bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk Assessment of Electronic Archive Services using Octave Allegro Method (Case Study: SIKN JIKN)
Authors: Herdianto R A , Ramli K , Suryanto Y
Published: March 2022

The National Archives Information System (SIKN) and the National Archives Information Network (JIKN) are the government national priority programs that aimed at providing web-based electronic archive treasury information facilities to the public. However, threat and disruption of critical information asset on electronic archives can cause interruption strategic objectives goals, vision, and mission of The National Archives of Indonesia (ANRI) in organizing archives that impact the network node, and the public. Therefore this research aims to analyze and identify risks in the SIKN JIKN electronic archive service and determine the potential risk of threats to important information assets. The OCTAVE Allegro method used to measure information security on five important information assets of the SIKN JIKN electronic archive information service. The results showed 64 areas of concerns analyzed, as many as 40 had to mitigate while the remaining 24 could be deferred or postponed. The conclusion of the risk assessment results in recommendations that must take to manage and protect critical assets in electronic archive services and supporting material for policymaking.
Forecasting of Freight Demand Transportation (Case Study in Lampung Province, Indonesia)
Authors: Junaedi T
Published: March 2022

Forecasting the volume of freight has a significant importance for future decisions for the entire economy, as well as its individual participants. The transportation of goods between Sumatra and Java using the highway mode that accumulate with local transportation will greatly burden roads in Lampung province. This research was conducted to predict the pattern and amount of movement of goods in the future. The modelling is conducted for the plan period up to 20 years based on growth predictions of geographical, social, economic and traffic flow. This study conducted a process of Sequential Demand Model (Planning Model 4 stages) by using software Transplan Version 8. Transportation patterns in 2040 is predicted will be dominated by continuous trips with domination of movement from Java to South Sumatra, or otherwise. Both the transportation between internal zones and external zone to internal zone have a significant increase. The most strategic main line freight in Lampung for today and in the future is along the Bakauheni-South Sumatra and Bengkulu-South Sumatra both through toll roads, national roads, and railways.
A complex-analytic approach to kinetic energy properties of irrotational flows
Authors: Constantin O. , Persson A.-M.
Published: March 2022

Using methods from complex analysis we obtain some qualitative results for the kinetic energy of two-dimensional irrotational water flows (monotonicity of horizontal averages with depth, location of the extrema).
Log-Brunn-Minkowski inequality under symmetry
Authors: Böröczky Károly , Kalantzopoulos Pavlos
Published: March 2022

We prove the log-Brunn-Minkowski conjecture for convex bodies with symmetries to

n
n

independent hyperplanes, and discuss the equality case and the uniqueness of the solution of the related case of the logarithmic Minkowski problem. We also clarify a small gap in the known argument classifying the equality case of the log-Brunn-Minkowski conjecture for unconditional convex bodies.
Nontransverse heterodimensional cycles: Stabilisation and robust tangencies
Authors: Díaz Lorenzo , Pérez Sebastián
Published: March 2022

We consider three-dimensional diffeomorphisms having simultaneously heterodimensional cycles and heterodimensional tangencies associated to saddle-foci. These cycles lead to a completely nondominated bifurcation setting. For every

r

⩾

2

r{\geqslant } 2

, we exhibit a class of such diffeomorphisms whose heterodimensional cycles can be

C
r

C^r

stabilised and (simultaneously) approximated by diffeomorphisms with

C
r

C^r

robust homoclinic tangencies. The complexity of our nondominated setting with plenty of homoclinic and heteroclinic intersections is used to overcome the difficulty of performing

C
r

C^r

perturbations,

r
⩾
2

r\geqslant 2

, which are remarkably more difficult than

C
1

C^1

ones. Our proof is reminiscent of the Palis-Takens’ approach to get surface diffeomorphisms with infinitely many sinks (Newhouse phenomenon) in the unfolding of homoclinic tangencies of surface diffeomorphisms. This proof involves a scheme of renormalisation along nontransverse heteroclinic orbits converging to a center-unstable Hénon-like family displaying blender-horseshoes. A crucial step is the analysis of the embeddings of these blender-horseshoes in a nondominated context.
A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations
Authors: Milite Salvatore , Bergamin Riccardo , Patruno Lucrezia , Calonaci Nicola , Caravagna Giulio
Published: March 2022

Motivation

Cancers are composed by several heterogeneous subpopulations, each one harbouring different genetic and epigenetic somatic alterations that contribute to disease onset and therapy response. In recent years, copy number alterations (CNAs) leading to tumour aneuploidy have been identified as potential key drivers of such populations, but the definition of the precise makeup of cancer subclones from sequencing assays remains challenging. In the end, little is known about the mapping between complex CNAs and their effect on cancer phenotypes.

Results

We introduce CONGAS, a Bayesian probabilistic method to phase bulk DNA and single-cell RNA measurements from independent assays. CONGAS jointly identifies clusters of single cells with subclonal CNAs, and differences in RNA expression. The model builds statistical priors leveraging bulk DNA sequencing data, does not require a normal reference and scales fast thanks to a GPU backend and variational inference. We test CONGAS on both simulated and real data, and find that it can determine the tumour subclonal composition at the single-cell level together with clone-specific RNA phenotypes in tumour data generated from both 10× and Smart-Seq assays.

Availability and implementation

CONGAS is available as 2 packages: CONGAS (https://github.com/caravagnalab/congas), which implements the model in Python, and RCONGAS (https://caravagnalab.github.io/rcongas/), which provides R functions to process inputs, outputs and run CONGAS fits. The analysis of real data and scripts to generate figures of this paper are available via RCONGAS; code associated to simulations is available at https://github.com/caravagnalab/rcongas_test.

Supplementary information

Supplementary data are available at Bioinformatics online.
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier
Authors: Kumar Ambuj , Khade Pranav M , Dorman Karin S , Jernigan Robert L
Published: March 2022

A new dynamic community identifier (DCI) is presented that relies upon protein residue dynamic cross-correlations generated by Gaussian elastic network models to identify those residue clusters exhibiting motions within a protein. A number of examples of communities are shown for diverse proteins, including GPCRs. It is a tool that can immediately simplify and clarify the most essential functional moving parts of any given protein. Proteins usually can be subdivided into groups of residues that move as communities. These are usually densely packed local sub-structures, but in some cases can be physically distant residues identified to be within the same community. The set of these communities for each protein are the moving parts. The ways in which these are organized overall can aid in understanding many aspects of functional dynamics and allostery. DCI enables a more direct understanding of functions including enzyme activity, action across membranes and changes in the community structure from mutations or ligand binding. The DCI server is freely available on a web site (https://dci.bb.iastate.edu/).

Supplementary information

Supplementary data are available at Bioinformatics online.
hacksig: a unified and tidy R framework to easily compute gene expression signature scores
Authors: Carenzo Andrea , Pistore Federico , Serafini Mara S , Lenoci Deborah , Licata Armando G , De Cecco Loris
Published: March 2022

Hundreds of gene expression signatures have been developed during the last two decades. However, due to the multitude of development procedures and sometimes a lack of explanation for their implementation, it can become challenging to apply the original method on custom data. Moreover, at present, there is no unified and tidy interface to compute signature scores with different single sample enrichment methods. For these reasons, we developed hacksig, an R package intended as a unified framework to obtain single sample scores with a tidy output as well as a collection of manually curated gene signatures and methods from cancer transcriptomics literature.

Availability and implementation

The hacksig R package is freely available on CRAN (https://CRAN.R-project.org/package=hacksig) under the MIT license. The source code can be found on GitHub at https://github.com/Acare/hacksig.

Supplementary information

Supplementary data are available at Bioinformatics online.
Compromised future thinking: another cognitive cost of temporal lobe epilepsy
Authors: Rayner Genevieve , Antoniou Mariana , Jackson Graeme , Tailby Chris
Published: March 2022

The ability to mentally travel forward through time allows humans to envisage a diverse array of possible events taking place in the future, helping us to choose which pathway to take in life. In epilepsy, we assume that patients use this cognitive ability when deciding between various treatment options, but this assumption has not been robustly tested. The temporal lobes are key contributors to this ‘future thinking’ and its building blocks include cognitive functions commonly impaired in temporal lobe epilepsy such as memory and language, giving rise to a hypothesis that ‘future thinking’ is impaired in this patient cohort. Participants were 68 adults: 37 with neurosurgically-naïve, unilateral temporal lobe epilepsy (51% right lateralized) and 31 healthy controls of similar age, sex and intellectual ability to the participants with epilepsy. Future thinking was measured using an imagined experiences task validated in other neurological populations. Tools well-established in temporal lobe epilepsy were used to measure potential cognitive correlates of future thinking. Analysis of variance revealed significantly impoverished future thinking in both left and right temporal lobe epilepsy relative to controls (P = 0.001, ηp2=0.206), with no difference between temporal lobe epilepsy groups (P > 0.05). Future thinking deficits in left temporal lobe epilepsy were paralleled by deficits in scene construction, whereas impoverished future thinking in right temporal lobe epilepsy occurred in the setting of intact scene construction. Deficits in future thinking were associated with reductions in lexical access and episodic autobiographic memory in both epilepsy groups. In sum, future thinking is compromised in both left and right temporal lobe epilepsy. The deficit in left temporal lobe epilepsy is largely explainable by dysfunction in verbal cognitive processes including scene construction. While the basis of the deficits observed with right temporal foci shares features with that of left temporal lobe epilepsy, their intact scene construction raises questions about the role of the left and right temporal lobes in future thinking and scene construction and the relationship between these two constructs, including whether right temporal lobe might play a specific role in future thinking in terms of creative processing. Clinicians should take impaired future thinking into account when counselling temporal lobe epilepsy patients about various treatment options, as they may struggle to vividly imagine what different outcomes might mean for their future selves.
Longitudinal tracking of axonal loss using diffusion magnetic resonance imaging in multiple sclerosis
Authors: Boonstra Frederique M. , Clough Meaghan , Strik Myrte , van der Walt Anneke , Butzkueven Helmut , White Owen B. , Law Meng , Fielding Joanne , Kolbe Scott C.
Published: March 2022

Axonal loss in the CNS is a key driver of progressive neurological impairments in people with multiple sclerosis. Currently, there are no established methods for tracking axonal loss clinically. This study aimed to determine the sensitivity of longitudinal diffusion MRI-derived fibre-specific measures of axonal loss in people with multiple sclerosis. Fibre measures were derived from diffusion MRI acquired as part of a standard radiological MRI protocol and were compared (i) to establish measures of neuro-axonal degeneration: brain parenchymal fraction and retinal nerve fibre layer thickness and (ii) between different disease stages: clinically isolated syndrome and early/late relapsing–remitting multiple sclerosis. Retrospectively identified data from 59 people with multiple sclerosis (18 clinically isolated syndrome, 22 early and 19 late relapsing–remitting) who underwent diffusion MRI as part of their routine clinical monitoring were collated and analysed. Twenty-six patients had 1-year and 14 patients had a 2-year follow-up. Brain parenchymal fraction was calculated from 3D MRI scans, and fibre-specific measures were calculated from diffusion MRI using multi-tissue constrained spherical deconvolution. At each study visit, patients underwent optical coherence tomography to determine retinal nerve fibre layer thickness, and standard neurological assessment expanded the disability status scale. We found a significant annual fibre-specific neuro-axonal degeneration (mean ± SD = −3.49 ± 3.32%, P < 0.001) that was ∼7 times larger than the annual change of brain parenchymal fraction (−0.53 ± 0.95%, P < 0.001), and more than four times larger than annual retinal nerve fibre layer thinning (−0.75 ± 2.50% P = 0.036). Only fibre-specific measures showed a significant difference in annual degeneration between the disease stages (P = 0.029). Reduced brain parenchymal fraction, retinal nerve fibre layer thickness and fibre-specific measures were moderately related to higher expanded disability status scale (rho = −0.368, rho = −0.408 and rho = −0.365, respectively). Fibre-specific measures can be measured from data collected within a standard radiological multiple sclerosis study and are substantially more sensitive to longitudinal change compared with brain atrophy and retinal nerve fibre layer thinning.
Methods for the identification and characterization of extracellular vesicles in cardiovascular studies: from exosomes to microvesicles
Authors: Davidson Sean M , Boulanger Chantal M , Aikawa Elena , Badimon Lina , Barile Lucio , Binder Christoph J , Brisson Alain , Buzas Edit , Emanueli Costanza , Jansen Felix , Katsur Miroslava , Lacroix Romaric , Lim Sai Kiang , Mackman Nigel , Mayr Manuel , Menasché Philippe , Nieuwland Rienk , Sahoo Susmita , Takov Kaloyan , Thum Thomas , Vader Pieter , Wauben Marca H M , Witwer Kenneth , Sluijter Joost P G
Published: March 2022

Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are released from cells of the cardiovascular system, and are considered important mediators of intercellular and extracellular communications. Two types of EVs of particular interest are exosomes and microvesicles, which have been identified in all tissue and body fluids and carry a variety of molecules including RNAs, proteins, and lipids. EVs have potential for use in the diagnosis and prognosis of cardiovascular diseases and as new therapeutic agents, particularly in the setting of myocardial infarction and heart failure. Despite their promise, technical challenges related to their small size make it challenging to accurately identify and characterize them, and to study EV-mediated processes. Here, we aim to provide the reader with an overview of the techniques and technologies available for the separation and characterization of EVs from different sources. Methods for determining the protein, RNA, and lipid content of EVs are discussed. The aim of this document is to provide guidance on critical methodological issues and highlight key points for consideration for the investigation of EVs in cardiovascular studies.
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation
Authors: Mazandu Gaston K , Hotchkiss Jade , Nembaware Victoria , Wonkam Ambroise , Mulder Nicola
Published: March 2022

The Sickle Cell Disease (SCD) Ontology (SCDO, https://scdontology.h3abionet.org/) provides a comprehensive knowledge base of SCD management, systems and standardized human and machine-readable resources that unambiguously describe terminology and concepts about SCD for researchers, patients and clinicians. The SCDO was launched in 2016 and is continuously updated in quantity, as well as in quality, to effectively support the curation of SCD research, patient databasing and clinical informatics applications. SCD knowledge from the scientific literature is used to update existing SCDO terms and create new terms where necessary. Here, we report major updates to the SCDO, from December 2019 until April 2021, for promoting interoperability and facilitating SCD data harmonization, sharing and integration across different studies and for retrospective multi-site research collaborations. SCDO developers continue to collaborate with the SCD community, clinicians and researchers to improve specific ontology areas and expand standardized descriptions to conditions influencing SCD phenotypic expressions and clinical manifestations of the sickling process, e.g. thalassemias.

Database URL: https://scdontology.h3abionet.org/
Pharmacokinetics, Safety and Efficacy of Intravenous Vedolizumab in Paediatric Patients with Ulcerative Colitis or Crohn’s Disease: Results from the Phase 2 HUBBLE Study
Authors: Hyams Jeffrey S , Turner Dan , Cohen Stanley A , Szakos Erzsébet , Kowalska-Duplaga Kinga , Ruemmele Frank , Croft Nicholas M , Korczowski Bartosz , Lawrence Promise , Bhatia Siddharth , Kadali Harisha , Chen Chunlin , Sun Wan , Rosario Maria , Kabilan Senthil , Treem William , Rossiter Guillermo , Lirio Richard A
Published: March 2022

Background and Aims

To date, there are no systematic pharmacokinetic [PK] data on vedolizumab in paediatric inflammatory bowel disease [IBD]. We report results from HUBBLE, a dose-ranging, phase 2 trial evaluating the PK, safety and efficacy of intravenous vedolizumab for paediatric IBD.

Methods

Enrolled patients [aged 2–17 years] with moderate to severe ulcerative colitis [UC] or Crohn’s disease [CD] and body weight ≥10 kg were randomized by weight to receive low- or high-dose vedolizumab [≥30 kg, 150 or 300 mg; <30 kg, 100 or 200 mg] on Day 1 and Weeks 2, 6 and 14. Week 14 assessments included PK, clinical response and exposure–response relationship. Safety and immunogenicity were assessed.

Results

Randomized patients weighing ≥30 kg [UC, n = 25; CD, n = 24] and <30 kg [UC, n = 19; CD, n = 21] had a baseline mean [standard deviation] age of 13.5 [2.5] and 7.6 [3.2] years, respectively. In almost all indication and weight groups, area under the concentration curve and average concentration increased ~2-fold from low to high dose; the trough concentration was higher in each high-dose arm compared with the low-dose arms. At Week 14, clinical response occurred in 40.0–69.2% of patients with UC and 33.3–63.6% with CD in both weight groups. Clinical responders with UC generally had higher trough concentration vs non-responders, while this trend was not observed in CD. Fourteen per cent [12/88] of patients had treatment-related adverse events and 6.8% [6/88] had anti-drug antibodies.

Conclusions

Vedolizumab exposure increased in an approximate dose-proportional manner. No clear dose–response relationship was observed in this limited cohort. No new safety signals were identified.
Revisiting the dual pathway hypothesis of Chorismate production in plants
Authors: Lynch Joseph H
Published: March 2022

The shikimate pathway, the seven enzymatic steps that synthesize chorismate from phosphoenolpyruvate and erythrose 4-phosphate, produces the last common precursor of the three aromatic amino acids. It is firmly established that all seven enzymes are present in plastids, and it is generally accepted that this organelle is likely the sole location for production of chorismate in plants. However, recently a growing body of evidence has provided support for a previous proposal that at least portions of the pathway are duplicated in the cytosol, referred to as the Dual Pathway Hypothesis. Here I revisit this obscure hypothesis by reviewing the findings that provided the original basis for its formulation as well as more recent results that provide fresh support for a possible extra-plastidial shikimate pathway duplication. Similarities between this possible intercompartmental metabolic redundancy and that of terpenoid metabolism are used to discuss potential advantages of pathway duplication, and the translational implications of the Dual Pathway Hypothesis for metabolic engineering are noted.
In Elimination Settings, Measles Antibodies Wane After Vaccination but Not After Infection: A Systematic Review and Meta-Analysis
Authors: Bolotin Shelly , Osman Selma , Hughes Stephanie L , Ariyarajah Archchun , Tricco Andrea C , Khan Sumaiya , Li Lennon , Johnson Caitlin , Friedman Lindsay , Gul Nazish , Jardine Rachel , Faulkner Maryrose , Hahné Susan J M , Heffernan Jane M , Dabbagh Alya , Rota Paul A , Severini Alberto , Jit Mark , Durrheim David N , Orenstein Walter A , Moss William J , Funk Sebastian , Turner Nikki , Schluter William , Jawad Jaleela S , Crowcroft Natasha S
Published: March 2022

Background

We conducted a systematic review to assess whether measles humoral immunity wanes in previously infected or vaccinated populations in measles elimination settings.

Methods

After screening 16 822 citations, we identified 9 articles from populations exposed to wild-type measles and 16 articles from vaccinated populations that met our inclusion criteria.

Results

Using linear regression, we found that geometric mean titers (GMTs) decreased significantly in individuals who received 2 doses of measles-containing vaccine (MCV) by 121.8 mIU/mL (95% confidence interval [CI], −212.4 to −31.1) per year since vaccination over 1 to 5 years, 53.7 mIU/mL (95% CI, −95.3 to −12.2) 5 to 10 years, 33.2 mIU/mL (95% CI, −62.6 to −3.9), 10 to 15 years, and 24.1 mIU/mL (95% CI, −51.5 to 3.3) 15 to 20 years since vaccination. Decreases in GMT over time were not significant after 1 dose of MCV or after infection. Decreases in the proportion of seropositive individuals over time were not significant after 1 or 2 doses of MCV or after infection.

Conclusions

Measles antibody waning in vaccinated populations should be considered in planning for measles elimination.
The Interplay Between Replication Capacity of HIV-1 and Surrogate Markers of Disease
Authors: Rindler Audrey E , Kusejko Katharina , Kuster Herbert , Neumann Kathrin , Leemann Christine , Zeeb Marius , Chaudron Sandra E , Braun Dominique L , Kouyos Roger D , Metzner Karin J , Günthard Huldrych F
Published: March 2022

Background

HIV-1 replication capacity (RC) of transmitted/founder viruses may influence the further course of HIV-1 infection.

Methods

RCs of 355 whole-genome primary HIV-1 isolates derived from samples acquired during acute and recent primary HIV-1 infection (PHI) were determined using a novel high-throughput infection assay in primary cells. The RCs were used to elucidate potential factors that could be associated with RC during PHI.

Results

Increased RC was found to be associated with increased set point viral load (VL), and significant differences in RCs among 13 different HIV-1 subtypes were discerned. Notably, we observed an increase in RCs for primary HIV-1 isolates of HIV-1 subtype B over a 17-year period. Associations were not observed between RC and CD4 count at sample date of RC measurement, CD4 recovery after initiation of antiretroviral treatment, CD4 decline in untreated individuals, and acute retroviral syndrome severity scores.

Conclusions

These findings highlight that RCs of primary HIV-1 isolates acquired during the acute and recent phase of infection are more associated with viral factors, that is set point VL, than with host factors. Furthermore, we observed a temporal increase in RC for HIV-1 subtype B viruses over a period of 17 years.

Clinical Trials Registration

NCT00537966.
Is combined surgical dislocation and proximal femoral osteotomy a safe procedure for correction of complex hip deformities?
Authors: Parilla Frank W , Nepple Jeffrey J , Pashos Gail E , Schoenecker Perry L , Clohisy John C
Published: March 2022

Complex deformities of the hip requiring intra-articular and proximal femoral correction are challenging with regard to surgical access and complication risk. Combined surgical dislocation and proximal femoral osteotomy (SD/PFO) is a surgical strategy that provides unrestricted access to the joint with the capability for adjunctive PFO. Although providing excellent surgical access, concerns over a potentially high risk of postoperative complications remain, and published information on the safety of this technique remain scarce. In this study, we defined the early complication profile of combined surgery across 48 hips with a variety of complex deformities using a standardized, validated complication grading scheme for hip preservation surgery. Patients were mean age 19.1 years 13–33 years and 60% had previous surgery. At the early mean follow-up of 2.9 years, considerable improvement was seen across all outcome scores. Major complications (Grade III or higher) occurred at a rate of 4.2% (n = 2). Both were osteotomy non-unions, and both were treated successfully with revision PFO and bone grafting at mean 1.1 years. To our knowledge, the current series of combined SD-PFO surgeries represents the largest to date for which detailed complication data have been reported. Given the complexity of these disorders, a major complication rate of 4.2% is acceptable. Our complication rates were comparable to those reported for isolated SD and PFO procedures. These rates did not vary significantly across morphologic variants or patient-specific characteristics. Additionally, our complication risk profile is consistent with previous, smaller reports, which supports the generalizability of these results among appropriately experienced surgeons.
Inner nuclear membrane protein TMEM201 maintains endothelial cell migration and angiogenesis by interacting with the LINC complex
Authors: Zhang Yutian , Kong Ya , Guo Haoran , Liu Yun , Zang Yi , Li Jia
Published: March 2022

The nuclear envelope comprises the outer nuclear membrane, inner nuclear membrane (INM), and nucleopore. Although ∼60 INM proteins have been identified, only a few of them have been well characterized, revealing their crucial roles. Our group focused on the INM protein transmembrane protein 201 (TMEM201), whose role in cellular function remains to be defined. In this study, we investigated the role of TMEM201 in endothelial cell migration and angiogenesis. Depletion of TMEM201 expression by short hairpin RNA-mediated interference impeded human umbilical vein endothelial cell (HUVEC) angiogenic behavior in tube formation and fibrin gel bead sprouting assays. Meanwhile, TMEM201-deficient HUVECs exhibited impaired migration ability. We next explored the underlying mechanism and found that the N-terminal of TMEM201 interacted with the linker of nucleoskeleton and cytoskeleton complex and was required for regulating endothelial cell migration and angiogenesis. These in vitro findings were further confirmed by using in vivo models. In Tmem201-knockout mice, retinal vessel development was arrested and aortic ring sprouting was defective. In addition, loss of tmem201 impaired zebrafish intersegmental vessel development. In summary, TMEM201 was shown to regulate endothelial cell migration and control the process of angiogenesis. This study is the first to reveal the role of INM proteins in the vascular system and angiogenesis.
Native pulmonary valve endocarditis requiring pulmonary valve replacement in adulthood: a case series
Authors: Mohamed S , Patel A J , Mazhar K , Osman A , Balacumaraswami L , Ridley P
Published: March 2022

Native pulmonary valve endocarditis is a rare phenomenon as native valve endocarditis tends to typically affect the left sided heart valves. However, the right-sided heart valves can be affected in patients with a history of intravenous drug use, whereby the tricuspid valve is most commonly affected. We present two cases who were diagnosed with native pulmonary valve endocarditis in the absence of congenital heart disease. In the first case, the native pulmonary valve endocarditis was probably a derivative of compounding factors of an enlarged underlying pulmonary artery and staphylococcal bacteraemia. In the second case, a common causal organism of native valve endocarditis following dental treatment and the resultant echocardiography findings was of significant interest. In summary, native pulmonary valve endocarditis is relatively rare complication in the adult population, especially in the absence of congenital heart disease.
Realizing the United Nations Sustainable Development Goals 7 and 13 in sub-Saharan Africa by 2030: synergizing energy and climate justice perspectives
Authors: Agbaitoro Godswill A , Oyibo Kester I
Published: March 2022

This article discusses how energy policy measures for realizing the United Nations Sustainable Development Goals (SDGs) 7 and 13 in sub-Saharan Africa (SSA) could be framed towards achieving energy justice by 2030. Both goals highlight interdependent and conflicting interactions that policymakers should be aware of whilst working to realize them. This position is quite challenging for developing countries that seek to simultaneously resolve the rising inequality of access to modern and affordable energy systems as stipulated in the SDG 7, whilst at the same time working to meet their international obligations towards the attainment of SDG 13. This article seeks to resolve this conflict by proposing some viable measures for a synergy between SDGs 7 and 13. It further examines the paradoxical situation faced by countries in the SSA region and argues for a contextualization of the two goals within the energy justice framework. The proposed approach entails a systematic transition from fossil fuels to low-carbon through socio-economic policies that take into account social injustices and further incorporate sustainable actions such as developing renewable energy technologies, diversification of energy options, energy efficiency, and regional alignments and/or cooperation. Overall, the measures outlined in this article aim to help the SSA region achieve energy justice towards 2030.
Reading in the mist: high-quality optical character recognition based on freely available early modern digitized books
Authors: Sangiacomo Andrea , Hogenbirk Hugo , Tanasescu Raluca , Karaisl , Antonia , White Nick
Published: March 2022

In this paper, we present a workflow for reworking digitized versions of early modern books, freely available in the public domain, in such a way that they will be capable of yielding high-quality optical character recognition (OCR) results suitable for computational text mining. Testing our method, we observed that anything above 90% OCR accuracy is sufficient for semantic analysis. In addition,the overall homogeneity in the OCR accuracy across the corpus proved to be more important than having perhaps only a few works with higher accuracy and the rest available in a lower quality. In terms of the OCR process, this paper illustrates how it was possible to reduce the processing time at maximum quality of a single book of average length (ca. 500 pages) from a minimum of 20 hrs to an average of about 3 hrs (though theoretically nearly infinitely reducible). This was achieved by replacing a step-by-step OCR process with a fully automated pipeline system run on an arbitrary number of servers, breaking up the full process of OCRing one book into minimal tasks that can be handled simultaneously by multiple servers.
Prospect of detecting X-ray haloes around middle-aged pulsars with eROSITA
Authors: Li Ben , Zhang Yi , Liu Teng , Liu Ruo-Yu , Wang Xiang-Yu
Published: March 2022

The detection of extended TeV γ-ray emission (dubbed ‘TeV haloes’) around Geminga and Monogem pulsars by High Altitude Water Cherenkov collaboration implies that the halo-like morphologies around middle-aged pulsars may be common. The γ-ray emission above 10 TeV is thought to arise from inverse Compton scattering of relativistic electrons/positrons in the pulsar haloes off cosmic microwave background photons. In the meanwhile, these electrons and positrons can produce X-ray synchrotron emission in the interstellar magnetic field, resulting in a diffuse emission in the X-ray band (namely X-ray haloes). Here, we study the prospect of detecting X-ray haloes with extended Roentgen Survey with an Imaging Telescope Array (eROSITA) from 10 middle-aged pulsars with characteristic age τc larger than tens of thousands of years in the Australia Telescope National Facility pulsar catalogue. Assuming a benchmark value (i.e. B = 3 $\mu$G) for the magnetic field, most of the X-ray haloes are found to be bright enough to be detected by eROSITA in the energy range of 0.5–2 keV with a 20 ks targeted survey. Among these pulsar haloes, four are detectable in the ongoing 4-yr eROSITA all-sky survey. Thanks to the large grasp in the soft X-ray band, eROSITA is expected to be able to measure the surface brightness profiles of the X-ray haloes from sub-pc up to tens of pc scales, which can be used to constrain the magnetic field and the diffusion coefficient in the pulsar haloes.
X-ray variability of transitional millisecond pulsars: a faint, stable, and fluctuating disc
Authors: Linares Manuel , De Marco Barbara , Wijnands Rudy , van der Klis Michiel
Published: March 2022

Transitional millisecond pulsars (tMSPs) have emerged in the last decade as a unique class of neutron stars at the crossroads between accretion- and rotation-powered phenomena. In their (sub-luminous) accretion disc state, with X-ray luminosities of order 1033–1034 erg s−1, they switch rapidly between two distinct X-ray modes: the disc-high (DH) and disc-low (DL) states. We present a systematic XMM–Newton and Chandra analysis of the aperiodic X-ray variability of all three currently known tMSPs, with a main focus on their disc state and separating DH and DL modes. We report the discovery of flat-topped broad-band noise in the DH state of two of them, with break frequencies of 2.8 mHz (PSR J1023 + 0038) and 0.86 mHz (M28-I). We argue that the lowest frequency variability is similar to that seen in disc-accreting X-ray binaries in the hard state, at typical luminosities at least two orders of magnitude higher than tMSPs. We find strong variability in the DH state around 1 Hz, not typical of hard state X-ray binaries, with fractional rms amplitudes close to 30 per cent. We discuss our results and use them to constrain the properties of the accretion disc, assuming that the X-ray variability is produced by fluctuations in mass accretion rate, and that the break frequency corresponds to the viscous time-scale at the inner edge of the disc. In this context, we find that the newly found break frequencies are broadly consistent with a disc truncated close to the light cylinder with $\dot{M}\simeq 10^{13}-5\times 10^{14}$ g s−1 and a viscosity parameter α ≳ 0.2.
Ultraviolet to far infrared self-consistent analysis of the stellar populations of massive starburst galaxies at intermediate redshifts
Authors: Espino-Briones Néstor , Pérez-González Pablo G , Zamorano Jaime , Rodríguez-Muñoz Lucía
Published: March 2022

We study in detail the properties of the stellar populations of 111 massive [log (M⋆/M⊙) ≥ 10] dusty [far-infrared (FIR)-selected] starburst (SFR/SFRMS > 2) galaxies at 0.7 < z < 1.2. For that purpose, we use self-consistent methods that analyse the UV-to-FIR broad-band observations in terms of the stellar light and dust re-emission with energy-balance techniques. We find that the emission of our starburst galaxies can be interpreted as a recent star formation episode superimposed on a more evolved stellar population. On average, the burst age is ∼80 Myr and its attenuation ∼2.4 mag. Assuming our starburst galaxies at half their lifetimes, we infer a duration of the starburst phase of ∼160 Myr. The median stellar mass and star formation rate (SFR) are log (M⋆/M⊙) ∼ 10.6 and ∼220 M⊙yr−1. Assuming this SFR and the inferred duration of the starburst phase, the stellar mass added during this phase corresponds to ∼40 per cent the median stellar mass of our sample. The young-population age determines the position of our galaxies in the M⋆–SFR plane. Galaxies located at the largest distances of the MS present shorter young-population ages. The properties of the underlying stellar population cannot be constrained accurately with our broad-band data. We also discuss the impact of including the FIR data and energy-balance techniques in the analysis of the properties of the stellar populations in starburst galaxies.
Radio and far-IR emission associated with a massive star-forming galaxy candidate atz≃ 6.8: a radio-loud AGN in the reionization era?
Authors: Endsley Ryan , Stark Daniel P , Fan Xiaohui , Smit Renske , Wang Feige , Yang Jinyi , Hainline Kevin , Lyu Jianwei , Bouwens Rychard , Schouws Sander
Published: March 2022

We report the identification of radio (0.144–3 GHz) and mid-, far-infrared, and sub-mm (24–850μm) emission at the position of one of 41 UV-bright ($\mathrm{M_{\mathrm{UV}}}^{ }\lesssim -21.25$) z ≃ 6.6–6.9 Lyman-break galaxy candidates in the 1.5 deg2 COSMOS field. This source, COS-87259, exhibits a sharp flux discontinuity (factor >3) between two narrow/intermediate bands at 9450 and 9700 Å and is undetected in all nine bands blueward of 9600 Å, as expected from a Lyman alpha break at z ≃ 6.8. The full multiwavelength (X-ray through radio) data of COS-87529 can be self-consistently explained by a very massive (M* = 1010.8 M⊙) and extremely red (rest-UV slope β = −0.59) z ≃ 6.8 galaxy with hyperluminous infrared emission (LIR = 1013.6 L⊙) powered by both an intense burst of highly obscured star formation (SFR ≈ 1800 M⊙ yr−1) and an obscured ($\tau _{_{\mathrm{9.7\mu m}}} = 7.7\pm 2.5$) radio-loud (L1.4 GHz ≈ 1025.4 W Hz−1) active galactic nucleus (AGN). The radio emission is compact (1.04 ± 0.12 arcsec) and exhibits an ultra-steep spectrum between 1.32 and 3 GHz ($\alpha =-1.57^{+0.22}_{-0.21}$) that flattens at lower frequencies ($\alpha = -0.86^{+0.22}_{-0.16}$ between 0.144 and 1.32 GHz), consistent with known z > 4 radio galaxies. We also demonstrate that COS-87259 may reside in a significant (11×) galaxy overdensity, as common for systems hosting radio-loud AGN. While we find that low-redshift solutions to the optical + near-infrared data are not preferred, a spectroscopic redshift will ultimately be required to establish the true nature of COS-87259 beyond any doubt. If confirmed to lie at z ≃ 6.8, the properties of COS-87259 would be consistent with a picture wherein AGN and highly obscured star formation activity are fairly common among very massive (M* > 1010 M⊙) reionization-era galaxies.
Observations of cold extragalactic gas clouds at z = 0.45 towards PKS 1610-771
Authors: Weng Simon , Sadler Elaine M , Foster Caroline , Péroux Céline , Mahony Elizabeth K , Allison James R , Moss Vanessa A , Su Renzhi , Whiting Matthew T , Yoon Hyein
Published: March 2022

We present results from MUSE observations of a 21-cm ${\rm H\, {\small I}}$ absorption system detected with the Australian Square Kilometre Array Pathfinder radio telescope at redshift z = 0.4503 towards the z = 1.71 quasar PKS 1610-771. We identify four galaxies (A, B, X, and Y) at the same redshift as the 21-cm ${\rm H\, {\small I}}$ Damped Lyman-α (DLA) absorption system, with impact parameters ranging from less than 10 kpc to almost 200 kpc from the quasar sightline. ${\rm Ca\, {\small II}}$ and ${\rm Na\, {\small I}}$ absorption is seen in the MUSE spectrum of the background QSO, with velocities coinciding with the initial ${\rm H\, {\small I}}$ 21-cm detection, but tracing less dense and warmer gas. This metal-line component aligns with the rotating ionized disc of galaxy B (impact parameter 18 kpc from the QSO) and appears to be corotating with the galaxy disc. In contrast, the 21-cm ${\rm H\, {\small I}}$ absorber is blueshifted relative to the galaxies nearest the absorber and has the opposite sign to the velocity field of galaxy B. Since galaxies A and B are separated by only 17 kpc on the sky and 70 km s−1 in velocity, it appears likely that the 21-cm detection traces extragalactic clouds of gas formed from their interaction. This system reveals that the cold 100 K neutral gas critical for star formation can be associated with complex structures beyond the galaxy disc, and is a first case study made in preparation for future large 21-cm absorption surveys like the ASKAP First Large Absorption Survey in ${\rm H\, {\small I}}$.
Metallicities of outer halo M31 globular clusters from integrated light calcium-II triplet spectroscopy
Authors: Sakari Charli M , Wallerstein George
Published: March 2022

This paper presents [Fe/H] ratios for globular clusters (GCs) in the outer halo of the Andromeda Galaxy, M31, based on moderate-resolution, integrated light (IL) spectroscopy of the calcium-II triplet (CaT) lines. The CaT strengths are measured by fitting Voigt profiles to the lines and integrating those profiles; integrations of defined bandpasses are also considered. The [Fe/H] ratios are determined using an empirical calibration with CaT line strength, as derived from another sample of M31 GCs that were previously studied at high-resolution. The [Fe/H] ratios for the new GCs reveal that the outer halo GCs are indeed generally more metal-poor than typical inner halo GCs, though there are several more metal-rich GCs that look to have been accreted from dwarf satellites. The metallicities of these GCs also place important constraints on the nature of the substructure in the outer halo and the dwarf satellites that created this substructure.
Thermal emission and scattering by aligned grains: Plane-parallel model and application to multiwavelength polarization of the HL Tau disc
Authors: Lin Zhe-Yu Daniel , Li Zhi-Yun , Yang Haifeng , Stephens Ian , Looney Leslie , Harrison Rachel , Fernández-López Manuel
Published: March 2022

Telescopes are now able to resolve dust polarization across circumstellar discs at multiple wavelengths, allowing the study of the polarization spectrum. Most discs show clear evidence of dust scattering through their unidirectional polarization pattern typically at the shorter wavelength of $\sim 870 \, \mu$m. However, certain discs show an elliptical pattern at ∼3 mm, which is likely due to aligned grains. With HL Tau, its polarization pattern at ∼1.3 mm shows a transition between the two patterns making it the first example to reveal such transition. We use the T-matrix method to model elongated dust grains and properly treat scattering of aligned non-spherical grains with a plane-parallel slab model. We demonstrate that a change in optical depth can naturally explain the polarization transition of HL Tau. At low optical depths, the thermal polarization dominates, while at high optical depths, dichroic extinction effectively takes out the thermal polarization and scattering polarization dominates. Motivated by results from the plane-parallel slab, we develop a simple technique to disentangle thermal polarization of the aligned grains T0 and polarization due to scattering S using the azimuthal variation of the polarization fraction. We find that, with increasing wavelength, the fractional polarization spectrum of the scattering component S decreases, while the thermal component T0 increases, which is expected since the optical depth decreases. We find several other sources similar to HL Tau that can be explained by azimuthally aligned scattering prolate grains when including optical depth effects. In addition, we explore how spirally aligned grains with scattering can appear in polarization images.
ExHaLe-jet: an extended hadro-leptonic jet model for blazars – I. Code description and initial results
Authors: Zacharias M , Reimer A , Boisson C , Zech A
Published: March 2022

The processes operating in blazar jets are still an open question. Modelling the radiation emanating from an extended part of the jet allows one to capture these processes on all scales. Kinetic codes solving the Fokker–Planck equation along the jet flow are well suited to this task, as they can efficiently derive the radiation and particle spectra without the need for computationally demanding plasma physical simulations. Here, we present a new extended hadro-leptonic jet code – ExHaLe-jet– which considers simultaneously the processes of relativistic protons and electrons. Within a pre-set geometry and bulk flow, the particle evolution is derived self-consistently. Highly relativistic secondary electrons (and positrons) are created through γ–γ pair production, Bethe–Heitler pair production, and pion/muon decay. These secondaries are entrained in the jet flow decreasing the ratio of protons to electrons with distance from the jet base. For particle–photon interactions, we consider all internal and many external photon fields, such as the accretion disc, broad-line region, and the dusty torus. The external fields turn out to be the most important source for particle–photon interactions governing the resulting photon and neutrino spectra. In this paper, we present the code and an initial parameter study, while in follow-up works we present extensions of the code and more specific applications.
CHANG-ES XXV: H iimaging of nearby edge-on galaxies – Data Release 4
Authors: Zheng Yun , Wang Jing , Irwin Judith , English Jayanne , Ma Qingchuan , Wang Ran , Wang Ke , Wang Q Daniel , Krause Marita , Randriamampandry Toky H , Li Jiangtao , Beck Rainer
Published: March 2022

We present the ${\rm H}\, {\small I}$ distribution of galaxies from the Continuum Haloes in Nearby Galaxies – an EVLA Survey (CHANG-ES). Though the observational mode was not optimized for detecting ${\rm H}\, {\small I}$, we successfully produce ${\rm H}\, {\small I}$ cubes for 19 galaxies. The moment-0 maps from this work are available on CHANG-ES data release website (i.e. https://www.queensu.ca/changes). Our sample is dominated by star-forming, ${\rm H}\, {\small I}$-rich galaxies at distances from 6.27 to 34.1 Mpc. ${\rm H}\, {\small I}$ interferometric images on two of these galaxies (NGC 5792 and UGC 10288) are presented here for the first time, while 12 of our remaining sample galaxies now have better ${\rm H}\, {\small I}$ spatial resolutions and/or sensitivities of intensity maps than those in existing publications. We characterize the average scale heights of the ${\rm H}\, {\small I}$ distributions for a subset of most inclined galaxies (inclination > 80 deg), and compare them to the radio continuum intensity scale heights, which have been derived in a similar way. The two types of scale heights are well correlated, with similar dependence on disc radial extension and star formation rate surface density but different dependence on mass surface density. This result indicates that the vertical distribution of the two components may be governed by similar fundamental physics but with subtle differences.