bluuebunny/crossref_metadata_2025 huggingface dataset:
Derivation of Top-Level Aircraft Requirements for Small Aircraft Transport by Modelling Demand in Europe
Authors: Will Florian , Flüthmann Nico , Eschmann Christian
Published: February 2022

Advancements in aircraft technologies and in the process of aircraft electrification allow for the design of new small aircraft transport (SAT) configurations with a significant impact on sustainability, travel time and operating cost. Additionally, the European Flightpath 2050 creates a European-wide political landscape to enable developments in that field to thrive. All this together provides an environment that promises to open new business opportunities in the form of new and revived mobility services. However, the described ecosystem raises the question of what demand exists for SAT and what top-level aircraft requirements (TLAR) need to be achieved to realize customer-centric SAT. Data of the existing traffic patterns in Europe is analyzed to create a demand model, derive the TLAR and ultimately lay the foundation for a successful European SAT transport system. Initially, traffic pattern data is collected with a resolution on county and city level, thereby ensuring a high accuracy of larger and smaller travel distances. Subsequently, to the data collection, the income distribution in European countries is analyzed and in combination with a Willingness To Pay (WTP) function the actual existing SAT demand is determined. The demand optimized TLAR are then derived by varying the demand models input parameters to maximize the demand. The above-described approach allows to extract the potential annual demand in Europe for a certain set of requirements, it also details how a single parameter effects the demand. Hence, it provides sensitivities to illuminate design focal points. In consideration of all the described factors the paper defines the TLAR, thereby enabling the design of new SAT configurations.
Key design and operation factors for high performance of C12A7:e-based cathodes
Authors: Post A. , Plaza J.F. , Toledo J. , Zschätzsch D. , Reitemeyer M. , Chen L. , Gurciullo A. , Siegel A. , Klar P. J. , Lascombes P. , Seifert B.
Published: February 2022

This work, based on an EU-funded project (NEMESIS), is summarising some of the results from the project activities on the research and development on electride-based cathode technology compatible with all kinds of electric propulsion (EP) systems requiring neutralization or electron emission. Further information describing in detail the performed tests and captured measurements can be found in the referenced documents of each section. Different cathode architectures and several emitter configurations with traditional and with alternative propellants are being developed and tested within the project, all of them using C12A7:e-electride material as thermionic electron source. Findings and conclusions derived from these multiple designs are allowing to figure out some of the key factors that determine the best performance of C12A7:e-electride based cathodes. In this work, a discussion of some of these key design and operation factors will be presented based both on the material characterization parameters, and on the performance tests carried out for the different cathode designs.
HERA Mission LIDAR Mechanical and Optical Design
Authors: Dias Nicole G. , Arribas Beltran N. , Gordo Paulo , Sousa Tiago , Marinho João , Melicio Rui , Amorim António , Livio Belegante , Michel Patrick
Published: February 2022

Near-Earth Objects (NEO) are the topic of several research studies, with objects smaller than 1km in size posing the most threats and being the less understood of this scientific domain. The Asteroid Impact and Deflection Assessment (AIDA) mission involves NASA and ESA with the main mission goal to perform and analyze the asteroid deflection using the Kinetic Impactor technique. The mission target is Didymos-B, a moon of a binary asteroid called Didymos. NASA oversees the Double Asteroid Redirection Test (DART probe), and ESA is responsible for HERA probe, that will measure the Dydimos-B deflection caused by the impact. The Light Detection and Ranging (LIDAR), the Radar, the Satellite-to-Satellite Doppler tracking, the Seismometer, and the Gravimeter are instruments integrated into HERA spacecraft. Information synergy between the instruments allows the detailed characterization of the asteroid including internal structure. This experiment allows further understanding and will provide important information to improve the current NEO understanding and modelling. In this paper, scientific advances related to the LIDAR instrument are reported, including the innovative optomechanical design resulting from thermal and mechanical optimizations. The LIDAR has a compact design and needs to withstand extreme conditions, such as radiative and thermal conditions, without compromise its high accuracy measurements. The LIDAR is a time-of-flight altimeter instrument that will measure the distances from the HERA spacecraft to the target. It provides information for a 3D topographic mapping and calculates the asteroid reflectivity. The measurements are to be performed at a distance from 500 m to 14 km while operations such as fly byes or landings remain a possibility.
Digital twins for prognostics of electro-hydraulic actuators: novel simplified fluid dynamic models for aerospace valves
Authors: Berri Pier Carlo , Vedova Matteo D.L. Dalla , Santaera Simone
Published: February 2022

In the design and development phases of electro-hydraulic actuators (EHAs) used for aircraft flight controls, it is often necessary to carry out accurate and high-fidelity fluid dynamics simulations to evaluate the system behaviour within its entire operating range and, if necessary, investigate its most critical issues. These high-fidelity simulations (nowadays achievable with different techniques and commercial software) generally become pretty expensive from a computational perspective. Therefore, especially in the preliminary design phases or implementing system health monitoring algorithms (in real-time), the need to adopt simplified models emerges definitely (albeit capable of guaranteeing the appropriate level of detail and accuracy). These simplified models are also essential for developing effective and reliable model-based prognostic strategies capable of performing early health assessments of EHA valves. This work proposes a new lumped-parameters simplified numerical model, which, despite having a very compact formulation and reduced computational costs, simulates the internal fluid dynamics of the valve, overcoming some critical issues typical of other models available in the literature. It evaluates valve performance as a function of spool position and environmental conditions (e.g. supply pressure), better-assessing flow rate feedback, internal leakages, and other operating conditions (e.g. spool fine adjustment, pressure supply variable, overpressure, or water hammer). The performance of this numerical model is evaluated comparing with other simplified models published in the literature. Moreover, it is validated with a high-fidelity digital twin that simulates the behaviour of the valve, taking into account the geometry of the spool, the properties of the hydraulic fluid, and the local internal fluid-dynamics (laminar or turbulent regime, cavitation, etc.).
Analytical Design of Conventional and Electrical Aircraft Environmental Control Systems
Authors: Munjulury Raghu Chaitanya , Devadurgam Hemanth , Rajagopal Soorya , Krus Petter
Published: February 2022

Environmental control systems hold vital importance as they are responsible for aircraft cabin air ventilation and passenger comfort. This paper presents an analytical design of both Conventional & Electrical environmental control systems. The result of the estimated design is represented in a geometrical model that gives freedom to visualize various options in the conceptual design process, using Knowledge-based engineering application as a base for the design and methodology. Flexibility in the model enables the user to control the size and positioning of the system and sub-systems associated with it. The number of passengers serves as the driving input and the three-dimensional model gives the exact representation concerning the volume occupied and dependencies on the number of passengers. It also provides a faster method to alter the system to user needs with respect to the number of air supply pipes, number of ducts, and pipe length.
Real Estate Advisory Drone (READ): system for autonomous indoor space appraisals, based on Deep Learning and Visual Inertial Odometry
Authors: Quattrini A , Mascheroni A , Vandone A , Coluzzi M , Barazzetti A , Cecconi F , Leidi T
Published: February 2022

The present paper describes the development of a mobile platform as a support of the real estate appraisal procedure. Currently, the estate evaluation is performed by an expert that manually collects data, performs measurements, and grabs pictures of the inspected unit to finally evaluate its commercial value. The READ project aims at automatizing this process by developing a solution based on a mobile unit (drone or tablet) able to navigate the indoor environment and record data, which will be later processed on the cloud. To accomplish all these tasks, the platform is equipped with cameras, a LiDAR sensor, and a data process unit, with the goal of 1) understanding its motion and localization; 2) reconstructing a 3D map of the inspected space; 3) performing image-based analyses applying AI algorithms enabling the identification of the indoor space (e.g. bedroom or kitchen), the counting and the classification of furniture objects, and the detection of building imperfections or frauds. Tests have been performed in different scenarios providing promising results, laying the foundations for bringing these technologies into a real operational context.
Resolved terahertz spectroscopy of tiny molecules employing tunable spoof plasmons in an otto prism configuration
Authors: Yao Haizi , Zhang Weiwei , Liu Wenfu , Mei Hongying
Published: February 2022

Sensitive detection of terahertz fingerprint absorption spectrum for tiny molecules is essential for bioanalysis. However, it is extremely challenging for traditional terahertz spectroscopy measurement because of the weak spectral response caused by the large mismatch between terahertz wavelengths and biomolecular dimensions. Here, we proposed a wideband-tunable metal plasmonic terahertz biosensor to detect tiny biomolecules, employing attenuated total reflection in an Otto prism configuration and tightly confined spoof surface plasmons on the grooved metal surface. Benefitting from the plasmonic electric field enhancement, such a biosensor is able to identify the molecular terahertz fingerprints. As a proof of concept, a hypothetical molecule modeled by the Lorentz model with two vibrational modes is used as the sensing analytes. Simulation results show that the absorption of two vibrational modes of analytes can be selectively enhanced up to ten times by plasmonic resonance, and their fingerprints can be resolved by sweeping incident angle in a wide waveband. Our work provides an effective approach for the highly sensitive identification of molecular fingerprints in fields of biochemical sensing for tiny analytes.
The characterization of a nanoscale MnNi cluster in thermally aged reactor pressure vessel steels
Authors: Liu Hailong , Li Qiulin
Published: February 2022

The MnNi-rich clusters or precipitates (MNPs) are one of the most important nanofeatures resulting in irradiation-induced embrittlement of reactor pressure vessel (RPV) steels. In this study, the microstructure and mechanical properties of the thermally-aged RPV steel were investigated by microhardness and tensile test, x-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atom probe tomography (APT), revealing the presence of a novel nanoscale B2 MnNi phase. The formation of these B2 MnNi phases was dominated by the thermodynamic of the RPV-steel system, and high-density dislocations could boost their formation and growth. Meanwhile, for samples aged for 2 h at 723 K, these ordered phases result in a yield-strengthening increment of 190 MPa. Although aged-induced ordered phases have a clear difference in terms of the lattice structure, nucleation rate, and thermal stability compared to irradiation-induced MNPs, the discovery of these B2 ordered phases helps us to establish a more comprehensive understanding of the nature and formation mechanism of MNPs produced by neutron irradiation.
Mechanical, light transmittance properties and simulation study of sustainable translucent lightweight aggregate concrete
Authors: Lian Fengmei , Yin Zhixiang
Published: February 2022

To investigate the engineering feasibility of translucent lightweight aggregate concrete (TLAC) in sustainable buildings, this paper focuses on testing the light transmission properties and mechanical performance of TLACs, the light transmission effect in building interiors is simulated and evaluated using automated steps seamlessly integrated with REVIT software and Radiance software. The preparation process of TLACs and the mixture proportions of raw materials were designed by combining translucent concrete technology with self-compacting mortar. The results indicate that the light transmission of TLAC increases with the volume of polymethylmethacrylate optical fiber (POF) incorporated and the diameter of POF, while the compressive strength tends to increase first and then decrease with the increasing volume fraction of POF in the TLAC samples. Moreover, the building lighting simulations show that indoor illuminance will improve significantly with the use of TLACs, which further illustrates the energy savings and structural performance improvements owing to the application of TLAC as a modern construction material.
Identifying robust functional modules using three-body correlations in Escherichia coli
Authors: Chen Tianlong , Singh Pramesh , Bassler Kevin E
Published: February 2022

Understanding the underlying structure of a gene regulatory network is crucial to understand the biological functions of genes or groups of genes. A common strategy to investigate it is to find community structure of these networks. However, methods of finding these communities are often sensitive to noise in the gene expression data and the inherent stochasticity of the community detection algorithms. Here we introduce an approach for identifying functional groups and their hierarchical organization in gene co-expression networks from expression data. A network describing the relatedness in the expression profiles of genes is first inferred using an information theoretic approach. Community structure within the inferred network is found by using modularity maximization. This community structure is further refined using three-body structural correlations to robustly identify important functional gene communities. We apply this approach to the expression data of E. coli genes and identify 25 robust groups, many of which show key associations with important biological functions as demonstrated by gene ontology term enrichment analysis. Thus, our approach makes specific and novel predictions about the function of these genes.
SATB2 Expression in Undifferentiated Pleomorphic Sarcomas of Bone
Authors: Warmke Laura M , Maloney Nolan , Leung Cheuk Hong , Lin Heather , Lazar Alexander J , Wang Wei-Lien
Published: February 2022

Objectives

SATB2 is a transcriptional regulator that plays an important role in osteoblastic differentiation. We examined the prevalence and potential significance of SATB2 expression in undifferentiated pleomorphic sarcoma (UPS) of bone.

Methods

We examined 38 cases of bone UPS without osteoid. The male-to-female ratio was 1:1.4, with a median age of 48 years (range, 23-83 years). Tumors occurred primarily in the femur (n = 8) and ilium (n = 8), with a median tumor size of 9.5 cm (range, 1.8-27.0 cm). The median follow-up was 24.7 months (range, 2-82 months): 11 patients developed local recurrences, and 18 patients had metastases, mainly to lung and bone.

Results

SATB2 expression (nuclear labeling ≥5%) was seen in 21 of 38 (55%) cases: 5 with focal (nuclear labeling 5%), 11 with patchy (nuclear labeling 5%-50%), and 5 with diffuse (nuclear labeling ≥50%) staining. Among this group, diffuse SATB2 expression demonstrated superior metastasis-free survival (P = .036) and event-free survival (P = .024). For comparison, 100 soft tissue UPS were stained; the majority were negative (75/100 [75%]).

Conclusions

UPS of bone demonstrated more frequent SATB2 expression compared with its soft tissue counterpart. In this series, diffuse SATB2 expression in UPS of bone was associated with better outcomes. Additional studies are still needed to determine its significance.
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction
Authors: Yao Junfeng , Sun Wen , Jian Zhongquan , Wu Qingqiang , Wang Xiaoli
Published: February 2022

Motivation

Polypharmacy is the combined use of drugs for the treatment of diseases. However, it often shows a high risk of side effects. Due to unnecessary interactions of combined drugs, the side effects of polypharmacy increase the risk of disease and even lead to death. Thus, obtaining abundant and comprehensive information on the side effects of polypharmacy is a vital task in the healthcare industry. Early traditional methods used machine learning techniques to predict side effects. However, they often make costly efforts to extract features of drugs for prediction. Later, several methods based on knowledge graphs are proposed. They are reported to outperform traditional methods. However, they still show limited performance by failing to model complex relations of side effects among drugs.

Results

To resolve the above problems, we propose a novel model by further incorporating complex relations of side effects into knowledge graph embeddings. Our model can translate and transmit multidirectional semantics with fewer parameters, leading to better scalability in large-scale knowledge graphs. Experimental evaluation shows that our model outperforms state-of-the-art models in terms of the average area under the ROC and precision–recall curves.

Availability and implementation

Code and data are available at: https://github.com/galaxysunwen/MSTE-master.
SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic
Authors: Knapp Adam C , Sordo Vieira Luis , Laubenbacher Reinhard , Chifman Julia
Published: February 2022

We introduce SteadyCellPhenotype, a browser-based interface for the analysis of ternary biological networks. It includes tools for deterministically finding all steady states of a network, as well as the simulation and visualization of trajectories with publication quality graphics. Simulations allow us to approximate the size of the basin for attractors and deterministic simulations of trajectories nearby specified points allow us to explore the behavior of the system in that neighborhood.

Availability and implementation

https://github.com/knappa/steadycellphenotype MIT License.
TransformerGO: predicting protein–protein interactions by modelling the attention between sets of gene ontology terms
Authors: Ieremie Ioan , Ewing Rob M , Niranjan Mahesan
Published: February 2022

Motivation

Protein–protein interactions (PPIs) play a key role in diverse biological processes but only a small subset of the interactions has been experimentally identified. Additionally, high-throughput experimental techniques that detect PPIs are known to suffer various limitations, such as exaggerated false positives and negatives rates. The semantic similarity derived from the Gene Ontology (GO) annotation is regarded as one of the most powerful indicators for protein interactions. However, while computational approaches for prediction of PPIs have gained popularity in recent years, most methods fail to capture the specificity of GO terms.

Results

We propose TransformerGO, a model that is capable of capturing the semantic similarity between GO sets dynamically using an attention mechanism. We generate dense graph embeddings for GO terms using an algorithmic framework for learning continuous representations of nodes in networks called node2vec. TransformerGO learns deep semantic relations between annotated terms and can distinguish between negative and positive interactions with high accuracy. TransformerGO outperforms classic semantic similarity measures on gold standard PPI datasets and state-of-the-art machine-learning-based approaches on large datasets from Saccharomyces cerevisiae and Homo sapiens. We show how the neural attention mechanism embedded in the transformer architecture detects relevant functional terms when predicting interactions.

Availability and implementation

https://github.com/Ieremie/TransformerGO.

Supplementary information

Supplementary data are available at Bioinformatics online.
Semi-automatic detection of honeybee brood hygiene—an example of artificial learning to facilitate ethological studies on social insects
Authors: Batz Philipp , Ruttor Andreas , Thiel Sebastian , Wegener Jakob , Zautke Fred , Schwekendiek Christoph , Bienefeld Kaspar
Published: February 2022

Machine-learning techniques are shifting the boundaries of feasibility in many fields of ethological research. Here, we describe an application of machine learning to the detection/measurement of hygienic behaviour, an important breeding trait in the honey bee (Apis mellifera). Hygienic worker bees are able to detect and destroy diseased brood, thereby reducing the reproduction of economically important pathogens and parasites such as the Varroa mite (Varroa destructor). Video observation of this behaviour on infested combs has many advantages over other methods of measurement, but analysing the recorded material is extremely time-consuming. We approached this problem by combining automatic tracking of bees in the video recordings, extracting relevant features, and training a multi-layer discriminator on positive and negative examples of the behaviour of interest. Including expert knowledge into the design of the features lead to an efficient model for identifying the uninteresting parts of the video which can be safely skipped. This algorithm was then used to semiautomatically identify individual worker bees involved in the behaviour. Application of the machine-learning method allowed to save 70% of the time required for manual analysis, and substantially increased the number of cell openings correctly identified. It thereby turns video-observation of individual cell opening events into an economically competitive method for selecting potentially resistant bees. This method presents an example of how machine learning can be used to boost ethological research, and how it can generate new knowledge by explaining the learned decision rule in form of meaningful parameters.
Admixture and selection patterns across the European distribution of Scots pine, Pinus sylvestris (Pinaceae)
Authors: Wachowiak Witold , Perry Annika , Zaborowska Julia , González-Martínez Santiago C , Cavers Stephen
Published: February 2022

We analysed data on nucleotide polymorphism at 78 nuclear genes to search for signatures of divergence and selection in populations from across the distribution of Pinus sylvestris in Europe. Data on variation at a large set of maternally inherited mitochondrial DNA markers were also analysed. Most nuclear loci showed homogeneous patterns of variation across populations from Spain, Central Europe, Nordic countries and Scotland. Mitochondrial markers did not reveal strong population structure but suggested admixture of samples carrying different mitochondrial lineages in certain parts of the distribution. At nuclear DNA loci, we found high nucleotide polymorphism, generally low population differentiation and weak signals of isolation by distance. Together with the mitochondrial DNA results, these patterns seem most likely to be associated with a process of colonization from multiple sources and efficient gene flow. The results are in line with demographic inference indicating establishment of Central European and Nordic populations before the Last Glacial Maximum and admixture of colonization fronts from mainland Europe in Scottish populations. Coalescent and outlier detection methods identified several genes showing molecular signatures of selection especially in response to temperature variation in ecologically and phenotypically divergent populations. The study provides a large set of markers for analysis of genetic diversity in populations of P. sylvestris, including candidate genes that are implicated in local adaptation and population divergence.
Surgeons, Infectious Diseases, and Twitter Hit a Home Run for Antibiotic Stewardship
Authors: Goff Debra A , Alverdy John , Gerlach Anthony T , Mayol Julio , Nwomeh Benedict
Published: February 2022

Many infectious diseases (ID) clinicians join Twitter to follow other ID colleagues or “like” people. While there is great value in engaging with people who have similar interests, there is equal value in engaging with “unlike” or non-ID people. Here, we describe how Twitter connected an ID pharmacist with a pediatric surgeon, a vice chair of surgery, a surgeon chief medical officer from Spain, and a surgical intensive care unit pharmacist. This Twitter collaboration resulted in several scholarly activities related to antibiotic resistance and antibiotic stewardship and served as a conduit for global collaboration.
Educational Impact of #IDJClub, a Twitter-Based Infectious Diseases Journal Club
Authors: Schwartz Ilan S , McCarty Todd , Woc-Colburn Laila E , Titanji Boghuma K , Cutrell James B , Cortes-Penfield Nicolas W
Published: February 2022

Background

Journal clubs have been an enduring mainstay of medical education, and hosting these on social media platforms can expand accessibility and engagement. We describe the creation and impact of #IDJClub, an infectious diseases (ID) Twitter journal club.

Methods

We launched #IDJClub in October 2019. Using the account @IDJClub, an ID physician leads a 1-hour open-access Twitter discussion of a recent publication. All participants use the hashtag #IDJClub. Sessions started monthly, but increased due to demand during the coronavirus disease 2019 (COVID-19) pandemic. We used Symplur ’s Healthcare Hashtag project to track engagement of #IDJClub per 60-minute discussion plus the following 30 minutes to capture ongoing conversations. We also conducted an online anonymous survey using Likert scales and open-ended questions to assess educational impact.

Results

In its first 20 months, 31 journal clubs were held, with medians of 42 (interquartile range [IQR], 28.5–60) participants and 312 (IQR, 205–427.5) tweets per session. 134 participants completed the survey, of whom 39% were ID physicians, 19% pharmacists, 13% ID fellows, and 10% medical residents. Most agreed or strongly agreed that #IDJClub provided clinically useful knowledge (95%), increased personal confidence in independent literature appraisal (72%), and was more educational than traditional journal clubs (72%). The format addressed several barriers to traditional journal club participation such as lack of access, subject experts, and time.

Conclusions

#IDJClub is an effective virtual journal club, providing an engaging, open-access tool for critical literature appraisal that overcomes several barriers to traditional journal club participations while fostering connectedness within the global ID community.
Soluble urokinase plasminogen activator receptor and decline in kidney function among patients without kidney disease
Authors: Iversen Esben , Kallemose Thomas , Hornum Mads , Bengaard Anne Kathrine , Nehlin Jan Olof , Rasmussen Line Jee Hartmann , Sandholdt Haakon , Tavenier Juliette , Feldt-Rasmussen Bo , Andersen Ove , Eugen-Olsen Jesper , Houlind Morten Baltzer
Published: February 2022

Background

Hospitalized patients are at an increased risk of developing kidney disease after discharge, often despite the absence of any clinical indicators during hospitalization. Soluble urokinase plasminogen activator receptor (suPAR) is a marker of systemic chronic inflammation that can be measured from routine blood samples. We determined whether elevated suPAR during hospitalization is associated with a decline in estimated glomerular filtration rate (eGFR) after discharge.

Methods

This was a retrospective longitudinal cohort study of patients without detectable kidney disease presenting to the emergency department on two separate occasions during a 3-year period. The association between suPAR and a decline in eGFR was assessed by linear mixed models for repeated measures adjusting for age, sex, C-reactive protein, sodium, diabetes, hypertension and cardiovascular disease.

Results

In total, 5124 patients (median age 65.9 years, 51.0% female) were included. The median suPAR was 2.9 ng/mL, the median time to readmission was 144 days and the expected rate of eGFR decline over this period was 5.1 mL/min/1.73 m2/year. Adjusting for other risk factors, patients with suPAR <3, 3–6 or ≥6 ng/mL had an expected eGFR decline of 4.3, 5.2 or 9.0 mL/min/1.73 m2/year, respectively. Similarly, patients with suPAR in the lowest (<2.4 ng/mL), middle (2.4–3.6 ng/mL) or highest (≥3.6 ng/mL) tertile had an expected eGFR decline of 4.2, 4.6 or 6.5 mL/min/1.73 m2/year, respectively. In both cases, a higher suPAR level was significantly and independently associated with a higher rate of eGFR decline (P < .001).

Conclusions

A higher suPAR level was associated with accelerated eGFR decline among patients presenting to the emergency department, suggesting that routine suPAR measurements may have utility for the early detection of kidney disease.
Evidence for acoustic discrimination in lemurs: A playback study on wild indrisIndri indri
Authors: Spezie Giovanni , Torti Valeria , Bonadonna Giovanna , De Gregorio Chiara , Valente Daria , Giacoma Cristina , Gamba Marco
Published: February 2022

Indris Indri indri are group-living lemurs that occupy stable territories over several years and perform remarkable long-distance vocal displays. Vocal exchanges between long-term territory neighbors may contribute to assessing reciprocal resource-holding potentials, thus adaptively reducing the costs of territorial defense by limiting aggressive escalation. Previous work showed that indris’ songs show distinctive acoustic features at individual and group level. However, the possibility that indris use such cues for individual or group-level recognition has never been investigated experimentally. We conducted a playback experiment to test whether indris discriminate between familiar and nonfamiliar songs. Our rationale lies in the hypothesis of the dear enemy phenomenon, which predicts that territorial animals will show reduced aggression levels toward familiar neighbors compared with novel rivals. We played back stimulus recordings to wild indris from their territory boundaries and examined their responses in terms of vocal and behavioral indicators of willingness to engage in a fight. In line with our predictions, focal animals responded more rapidly and approached more often the speaker in response to playback stimuli of nonfamiliar individuals than to stimuli of neighboring groups. These results indicate that indris can discriminate between different classes of intruders based on distinctive acoustic features of their song choruses. We suggest that increased aggression directed toward unfamiliar intruders may be explained by higher threat levels associated with dispersal and group formation dynamics. We further discuss the relevance of these findings in a strepsirrhine primate model for comparative studies of vocal communication and sociality.
ST-segment elevation myocardial infarction with plaque erosion, to stent or not to stent: utility of intracoronary optical coherence tomography (OCT) imaging—a case report
Authors: Khan Kumail Abbas , Osheiba Mohammed , Mechery Anthony , Khan Sohail Q
Published: February 2022

Background

Treating acute myocardial infarction in the setting of insignificant coronary obstruction is an emerging challenge especially with the application of intracoronary imaging like intravascular ultrasound and optical coherence tomography (OCT). The cardiologists dealing with such patients may consider not to stent if there is intracoronary imaging evidence of minimal thrombus without plaque rupture and the vessel appears patent with settling of chest pain and electrocardiogram (ECG) changes.

Case summary

A 47-year-old gentleman presented direct to the emergency department after experiencing retrosternal chest pain with an ECG showing hyperacute anterior T waves. He had ongoing chest pain and was therefore brought to the cardiac cath lab on the primary percutaneous coronary intervention (PCI) pathway. The first picture showed that the proximal left anterior descending (LAD) was occluded (TIMI 0 flow) with evidence of large thrombus burden. Pre-dilating with a 2.5 × 15 mm balloon did not change flow. Aspiration with an Export catheter was carried out for several runs. Most of the thrombus was successfully removed; however, some of it did go into the distal LAD but was successfully retrieved with aspiration catheter. The diagonal branch was occluded with thrombus which was wired followed by thrombus aspiration establishing TIMI II flow. The procedure was covered with Eptifibatide boluses and heparin. After thrombectomy, angiographically there was no obvious lesion present within the LAD. Optical coherence tomography confirmed only mild atheroma with a small amount of plaque and minimal thrombus. There was OCT evidence of plaque erosion without any plaque rupture. The area was above 9 mm2 and we decided not to treat that with a stent. The right coronary artery had an anterior take-off and was unobstructed. In conclusion, the patient had successful primary PCI to LAD with thrombus aspiration and balloon angioplasty only. He was placed on 12 months of dual antiplatelets therapy with Aspirin and Prasugrel.

Discussion

This case highlights the rare presentation of patients with acute myocardial infarction with plaque erosion and the usefulness of OCT in formulating a management plan.
Systemic sclerosis complicated by chronic thromboembolic pulmonary hypertension treated with balloon pulmonary angioplasty: a case report
Authors: Matsui Tomoyo , Kikuchi Noriko , Serizawa Naoki , Hagiwara Nobuhisa
Published: February 2022

Background

Systemic sclerosis (SSc) is known to induce pulmonary hypertension (PH), resulting in poor prognosis. Pulmonary hypertension secondary to connective tissue disease is usually classified as Group 1. In patients with SSc, PH owing to left heart failure (Group 2) and interstitial pneumonia (Group 3) are also known; however, there have been limited reports on chronic thromboembolic PH (CTEPH), which corresponds to Group 4.

Case summary

A 39-year-old female with SSc was admitted with shortness of breath on exertion for the past 4 months. Right heart catheterization revealed severe PH. Group 1 PH secondary to collagen tissue disease was suspected; however, thoracic computed tomography and lung perfusion scan led to the diagnosis of CTEPH of Group 4. We treated the PH with several medications and balloon pulmonary angioplasty (BPA), which improved the PH and right heart failure. Consequently, her overall condition also improved.

Discussion

This is a rare case report of SSc complicated by CTEPH, which was treated with BPA. Patients with SSc are prone to complications of various type of PH. Thus, it is important to distinguish CTEPH in terms of treatment choice and prognosis.
Single-centre outcome of extracorporeal membrane oxygenation after the neonatal Norwood procedure
Authors: Mayr Benedikt , Kido Takashi , Holder Samantha , Wallner Marie , Vodiskar Janez , Strbad Martina , Ruf Bettina , Hager Alfred , Ewert Peter , Hörer Jürgen , Lange Rüdiger , Ono Masamichi
Published: February 2022

OBJECTIVES

Despite improvements in the surgical management of the hypoplastic left heart syndrome and its variant, the Norwood procedure is still associated with substantial mortality and morbidity and extracorporeal membrane oxygenation support is required in some patients.

METHODS

We reviewed patients with the Norwood procedure between 2007 and 2019. The primary end point of the study was mortality during extracorporeal membrane oxygenation. Secondary end points included morbidity, bidirectional cavopulmonary shunt and Fontan completion.

RESULTS

Of the 257 patients in whom the Norwood procedure was performed, mechanical support was required in 41 patients (16%). Indications for extracorporeal membrane oxygenation were low cardiac output (n = 16, 39%), hypoxaemia (n = 12, 29%) and inability to wean from cardiopulmonary bypass (n = 9, 22%). The median age at extracorporeal membrane oxygenation was 10.9 days (interquartile range, 7.9–21.2) and veno-arterial support was required in 37 patients (90.2%). Weaning from extracorporeal membrane oxygenation was achieved in 61% (n = 25). Survival to hospital discharge and 1-year survival was 34.6% (standard deviation: 17.1) and 25.7% (standard deviation: 7), respectively. Bidirectional cavopulmonary shunt was performed in 24% (n = 10) and Fontan completion in 7% (n = 3). Preoperative moderate or greater atrioventricular valve regurgitation was independently associated with mechanical support. Implantation of extracorporeal membrane oxygenation in the paediatric catheter laboratory was identified as an independent risk factor for mortality.

CONCLUSIONS

Moderate or greater atrioventricular valve regurgitation is an independent risk factor for mechanical support after the Norwood procedure. Mechanical support is associated with substantial in-hospital mortality; however, successful Fontan completion was accomplished in some patients.
Commissural closure to treat severe mitral regurgitation: standing the test of time
Authors: Carino Davide , Lorusso Roberto , Lapenna Elisabetta , Del Forno Benedetto , Sala Alessandra , Zancanaro Edoardo , Ruggeri Stefania , Abboud Sabrin , Schiavi Davide , Ascione Guido , Castiglioni Alessandro , Alfieri Ottavio , Maisano Francesco , De Bonis Michele
Published: February 2022

OBJECTIVES

Mitral regurgitation (MR) due to commissural prolapse or flail represents a pattern of valve dysfunction that can be treated, among other techniques, by suturing the margins of the anterior and posterior leaflets in the commissural area (commissural closure). The very long-term results of this technique have not been reported so far and represent the objective of this study.

METHODS

A retrospective review of our institutional database was carried on querying for patients who underwent commissural closure and ring annuloplasty within the time frame 1997–2007 to provide a robust long-term assessment. Cumulative incidence function (CIF) using death as a competitive outcome was used to estimate cardiac death and reoperation for mitral valve replacement. To describe the time course of MR, we performed a longitudinal analysis using generalized estimating equations with a random intercept for correlated data.

RESULTS

A total of 125 patients were included. At 15 years, the CIF for cardiac death, with non-cardiac death as a competitive event, was 8.0 ± 2.57% (95% confidence interval [3.88–13.93]). At 15 years, the CIF for reintervention for a mitral valve replacement with death as a competitive event was 5.0 ± 1.98%, 95% confidence interval [2.04–9.89]. No significant predictors of reintervention for mitral valve replacement were identified. At 5 years, the predicted rate of MR ≥3+ recurrence was 2.53% while it was 8.22% at 15 years. In no case a more than mild mitral stenosis was detected.

CONCLUSIONS

Severe MR due to commissural prolapse/flail can be effectively treated with commissural closure and ring annuloplasty. In our series, the rate of reoperation in the very long term was extremely low. Similarly, longitudinal analysis demonstrated a very low rate of MR ≥3+ recurrence.
Population divergence time estimation using individual lineage label switching
Authors: Beerli Peter , Ashki Haleh , Mashayekhi Somayeh , Palczewski Michal
Published: February 2022

Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayesian inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as Migrate. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a reanalysis of a dataset of 5 populations consisting of 3 present-day populations (Africans, Europeans, Asian) and 2 archaic samples (Altai and Ust’Isthim). Evaluations of simple divergence models without subsequent geneflow show high accuracy, whereas the accuracy of the results of isolation with migration models depends on the magnitude of the immigration rate. High immigration rates lead to a time of the most recent common ancestor of the sample that, looking backward in time, predates the divergence time. Even with many independent loci, accurate estimation of the divergence time with high immigration rates becomes problematic. Our comparison to other software tools reveals that our lineage-switching method, implemented in Migrate, is comparable to IMa2p. The software Migrate can run large numbers of sequence loci (>1,000) on computer clusters in parallel.
Maternal plasma lipids are involved in the pathogenesis of preterm birth
Authors: Chen Yile , He Bing , Liu Yu , Aung Max T , Rosario-Pabón Zaira , Vélez-Vega Carmen M , Alshawabkeh Akram , Cordero José F , Meeker John D , Garmire Lana X
Published: February 2022

Background

Preterm birth is defined by the onset of labor at a gestational age shorter than 37 weeks, and it can lead to premature birth and impose a threat to newborns’ health. The Puerto Rico PROTECT cohort is a well-characterized prospective birth cohort that was designed to investigate environmental and social contributors to preterm birth in Puerto Rico, where preterm birth rates have been elevated in recent decades. To elucidate possible relationships between metabolites and preterm birth in this cohort, we conducted a nested case-control study to conduct untargeted metabolomic characterization of maternal plasma of 31 women who experienced preterm birth and 69 controls who underwent full-term labor at 24–28 gestational weeks.

Results

A total of 333 metabolites were identified and annotated with liquid chromatography/mass spectrometry. Subsequent weighted gene correlation network analysis shows that the fatty acid and carene-enriched module has a significant positive association (P = 8e−04, FDR = 0.006) with preterm birth. After controlling for potential clinical confounders, a total of 38 metabolites demonstrated significant changes uniquely associated with preterm birth, where 17 of them were preterm biomarkers. Among 7 machine-learning classifiers, the application of random forest achieved a highly accurate and specific prediction (AUC = 0.92) for preterm birth in testing data, demonstrating their strong potential as biomarkers for preterm births. The 17 preterm biomarkers are involved in cell signaling, lipid metabolism, and lipid peroxidation functions. Additional modeling using only the 19 spontaneous preterm births (sPTB) and controls identifies 16 sPTB markers, with an AUC of 0.89 in testing data. Half of the sPTB overlap with those markers for preterm births. Further causality analysis infers that suberic acid upregulates several fatty acids to promote preterm birth.

Conclusions

Altogether, this study demonstrates the involvement of lipids, particularly fatty acids, in the pathogenesis of preterm birth.
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
Authors: Fahrner Matthias , Föll Melanie Christine , Grüning Björn Andreas , Bernt Matthias , Röst Hannes , Schilling Oliver
Published: February 2022

Background

Data-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging owing to the high complexity and large data and sample size, which require specialized software and vast computing infrastructures. Most available open-source DIA software necessitates basic programming skills and covers only a fraction of a complete DIA data analysis. In consequence, DIA data analysis often requires usage of multiple software tools and compatibility thereof, severely limiting the usability and reproducibility.

Findings

To overcome this hurdle, we have integrated a suite of open-source DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef, and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their use on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate the usability of an all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training material is provided to further increase access for the proteomics community.

Conclusion

The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework in combination with extensive training material empowers a broad community of researches to perform reproducible and transparent DIA data analysis.
Surface aggregations ofCalanus finmarchicusduring the polar night
Authors: Espinasse Boris , Daase Malin , Halvorsen Elisabeth , Reigstad Marit , Berge Jørgen , Basedow Sünnje L
Published: February 2022

While marine ecosystems in polar areas were thought to be mostly inactive during the polar night, recent observations in the Arctic highlight that dynamic biological interactions occur across all trophic levels. One particularly interesting observation made repeatedly is the occurrence of Calanus finmarchicus, a key species at the base of the food web, in the upper part of the water column in early January. This contrasts with the confirmed life cycle of this copepod, which predicts descent to overwintering depths in autumn and ascent at the end of the winter. Here, we compiled 6 years of data from the polar night to explore this unusual behaviour and to investigate the underlying mechanisms that may cause these surface aggregations. Highest abundance of C. finmarchicus in surface waters was closely related to Polar Surface Water in the vicinity of the sea ice edge. A total of six hypotheses are assessed to explain this distribution pattern, which includes passive transport and active behaviour as a way to improve survival chances or food access. In the context of climate change and sea ice decrease, the presence of lipid-rich copepods in cold surface waters could be a key parameter in driving the spatial distributions of top predators in the Arctic.