bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilisation of pre-exposure prophylaxis (PrEP) for HIV prevention in the Australian general practice setting: a longitudinal observational study
Authors: Chidwick Kendal , Pollack Allan , Busingye Doreen , Norman Sarah , Grulich Andrew , Bavinton Benjamin , Guy Rebecca , Medland Nick 
Published: April 2022

Background Pre-exposure prophylaxis (PrEP) became available through the Australian Pharmaceutical Benefits Scheme (PBS) on 1 April 2018 for HIV infection prevention in patients ≥18 years at medium-to-high HIV risk. The aims were to investigate PrEP utilisation in general practice since PBS listing, and factors associated with discontinuation. Methods This longitudinal study included patients aged 18–74 years attending general practices participating in MedicineInsight, a large-scale national primary care database of deidentified electronic health records, between October 2017 and September 2019. Results PrEP utilisation increased 10-fold following PBS listing. On average, patients had 9.7 PrEP prescriptions per year; a medication possession ratio of 80.8%. Of 1552 patients prescribed PrEP from April 2018, most were male (98.3%), aged 18–39 years (59.3%), resided in major cities (86.7%) and in the two most socioeconomically advantaged quintiles (70.0%). Almost half (49.1%) of the patients were identified as new to PrEP. At study end, 65.1% were on active PrEP (16.5%, of whom had non-continuous use), 19.2% had discontinued PrEP and 15.7% were lost to follow up. Patients who discontinued were more likely to attend low rather than high PrEP caseload practices (adjusted odds ratio [aOR] 1.7; 95% CI: 1.0–2.8; P = 0.047). The odds of non-continuous therapy was 2.9-fold higher in patients with bipolar disorder (aOR 2.89; 95% CI: 1.10–7.6; P = 0.045). Conclusions Following PBS listing, PrEP utilisation increased and stopping therapy was associated with attending low caseload practices. General practice education, particularly among low caseload practices, could help address these disparities.
Copying form without content
Authors: Pakendorf Brigitte 
Published: April 2022

AbstractTwo major types of change are generally distinguished in language contact studies: the transfer of linguistic form (frequently taken to include transfer of concomitant meaning or function) and the transfer of structural and semantic patterns by themselves, without attendant form. A type of change that is less frequently discussed is so-called relexification. This involves the transfer of form without model-language semantic or syntactic specifications that is grafted onto an equivalent recipient-language lemma. Relexification has been suggested to play a role in the development of mixed languages or creoles, but as is shown here, it can also be identified in several ordinary situations of language contact from around the world. This type of change represents a mirror image of the transfer of patterns without lexical material and supports recent models of language selection in bilinguals.
Aphanomyces euteiches (Aphanomyces root rot).
Authors:   UK, CABI
Published: April 2022

Abstract

A. euteiches can cause considerable yield losses especially in the production of processing peas. Overall yearly losses of 10% are reported from the USA (Hagedorn, 1984) and in the European parts of the former USSR, losses can amount to 50% or more (Tsvetkova and Kotova, 1982). Infection of a pea crop causes uneven maturation, inferior pea quality and the crop may not even be harvested. The losses caused by A. euteiches-infected snap bean grown without rotation can be severe after 2 years in irrigated conditions (Pfender and Hagedorn, 1982). Lucerne grown in wet conditions can suffer from Aphanomyces root rot with subsequent losses in forage yield (Wiersma et al., 1997). In permanent pastures of subterranean clover, A. euteiches causes a decline in forage production (Greenhalgh et al., 1985).
Subpulse Drifting of PSR J1110–5637
Authors: Dang S. J. , Shang L. H. , Lin L. , Zhi Q. J. , Zhao R. S. , Wu C. B. , You Z. Y. , Dong A. J. , Bai J. T. , Xu X. , Zhang D. D. , Yang H. , Lin Q. W. 
Published: April 2022

Abstract
We report a detailed study of polarization characteristics and subpulse drifting in PSR J1110−5637 with the observations of the Parkes 64 m radio telescope at 1369 MHz. The observations revealed that the trailing component of the pulse profile has obvious subpulse drifting, while the leading component has no subpulse drifting. Using the two-dimensional fluctuation spectrum (2DFS), we detected three distinct emission modes in the trailing component (modes A, B and C). The emission in mode A is chaotic and indistinguishable, while modes B and C have obvious subpulse drifting. The vertical modulation periods P3 of modes B and C are around the mean values of 12 P and 8 P, respectively. The subpulse drifting of PSR J1110−5637 will expand the pulsar sample with multiple subpulse drifting rates, and this will help future systematic studies on the physical origin of the subpulse drifting phenomenon.
Statistical Properties of X-Ray Flares from the Supergiant Fast X-Ray Transients
Authors: Zhang Wen-Long , Yi Shuang-Xi , Yang Yu-Peng , Qin Ying 
Published: April 2022

Abstract
Supergiant fast X-ray transients are a sub-class of high mass X-ray binaries, in which the compact object is a neutron star and it is accreting materials from its non-degenerate companion star. The sample of supergiant fast X-ray transients from XMM-Newton public observations have been intensively studied, and hence the corresponding parameters for identifying X-ray flares have been obtained by Sidoli et al., such as the rise time, the decay time, the duration time, the waiting time, the peak luminosity, the isotropic energy and the mean luminosity. In order to investigate the origin of the X-ray flares from the supergiant fast X-ray transients, we apply the cumulative distribution method with the power-law index

dN

(
x
)

/

dx
∝
(
x
+

x

0

)

−

α

x

to the target sample. We then find that the relevant parameters can be well described by the cumulative distribution with indices 1.0–1.9 for IGR J16418-4532, IGR J16328-4726 and IGR J18450-0435, respectively. This finding indicates that the X-ray flares are likely to be produced by the self-organizing critical process, one possible scenario may be due to reconnection in magnetized stellar wind blobs approaching into the magnetosphere of magnetized neutron star. Therefore, we suggest that the high mass X-ray binaries with similar X-ray flares likely belong to the self-organized criticality systems.
Thienoguanosine brightness in DNA duplexes is governed by the localization of its ππ* excitation in the lowest energy absorption band
Authors: Ciaco Stefano , Gavvala Krishna , Greiner Vanille , Mazzoleni Viola , Didier Pascal , Ruff Marc , Martinez-Fernandez Lara , Improta Roberto , Mély Yves 
Published: April 2022

Abstract
Thienoguanosine (thG) is an isomorphic fluorescent guanosine (G) surrogate, which almost perfectly mimics the natural G in DNA duplexes and may therefore be used to sensitively investigate for example protein-induced local conformational changes. To fully exploit the information given by the probe, we carefully re-investigated the thG spectroscopic properties in 12-bp duplexes, when the Set and Ring Associated (SRA) domain of UHRF1 flips its 5′ flanking methylcytosine (mC). The SRA-induced flipping of mC was found to strongly increase the fluorescence intensity of thG, but this increase was much larger when thG was flanked in 3′ by a C residue as compared to an A residue. Surprisingly, the quantum yield and fluorescence lifetime values of thG were nearly constant, regardless of the presence of SRA and the nature of the 3′ flanking residue, suggesting that the differences in fluorescence intensities might be related to changes in absorption properties. We evidenced that thG lowest energy absorption band in the duplexes can be deconvoluted into two bands peaking at ∼350 nm and ∼310 nm, respectively red-shifted and blue-shifted, compared to the spectrum of thG monomer. Using quantum mechanical calculations, we attributed the former to a nearly pure ππ* excitation localized on thG and the latter to excited states with charge transfer character. The amplitude of thG red-shifted band strongly increased when its 3′ flanking C residue was replaced by an A residue in the free duplex, or when its 5′ flanking mC residue was flipped by SRA. As only the species associated with the red-shifted band were found to be emissive, the highly unusual finding of this work is that the brightness of thG in free duplexes as well as its changes on SRA-induced mC flipping almost entirely depend on the relative population and/or absorption coefficient of the red-shifted absorbing species.
Simulation of Bragg coherent diffraction imaging
Authors: Mokhtar A H , Serban D , Newton M C 
Published: April 2022

Abstract
The arrangement of atoms within a crystal and information on deviations from the ideal lattice is encoded in the diffraction pattern obtained from an appropriately conducted Bragg coherent diffraction imaging (BCDI) experiment. A foreknowledge of how specific displacements of atoms within the unit cell alter the BCDI diffraction pattern and the subsequent real-space image is often useful for interpretation and can provide valuable insight for materials design. Here we report on an atomistic approach to efficiently simulate BCDI diffraction patterns by factorising and eliminating certain redundancies in the conventional approach. Our method is able to reduce the computation time by several orders of magnitude without compromising the recovered phase information and therefore enables feasible atomistic simulations on nanoscale crystals with arbitrary lattice distortions.
High-sensitivity pattern discovery in large, paired multiomic datasets
Authors: Ghazi Andrew R , Sucipto Kathleen , Rahnavard Ali , Franzosa Eric A , McIver Lauren J , Lloyd-Price Jason , Schwager Emma , Weingart George , Moon Yo Sup , Morgan Xochitl C , Waldron Levi , Huttenhower Curtis 
Published: April 2022

AbstractMotivationModern biological screens yield enormous numbers of measurements, and identifying and interpreting statistically significant associations among features are essential. In experiments featuring multiple high-dimensional datasets collected from the same set of samples, it is useful to identify groups of associated features between the datasets in a way that provides high statistical power and false discovery rate (FDR) control.ResultsHere, we present a novel hierarchical framework, HAllA (Hierarchical All-against-All association testing), for structured association discovery between paired high-dimensional datasets. HAllA efficiently integrates hierarchical hypothesis testing with FDR correction to reveal significant linear and non-linear block-wise relationships among continuous and/or categorical data. We optimized and evaluated HAllA using heterogeneous synthetic datasets of known association structure, where HAllA outperformed all-against-all and other block-testing approaches across a range of common similarity measures. We then applied HAllA to a series of real-world multiomics datasets, revealing new associations between gene expression and host immune activity, the microbiome and host transcriptome, metabolomic profiling and human health phenotypes.Availability and implementationAn open-source implementation of HAllA is freely available at http://huttenhower.sph.harvard.edu/halla along with documentation, demo datasets and a user group.Supplementary informationSupplementary data are available at Bioinformatics online.
Attaining biochemical euthyroidism early after total thyroidectomy in Graves’ disease may lower long-term morbidity risk
Authors: Liu Xiaodong , Wong Carlos K H , Chan Wendy W L , Tang Eric H M , Woo Yu Cho , Liu Shirley Y W , Lam Cindy L K , Lang Brian H H 
Published: April 2022

Abstract

Background
The relationship between good early control of thyroid hormone levels after thyroidectomy for Graves’ disease (GD) and subsequent risks of mortality and morbidities is not well known. The aim of this study was to examine the association between thyroid hormone levels within a short interval after surgery and long-term mortality and morbidity risks from a population-based database.

Methods
Patients with GD who underwent complete/total thyroidectomy between 2006 and 2018 were selected from the Hong Kong Hospital Authority clinical management system. All patients were classified into three groups (euthyroidism, hypothyroidism, and hyperthyroidism) according to their thyroid hormone levels at 6, 12, and 24 months after surgery. Cox proportional hazards models were performed to compare the risks of all-cause mortality, cardiovascular disease (CVD), Graves’ ophthalmopathy, and cancer.

Results
Over a median follow-up of 68 months with 5709 person-years, 949 patients were included for analysis (euthyroidism, n = 540; hypothyroidism, n = 282; and hyperthyroidism, n = 127). The hypothyroidism group had an increased risk of CVD (HR = 4.20, 95 per cent c.i. 2.37 to 7.44, P &lt; 0.001) and the hyperthyroidism group had an increased risk of cancer (HR = 2.14, 95 per cent c.i. 1.55 to 2.97, P &lt; 0.001) compared with the euthyroidism group. Compared with patients obtaining euthyroidism both at 6 months and 12 months, the risk of cancer increased in patients who achieved euthyroidism at 6 months but had an abnormal thyroid status at 12 months (HR = 2.33, 95 per cent c.i. 1.51 to 3.61, P &lt; 0.001) and in those who had abnormal thyroid status at 6 months but achieved euthyroidism at 12 months (HR = 2.52, 95 per cent c.i. 1.60 to 3.97, P &lt; 0.001).

Conclusions
This study showed a higher risk of CVD in postsurgical hypothyroidism and a higher risk of cancer in hyperthyroidism compared with achieving euthyroidism early after thyroidectomy. Patients who were euthyroid at 6 months and 12 months had better outcomes than those achieving euthyroidism only at 6 months or 12 months. Attaining biochemical euthyroidism early after thyroidectomy should become a priority.
Risk factors associated with immune checkpoint inhibitor–induced acute kidney injury compared with other immune-related adverse events: a case–control study
Authors: Gérard Alexandre O , Barbosa Susana , Parassol Nadège , Andreani Marine , Merino Diane , Cremoni Marion , Laurain Audrey , Pinel Sylvine , Bourneau-Martin Delphine , Rocher Fanny , Esnault Vincent L M , Borchiellini Delphine , Sicard Antoine , Drici Milou-Daniel ,   French Network of Pharmacovigilance Centers
Published: April 2022

ABSTRACT

Background
Immune checkpoint inhibitors (ICIs) foster anti-cancer immune responses. Their efficacy comes at the cost of immune-related adverse events (IRAEs). The latter affects various organs, including kidneys, mostly as acute tubulointerstitial nephritis, the pathophysiology of which remains unclear. We conducted a multicentre case–control study to compare the characteristics of patients with renal IRAEs (ICI-AKI) with those of patients diagnosed with other IRAEs.

Methods
We queried the French pharmacovigilance database for all adverse events involving ICIs. Reports were classified as ICI-AKI or extrarenal IRAE. For each ICI-AKI report, four reports of extrarenal IRAEs were randomly included (control group, 4:1 ratio). Variables showing an association with a P &lt; 0.05 were included as covariates in a multivariate analysis.

Results
Therefore, 167 ICI-AKI reports were compared with 668 extrarenal IRAEs. At least one concomitant extrarenal IRAE was mentioned in 44.3% of ICI-AKI reports. Patients with ICI-AKI were significantly older than patients with extrarenal IRAEs (69.1 versus 64.6 years; P = 0.0135), and chronic kidney disease was significantly more prevalent (12.0% versus 3.3%; P = 0.0125). Patients with ICI-AKI were significantly more likely to be treated with fluindione [adjusted odds ratio (OR) 6.53, 95% confidence interval (95% CI) 2.21–19.31; P = 0.0007], a non-steroidal anti-inflammatory drug (NSAID, OR 3.18, 95% CI 1.07–9.4; P = 0.0368) or a proton-pump inhibitor (PPI, OR 2.18, 95% CI 1.42–3.34; P = 0.0004).

Conclusion
This study is limited by a lack of data, preventing confirmation of numerous reports therefore not included in the analysis. We are unable to draw definite pathophysiological conclusions from our data. Nonetheless, we suggest that ICIs may be a ‘second-hit’ that precipitates acute kidney injury caused by another concomitant drug (fluindione, NSAID or PPI).
Response to acute vasodilator challenge and haemodynamic modifications after MitraClip in patients with functional mitral regurgitation and pulmonary hypertension
Authors: Mandurino-Mirizzi Alessandro , Munafò Andrea , Raineri Claudia , Magrini Giulia , Frassica Romina , Arzuffi Luca , Scelsi Laura , Turco Annalisa , Ferlini Marco , Gazzoli Fabrizio , Ferrario Maurizio , Ghio Stefano , Oltrona-Visconti Luigi , Crimi Gabriele 
Published: April 2022

Abstract
The effectiveness of transcatheter edge-to-edge repair (TEER) in patients with functional mitral regurgitation (FMR) and pulmonary hypertension (PH) is still debated and pre-procedural predictors of haemodynamic improvement after TEER in this setting are currently unknown. We investigated whether normalization of pulmonary artery wedge pressure (PAWP) in response to sodium nitroprusside (SNP) during baseline right heart catheterization might be predictive of a favourable haemodynamic response to MitraClip in patients with FMR and PH. Among 22 patients enrolled, 13 had a positive response to SNP (responders), nine were non-responders. At 6-months follow-up, responders showed a 33% reduction in PAWP and a 25% reduction in mean pulmonary artery pressure (PAP) (P = 0.002 and 0.004, respectively); no significant change occurred in non-responders. In patients with FMR and PH, pre-procedural vasodilator challenge with SNP may help define patients who may have haemodynamic improvement after TEER.
Percutaneous closure of a ‘whale tail’ left atrial appendage with a Watchman FLX device and pre-procedural FEops HEARTguide patient-specific computational simulation: a case report
Authors: Di Muro Francesca Maria , Stolcova Miroslava , Di Mario Carlo , Meucci Francesco 
Published: April 2022

Abstract

Background
Percutaneous left atrial appendage closure (LAAC) is an emerging alternative to oral anticoagulation for stroke prevention in atrial fibrillation (AF) in patients with AF, elevated stroke risk and contraindications to long-term anticoagulation treatment. Optimal pre-procedural planning is essential to ensure optimal procedural results.

Case summary
We report the case of a 62-year-old man with a history of right cerebellar haematoma referred for LAA closure. We describe the first use of FEops HEARTguide patient-specific computational simulation in the planning of LAAC with the Watchman Flex device (Boston Scientific, Marlborough, MA, USA) in an unusual ‘whale tail’-like LAA anatomy.

Discussion
Percutaneous left atrial appendage (LAA) closure is feasible in the majority of patients. However, certain LAA anatomies may pose substantial technical challenges. This case shows the crucial role of a pre-procedural assessment based on patient-specific computational simulations for LAA closure in difficult scenarios resulting in a more efficient procedure with the optimal result and good clinical outcomes.
Paradoxical sinus deceleration during dobutamine stress echocardiography: case series and review of the literature
Authors: Sulo Enxhela , Davidsen Einar Skulstad , Lønnebakken Mai Tone , Bleie Øyvind , Saeed Sahrai 
Published: April 2022

Abstract

Background
Dobutamine stress echocardiography is an established diagnostic modality for assessing myocardial ischaemia in patients with known or suspected coronary artery disease. Dobutamine infusion causes dose-dependent increase in heart rate and contractility. However, in some cases, it induces paradoxical sinus deceleration, whose underlying mechanism and clinical significance are not fully understood.

Case summary
We present episodes of paradoxical sinus deceleration observed during dobutamine stress echocardiography in six (four males and two females) patients and described its patterns of occurrence and clinical and echocardiographic characteristics.

Discussion
Paradoxical sinus deceleration occurred mostly at maximal dobutamine infusion was accompanied with a decline in blood pressure and resolved spontaneously following cessation of dobutamine infusion. Individuals experiencing paradoxical sinus deceleration had in common abnormal left ventricle geometry but differed with regard to age, sex, and cardiometabolic risk factors.
Impact of source and receiver distributions on imaging of dipping reflectors with passive reflection seismic interferometry
Authors: Beckel Ruth A , Juhlin Christopher 
Published: April 2022

SUMMARY
Passive reflection seismic interferometry (PRSI) facilitates imaging the subsurface structure using passive sources but according to the general theory, the target needs to be illuminated equally from all directions to obtain a kinematically correct result. In practice, this requirement is almost impossible to meet which can introduce artefacts into the PRSI results. Our study was motivated by an unsuccessful attempt to image a couple of known dipping reflectors by applying PRSI to a data set of local microearthquakes clustering around the glacially triggered Burträsk fault. Dipping reflectors are a special case since they introduce a directionality into the seismic-interferometry problem that makes the results especially sensitive to the source azimuths. To investigate which source distributions are favourable in such a case and to study the range of artefacts occurring, we analyse a number of acoustic and elastic synthetic data sets calculated using a simple model of a dipping fault. Our results show that the main contribution for imaging such a fault with PRSI comes from sources in the hangingwall whereas contributions from the footwall are often weak and kinematically incorrect. The type and position of the occurring artefacts depend upon both the source azimuth and the type of modelling. In the acoustic case, the main artefact is a gently dipping reflection caused by insufficient cancellation of the direct reflection at the fault. In the elastic case, the artefacts are dominated by a set of both gently and steeply dipping reflections related to P–S converted waves. These artefacts are present even for ideal illumination due to the use of source records containing both P- and S-wave contributions. During interpretation, it is essential to be able to distinguish between physically meaningful reflections and artefacts. We found that both acoustic and elastic artefacts stack best at lower than expected normal moveout velocities. If data quality is insufficient for velocity analysis, our results can serve as a reference point for the interpretation of dipping features in PRSI images.
Two-Dimensional Gross–Pitaevskii Equation With Space-Time White Noise
Authors: de Bouard Anne , Debussche Arnaud , Fukuizumi Reika 
Published: April 2022

Abstract
In this paper we consider the two-dimensional stochastic Gross–Pitaevskii equation, which is a model to describe Bose–Einstein condensation at positive temperature. The equation is a complex Ginzburg–Landau equation with a harmonic potential and an additive space-time white noise. We study the global well posedness of the model using an inhomogeneous Wick renormalization due to the potential and prove the existence of an invariant measure.