The null should be tested against alternative vector or host roles in pathogen transmission to better inform disease management. We propose a re-evaluation of what is necessary to identify and confirm hosts, reservoirs and vectors associated with environmental pathogen replication, dispersal and transmission; critically review alternative environmental sources of MU that may be important for transmission, including invertebrate and vertebrate species, plants and biofilms on aquatic substrates; and conclude with placing BU within the context of other neglected and emerging infectious diseases with intricate ecological relationships that lead to disease in humans, wildlife and domestic animals.
An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets
Authors: Rangel Luiz Thibério , Soucy Shannon M , Setubal João C , Gogarten Johann Peter , Fournier Gregory P
Published: August 2021

Assessing the compatibility between gene family phylogenies is a crucial and often computationally demanding step in many phylogenomic analyses. Here, we describe the Evolutionary Similarity Index (IES), a means to assess shared evolution between gene families using a weighted orthogonal distance regression model applied to sequence distances. The utilization of pairwise distance matrices circumvents comparisons between gene tree topologies, which are inherently uncertain and sensitive to evolutionary model choice, phylogenetic reconstruction artifacts, and other sources of error. Furthermore, IES enables the many-to-many pairing of multiple copies between similarly evolving gene families. This is done by selecting non-overlapping pairs of copies, one from each assessed family, and yielding the least sum of squared residuals. Analyses of simulated gene family data sets show that IES’s accuracy is on par with popular tree-based methods while also less susceptible to noise introduced by sequence alignment and evolutionary model fitting. Applying IES to an empirical data set of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. The most cohesive cluster consisted of 62 genes with compatible evolutionary signal, which occur as both single-copy and multiple homologs per genome; phylogenetic analysis of concatenated alignments from this cluster produced a tree closely matching previously published species trees for Archaea. Four other clusters are mainly composed of accessory genes with limited distribution among Archaea and enriched toward specific metabolic functions. Pairwise evolutionary distances obtained from these accessory gene clusters suggest patterns of interphyla horizontal gene transfer. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.
Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture
Authors: Han Shunhua , Basting Preston J , Dias Guilherme B , Luhur Arthur , Zelhof Andrew C , Bergman Casey M
Published: August 2021

Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabeling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here, we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of long-terminal repeat retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.
An integrative 3-D model of the deep lithospheric structure beneath Dolsk and Odra fault zones as a result of magnetotelluric data interpretation
Authors: Oryński Szymon , Jóźwiak Waldemar , Nowożyński Krzysztof
Published: August 2021

Long-period magnetotelluric soundings were carried out in the eastern part of the Fore-Sudetic Monocline in central Europe to determine the deep geoelectrical structure. It is an important area in the contact zone of the Palaeozoic terranes of Western Europe and the Proterozoic East European Craton. The research area includes the Dolsk fault zone and the Odra fault zone, which are essential geological boundaries of a regional nature separating crustal blocks of various origins. There were conducted 51 soundings on the quasi-regular mesh 150 km in SE and 225 km in NE. The research region is highly urbanized, and hence some of the data were strongly disturbed. Careful processing of data was required, and sometimes measurements had to be repeated at other locations. The collected data allow constructing 3-D models of the electrical conductivity distribution. A parallel version of the ModEM 3-D inversion code was used for modelling. The information contained in each used transfer function was also examined by performing a separate inversion of these functions. The obtained resistivity distribution models confirm the Dolsk and Odra faults' location as postulated previously by geologists. They also show that these very deep faults are reaching the lower crust. However, they do not clearly state how far the contemporary lowering of the Baltica reaches under cover of younger Palaeozoic sediments.
The influence of trawl efficiency assumptions on survey-based population metrics
Authors: Dean Micah J , Hoffman William S , Buchan Nicholas C , Cadrin Steven X , Grabowski Jonathan H
Published: August 2021

Catch data from bottom trawl surveys are used in various ways (e.g. stock assessments, fisheries management, and ecosystem studies) to represent trends in fish populations across space, time, season, or size. Relative abundance indices assume constant capture efficiency, and area-swept abundance requires an estimate of capture efficiency. Therefore, it is important to develop a predictive understanding of the interaction between fish and survey gear. We conducted experiments to test two primary factors that influence the efficiency of survey trawls at capturing demersal groundfish: (1) footrope escapement—estimated by attaching a collection bag beneath the primary trawl, and (2) herding of the sweeps/doors—estimated by varying sweep length. Random forest models were used to disentangle the herding effect from patterns caused by environmental variables. Contrary to common assumptions, footrope efficiency was incomplete (< 100%) and herding was non-trivial (> 0%), which introduces a bias in population metrics that rely on such assumptions. This bias varied by species and depended upon the relative strength of the counteracting effects of footrope escapement and herding. Our findings suggest that trawl efficiency should be estimated (not assumed) to derive area-swept abundance, and relative abundance indices should account for size-based efficiency and changing size compositions.
Applying Bayesian model selection to determine ecological covariates for recruitment and natural mortality in stock assessment
Authors: Trochta John T , Branch Trevor A
Published: August 2021

Incorporating ecological covariates into fishery stock assessments may improve estimates, but most covariates are estimated with error. Model selection criteria are often used to identify support for covariates, have some limitations and rely on assumptions that are often violated. For a more rigorous evaluation of ecological covariates, we used four popular selection criteria to identify covariates influencing natural mortality or recruitment in a Bayesian stock assessment of Pacific herring (Clupea pallasii) in Prince William Sound, Alaska. Within this framework, covariates were incorporated either as fixed effects or as latent variables (i.e. covariates have associated error). We found most support for pink salmon increasing natural mortality, which was selected by three of four criteria. There was ambiguous support for other fixed effects on natural mortality (walleye pollock and the North Pacific Gyre Oscillation) and recruitment (hatchery-released juvenile pink salmon and a 1989 regime shift). Generally, similar criteria values among covariates suggest no clear evidence for a consistent effect of any covariate. Models with covariates as latent variables were sensitive to prior specification and may provide potentially very different results. We recommend using multiple criteria and exploring different statistical assumptions about covariates for their use in stock assessment.
Converging Lexicography and Neology
Authors: Klosa-Kückelhaus Annette , Kernerman Ilan
Published: August 2021

This introduction summarizes general issues combining lexicography and neology in the context of the Globalex Workshop on Lexicography and Neology series. We present each of the six papers composing this Special Issue, featuring two Slavic languages (Czech and Slovak) and two Romance ones (Brazilian Portuguese and Spanish in its European and Latin American varieties) and their diverse lexicographic research and representation, in specialized dictionaries of neologisms or general language ones, in monolingual, bilingual and multilingual lexical resources, and in print and digital dictionaries.
Non-uniform ISS small-gain theorem for infinite networks
Authors: Mironchenko Andrii
Published: August 2021

We introduce the concept of non-uniform input-to-state stability for networks. It combines the uniform global stability with the uniform attractivity of any subnetwork while it allows for non-uniform convergence of all components. For an infinite network consisting of input-to-state stable subsystems, which do not necessarily have a uniform $\mathscr{K}\mathscr{L}$-bound on the transient behaviour, we show the following: if the gain operator satisfies the uniform small-gain condition, then the whole network is non-uniformly input-to-state stable and all its finite subnetworks are input-to-state stable.
A comprehensive digital phenotype for postpartum hemorrhage
Authors: Zheutlin Amanda B , Vieira Luciana , Shewcraft Ryan A , Li Shilong , Wang Zichen , Schadt Emilio , Kao Yu-Han , Gross Susan , Dolan Siobhan M , Stone Joanne , Schadt Eric , Li Li
Published: August 2021

Objective

We aimed to establish a comprehensive digital phenotype for postpartum hemorrhage (PPH). Current guidelines rely primarily on estimates of blood loss, which can be inaccurate and biased and ignore complementary information readily available in electronic medical records (EMR). Inaccurate and incomplete phenotyping contributes to ongoing challenges in tracking PPH outcomes, developing more accurate risk assessments, and identifying novel interventions.

Materials and Methods

We constructed a cohort of 71 944 deliveries from the Mount Sinai Health System. Estimates of postpartum blood loss, shifts in hematocrit, administration of uterotonics, surgical interventions, and diagnostic codes were combined to identify PPH, retrospectively. Clinical features were extracted from EMRs and mapped to common data models for maximum interoperability across hospitals. Blinded chart review was done by a physician on a subset of PPH and non-PPH patients and performance was compared to alternate PPH phenotypes. PPH was defined as clinical diagnosis of postpartum hemorrhage documented in the patient’s chart upon chart review.

Results

We identified 6639 PPH deliveries (9% prevalence) using our phenotype—more than 3 times as many as using blood loss alone (N = 1,747), supporting the need to incorporate other diagnostic and intervention data. Chart review revealed our phenotype had 89% accuracy and an F1-score of 0.92. Alternate phenotypes were less accurate, including a common blood loss-based definition (67%) and a previously published digital phenotype (74%).

Conclusion

We have developed a scalable, accurate, and valid digital phenotype that may be of significant use for tracking outcomes and ongoing clinical research to deliver better preventative interventions for PPH.
Shotgun proteomics of homogenate milk reveals dynamic changes in protein abundances between colostrum, transitional, and mature milk of swine
Authors: Bradshaw Christina V , Suarez Trujillo Aridany , Luecke Sarah M , Logan Lea D , Mohallem Rodrigo , Aryal Uma K , Stewart Kara R , Casey Theresa M , Minor Radiah C
Published: August 2021

Milk is an easily digestible source of nutrients and bioactive factors, its composition reflects the neonate’s needs, and changes from colostrum to transitional and mature milk. Our objective was to measure milk fat, lactose, total carbohydrate, and protein content in parallel with global proteome of homogenate milk samples to characterize changes across the three phases of swine lactation. Milk samples were collected from multiparous sows (n = 9) on postnatal day 0 (D0; colostrum), 3 (D3; early transitional), 7 (D7; late transitional), and 14 (D14; mature). On D3, percent fat (16 ± 2.1) and lactose (3.8 ± 0.3) were higher (P < 0.05) than on D0 (10 ± 3.9 and 1.5 ± 0.3, respectively). Levels of fat and lactose were not different between D3 and D14. Percent total protein decreased (P < 0.05) between D0 (11 ± 2.1) and D3 (5 ± 0.7), but there was no significant change in percent protein between D3 and D14. Total carbohydrates increased (P < 0.05) between D3 (944 ± 353 µg/mL) and D14 (1,150 ± 462 µg/mL). Quantitative proteomic analysis using liquid chromatography tandem mass spectrometry (LC-MS/MS) of homogenate D0, D3, and D14 milk samples (n = 6) identified 772 protein groups which corresponded to 501 individual protein-coding genes. A total of 207 high confidence proteins were detected in n = 3 sows/day. Of the high confidence proteins, 81 proteins were common among all 3 days of lactation. Among the proteins that decreased between the days (false discovery rate; FDR < 0.05) were multiple apolipoproteins and XDH which decreased between D0 to D3. Proteins that increased across the days (FDR < 0.05) were complement factors and 14-3-3 proteins (YWHAQ, YWHAE). Our data provide a good characterization of milk proteome changes that likely reflect mammary function as well as the neonate’s phase-specific developmental needs. This data may be useful in developing approaches to enhance the health and welfare of swine.
International comparison of trends in cancer mortality: Japan has fallen behind in screening-related cancers
Authors: Katanoda Kota , Ito Yuri , Sobue Tomotaka
Published: August 2021

While the age-standardized mortality rate in Japan is decreasing for all cancers as a whole, this is not the case for some major site-specific cancers. We descriptively compared trends in all-cancer and site-specific cancer mortality in Japan and selected countries. Data on age-standardized cancer mortality rates in six countries (Japan, the USA, the UK, Canada, Australia and the Republic of Korea) in 1980–2016 were obtained from the World Health Organization mortality database. While stomach and liver cancer mortality rates in Japan and Korea were initially much higher than those in non-Asian countries, they have rapidly decreased over the long term. By contrast, colorectal, pancreatic and cervical cancer mortality rates in Japan, which were initially lower than those in other countries, have increased such that they are now similar or higher than the rates in non-Asian countries. For male lung cancer, Japan’s initially lower mortality rate is now comparable to that in non-Asian countries as a result of slower decline. Meanwhile, the mortality rate of female breast cancer in Japan and Korea has increased and is nearing the rates observed in non-Asian countries, which by contrast have shown a steady decrease. Thus, while Japan has been successful in reducing the burden of stomach and liver cancers, it is falling behind in reducing the mortality rate of screening-related cancers such as colorectal, female breast and cervical cancers. Control measures for these cancers need to be strengthened.