bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract

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; &lt;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 &lt;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

AbstractThe 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

Abstract

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

Abstract

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

ABSTRACT
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT
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

ABSTRACTTransitional 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

ABSTRACT
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 &gt; 2) galaxies at 0.7 &lt; z &lt; 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

ABSTRACTWe 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 &gt;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 &gt; 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* &gt; 1010 M⊙) reionization-era galaxies.