bluuebunny/crossref_metadata_2025_split huggingface dataset:
HQAlign: aligning nanopore reads for SV detection using current-level modeling
Authors: Joshi Dhaivat , Diggavi Suhas , Chaisson Mark J P , Kannan Sreeram 
Published: September 2023

Abstract

Motivation
Detection of structural variants (SVs) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate alignment of these long reads play an important role in identifying novel SVs. Long-read sequencers, such as nanopore sequencing, can address this problem by providing very long reads but with high error rates, making accurate alignment challenging. Many errors induced by nanopore sequencing have a bias because of the physics of the sequencing process and proper utilization of these error characteristics can play an important role in designing a robust aligner for SV detection problems. In this article, we design and evaluate HQAlign, an aligner for SV detection using nanopore sequenced reads. The key ideas of HQAlign include (i) using base-called nanopore reads along with the nanopore physics to improve alignments for SVs, (ii) incorporating SV-specific changes to the alignment pipeline, and (iii) adapting these into existing state-of-the-art long-read aligner pipeline, minimap2 (v2.24), for efficient alignments.

Results
We show that HQAlign captures about 4%–6% complementary SVs across different datasets, which are missed by minimap2 alignments while having a standalone performance at par with minimap2 for real nanopore reads data. For the common SV calls between HQAlign and minimap2, HQAlign improves the start and the end breakpoint accuracy by about 10%–50% for SVs across different datasets. Moreover, HQAlign improves the alignment rate to 89.35% from minimap2 85.64% for nanopore reads alignment to recent telomere-to-telomere CHM13 assembly, and it improves to 86.65% from 83.48% for nanopore reads alignment to GRCh37 human genome.

Availability and implementation
https://github.com/joshidhaivat/HQAlign.git.
East is East? Beyond the Global North and Global South in Criminology
Authors: Piacentini Laura , Slade Gavin 
Published: September 2023

Abstract
This paper identifies an absence in currently constituted criminological discourse on the Global North and Global South. This absence is the Global East. The Global East is not a defined region but a relation of betweenness, geographically and geo-politically, within and between the South and North, representing peoples from countries and societies which fit imperfectly into a North/South binary. We focus on the Eastern European and Eurasian regions to demonstrate this point, concentrating specifically on its omission in punishment and society studies. Our paper makes a positive argument for the Global East concept, disrupting the assumed categories of North and South and producing a strategic essentialism to help better represent peoples thus far overlooked in southern criminology.
Bedside Intestinal Ultrasound Performed in an Inflammatory Bowel Disease Urgent Assessment Clinic Improves Clinical Decision-Making and Resource Utilization
Authors: St-Pierre Joëlle , Delisle Maxime , Kheirkhahrahimabadi Hengameh , Goodsall Thomas M , Bryant Robert V , Christensen Britt , Vaughan Rose , Al-Ani Aysha , Ingram Richard J M , Heatherington Joan , Carter Dan , Lu Cathy , Ma Christopher , Novak Kerri L 
Published: September 2023

AbstractBackgroundPatients with inflammatory bowel disease (IBD) require accessible, timely, and noninvasive strategies to monitor disease. The aim was to assess the integration of intestinal ultrasound (IUS) on decision-making and endoscopy utilization in a standardized care pathway.MethodsThis prospective, multicenter, international, observational cohort study included patients seen within a centralized model for IBD care was conducted during the COVID pandemic. Patients were evaluated with IUS alone or in combination with an in-clinic, unsedated sigmoidoscopy. Demographic, clinical, laboratory, and imaging data, clinical decisions, and need for urgent endoscopy, hospitalization, and surgeries were recorded.ResultsOf the 158 patients included, the majority had an established diagnosis of Crohn’s disease (n = 123, 78%), and 47% (n = 75) of patients were on biologic therapy. IUS identified active inflammation in 65% (n = 102) of patients, and strictures in 14% (n = 22). Fecal calprotectin levels correlated with inflammation detected on IUS (median of 50 μg/g [Q1–Q3: 26–107 μg/g] without inflammation and 270 μg/g [Q1–Q3: 61–556 μg/g] with inflammation; p = 0.0271). In the majority of patients, clinical assessment with IUS led to an acute change in IBD-specific medications (57%, n = 90) and avoided or delayed the need for urgent endoscopy (85%, n = 134). Four patients were referred for urgent surgical consultation.ConclusionsPoint-of-care IUS used in a flare clinic pathway is a useful strategy to improve effective IBD care delivery and to assist in therapeutic management decisions, in many cases avoiding the acute need for endoscopy.
Prevalence and severity of abdominal bloating in patients with gastroesophageal reflux disease
Authors: Shacker Mark , Latorre-Rodríguez Andrés R , Mittal Sumeet K 
Published: September 2023

Summary
Abdominal bloating (AB) is a common symptom among patients with gastroesophageal reflux disease (GERD); however, in clinical practice, its prevalence is likely underestimated due to the lack of objective tools to measure its frequency and severity. It is associated with dissatisfaction and worse quality of life, but data on its prevalence before and after mechanical control of GERD (i.e. fundoplication, magnetic sphincter augmentation, and antireflux mucosectomy) are lacking. To assess and determine the pre- and postoperative prevalence and severity of AB among patients with GERD, we conducted a structured literature search using MeSH and free-text terms in MEDLINE (via Pubmed), EMBASE, and Taylor & Francis Online between January 1977 and October 2022. Fifteen articles reporting the prevalence or severity of AB using quality-of-life questionnaires before or after antireflux surgery (ARS) were included. Overall, a high prevalence of AB before ARS was found. A decline in the prevalence and severity of AB was documented postoperatively in most cases independent of the surgical approach. Among surgical approaches, a complete fundoplication had the highest reported postoperative AB. Overall, patients reported less severe and less frequent AB after ARS than before. The traditional belief that postoperative bloating is a sequela of ARS should be reevaluated.
A multimodality approach to a rare case of ruptured sinus of Valsalva aneurysm with tricuspid valve involvement: a case report
Authors: Wilson Vindhya C , Jacob Anita , van der Walt Liezl M , Sasse Alexander 
Published: September 2023

Abstract

Background
Ruptured sinus of Valsalva aneurysm is a rare disease entity that is potentially life-threatening if left untreated. While imaging is the mainstay of diagnosis, resultant tricuspid valve involvement may mask typical findings providing a diagnostic challenge. Disruption of the tricuspid valve during ruptured sinus of Valsalva aneurysm with consequent tricuspid regurgitation is rare and infrequently described in the literature. Description of the utility and limitations of multimodality imaging in this scenario is equally scarce.

Case summary
We review the case of a young patient presenting with acute ruptured sinus of Valsalva aneurysm and involvement of the tricuspid valve on a background of severe aortic regurgitation requiring multimodality imaging for diagnostic and pre-surgical assessment.

Discussion
In young patients presenting with acute decompensation and pre-existing bicuspid aortic valve regurgitation, an increased clinical suspicion of a sinus of Valsalva aneurysm rupture is imperative. Doppler and 3D transoesophageal echocardiographic assessment should be pursued to characterize abnormal flows and clarify aetiology in the context of tricuspid involvement and resultant tricuspid regurgitation. A large-volume left–right shunt in proximity to the tricuspid annulus may result in disproportionately severe tricuspid regurgitation in the absence of annular disruption due to forced systolic opening of the leaflets by shunt flow and ‘windsock’ prolapse. Multimodality imaging can be essential in these cases to adequately assess the extent of the ruptured sinus of Valsalva aneurysm and overcome limitations of single modality imaging.
Usefulness of catheter pressure measurement using the Navvus RXi system to determine left ventricular outflow tract obstruction and aortic stenosis severity: a case report
Authors: Yashige Masaki , Zen Kan , Kataoka Eisuke , Matoba Satoaki 
Published: September 2023

Abstract

Background
Left ventricular outflow tract obstruction (LVOTO) sometimes presents with aortic stenosis (AS). Echocardiography is used to assess the diagnosis and severity of LVOTO or AS. However, LVOTO is one of the conditions that makes AS assessment difficult, and catheter pressure measurement is frequently useful in such cases.

Case summary
An 84-year-old female patient presented with New York Heart Association functional Class III dyspnoea. Transthoracic echocardiography revealed LVOTO caused by upper septal hypertrophy, mitral valve systolic anterior motion with moderate mitral regurgitation, and a highly calcified aortic valve, which suggested the possibility of severe AS. The continuous Doppler echocardiography revealed a late-systolic peaking dagger-shaped profile with a peak jet velocity of 5.6 m/s. Cardiac catheterization was performed to determine the contribution of AS or LVOTO to her symptoms. Catheter pressures were measured at the ascending aorta (using a coronary catheter) and the LV (using the Navvus RXi system). The initial mean pressure gradient between the apex of the LV, just below the aortic valve and aorta, was measured at 65 and 25 mmHg, respectively. The mean pressure gradient between the apex and the aorta decreased from 65 to 40 mmHg after a 50 mg disopyramide administration. Oral medication therapy effectively stabilized her symptom after catheterization.

Discussion
To the best of our knowledge, this is the first reported case of assessing the severity of LVOTO and AS using the Navvus RXi system. Catheter pressure measurement using the Navvus RXi system is a useful method of determining the severity of LVOTO and AS.
Unintended Consequences of Central Bank Lending in Financial Crises
Authors: van der Kwaak Christiaan 
Published: September 2023

Abstract
I investigate the macroeconomic impact of central bank funding becoming a more attractive funding source to financial intermediaries in times of crisis. I show that the requirement to pledge collateral has a contractionary effect on private credit, everything else equal, and thereby reduces the expansionary effect that such lending otherwise has. I use an estimated New Keynesian model with financial frictions to show that the collateral effect explains the limited growth of Italian banks’ private credit in response to the European Central Bank’s three-year longer-term refinancing operations. Finally, I explore whether changes in lending policy can offset the cumulative negative effects from the collateral effect.
The effect of cumulative childhood exposure to neighbourhood socioeconomic disadvantage on school performance—a register-based study on neighbourhoods, schools, and siblings
Authors: Tarkiainen Lasse , Kemppainen Teemu , Lahtinen Hannu , Bernelius Venla , Martikainen Pekka 
Published: September 2023

Abstract
Several studies show that exposure to neighbourhood disadvantage predicts poorer educational outcomes among adolescents. Selective sorting into neighbourhoods, other unobserved childhood family characteristics, and failing to account for other relevant social contexts such as schools inhibit strong causal inference from the associations reported in previous studies. Based on longitudinal register data on the total population of Finnish children in major cities, we studied the extent to which variation in grade point average (GPA) was attributable to schools, neighbourhoods, and families. We also sought to determine whether exposure to neighbourhood disadvantage predicted GPA after accounting for non-random selection into neighbourhoods by comparing siblings with differential exposure to neighbourhoods. Overall, we observed no effect of neighbourhood disadvantage on GPA after accounting for observed and unobserved family characteristics in the general population. However, we did observe a non-negligible but not statistically significant effect of neighbourhood disadvantage among children of parents with only basic education. Family factors accounted for most of the variation in GPA, and only around 1 per cent of the variance was attributable to the neighbourhood. This weak relevance of the neighbourhood to educational outcomes may reflect the success of educational and other social policies limiting the emergence of neighbourhood effects.
Atrial fibrillation cryoablation is an effective day case treatment: the UK PolarX vs. Arctic Front Advance experience
Authors: Honarbakhsh Shohreh , Martin Claire A , Mesquita Joao , Herlekar Rahul , Till Richard , Srinivasan Neil T , Duncan Edward , Leong Fong , Dulai Rajdip , Veasey Rick , Panikker Sandeep , Paisey John , Ramgopal Balasubramanian , Das Moloy , Ahmed Wissam , Sahu Jonathan , Earley Mark J , Finlay Malcolm C , Schilling Richard J , Hunter Ross J 
Published: September 2023

Abstract

Aims
Pulmonary vein isolation (PVI) is the cornerstone of catheter ablation for atrial fibrillation (AF). There are limited data on the PolarX Cryoballoon. The study aimed to establish the safety, efficacy, and feasibility of same day discharge for Cryoballoon PVI.

Methods and results
Multi-centre study across 12 centres. Procedural metrics, safety profile, and procedural efficacy of the PolarX Cryoballoon with the Arctic Front Advance (AFA) Cryoballoon were compared in a cohort large enough to provide definitive comparative data. A total of 1688 patients underwent PVI with cryoablation (50% PolarX and 50% AFA). Successful PVI was achieved with 1677 (99.3%) patients with 97.2% (n = 1641) performed as day case procedures with a complication rate of &lt;1%. Safety, procedural metrics, and efficacy of the PolarX Cryoballoon were comparable with the AFA cohort. The PolarX Cryoballoon demonstrated a nadir temperature of −54.6 ± 7.6°C, temperature at 30 s of −38.6 ± 7.2°C, time to −40°C of 34.1 ± 13.7 s, and time to isolation of 49.8 ± 33.2 s. Independent predictors for achieving PVI included time to reach −40°C [odds ratio (OR) 1.34; P &lt; 0.001] and nadir temperature (OR 1.24; P &lt; 0.001) with an optimal cut-off of ≤34 s [area under the curve (AUC) 0.73; P &lt; 0.001] and nadir temperature of ≤−54.0°C (AUC 0.71; P &lt; 0.001), respectively.

Conclusions
This large-scale UK multi-centre study has shown that Cryoballoon PVI is a safe, effective day case procedure. PVI using the PolarX Cryoballoon was similarly safe and effective as the AFA Cryoballoon. The cryoablation metrics achieved with the PolarX Cryoballoon were different to that reported with the AFA Cryoballoon. Modified cryoablation targets are required when utilizing the PolarX Cryoballoon.
Insight into the relationship between resting heart rate and atrial fibrillation: a Mendelian randomization study
Authors: Klevjer Marie , Rasheed Humaira , Romundstad Pål R , Madssen Erik , Brumpton Ben M , Bye Anja 
Published: September 2023

Abstract

Aims
A low resting heart rate (RHR) implies a more efficient heart function and a lower risk of cardiovascular disease. However, observational studies have reported a U-shaped association between RHR and atrial fibrillation (AF). In contrast, Mendelian randomization (MR) studies have found an inverse causal association between RHR and AF. Hence, the causal nature of the relationship is not clear. The aim is to investigate the causal association and its shape between RHR on AF using linear and non-linear MR (NLMR).

Methods and results
Linear and non-linear MR were performed on individual-level data in the Trøndelag Health Study (HUNT) and UK Biobank (UKB). HUNT consists of 69 155 individuals with 7,062 AF cases, while UKB provides data on 431 852 individuals with 20 452 AF cases. The linear MR found an inverse relationship between RHR and AF with an OR = 0.95 [95% confidence interval (CI): 0.93–0.98] and OR = 0.96 (95% CI: 0.95–0.97) per unit decrease in RHR in HUNT and UKB, respectively. The NLMR was supportive of an inverse linear relationship in both HUNT and UKB for RHR values &lt;90 beats per minute (bpm). Several sensitivity analyses were also consistent.

Conclusion
In contrast with the current observational knowledge of RHR and AF, an inverse causal association between RHR and AF was demonstrated in both linear and non-linear MR for RHR values up to 90 bpm. Further exploring the underlying mechanisms of the genetic instrument for RHR may shed light on whether pleiotropy is biasing this association.
Long-term evolution of antibiotic tolerance in Pseudomonas aeruginosa lung infections
Authors: Ghoul Melanie , Andersen Sandra B , Marvig Rasmus L , Johansen Helle K , Jelsbak Lars , Molin Søren , Perron Gabriel , Griffin Ashleigh S 
Published: September 2023

Abstract
Pathogenic bacteria respond to antibiotic pressure with the evolution of resistance but survival can also depend on their ability to tolerate antibiotic treatment, known as tolerance. While a variety of resistance mechanisms and underlying genetics are well characterized in vitro and in vivo, an understanding of the evolution of tolerance, and how it interacts with resistance in situ is lacking. We assayed for tolerance and resistance in isolates of Pseudomonas aeruginosa from chronic cystic fibrosis lung infections spanning up to 40 years of evolution, with 3 clinically relevant antibiotics: meropenem, ciprofloxacin, and tobramycin. We present evidence that tolerance is under positive selection in the lung and that it can act as an evolutionary stepping stone to resistance. However, by examining evolutionary patterns across multiple patients in different clone types, a key result is that the potential for an association between the evolution of resistance and tolerance is not inevitable, and difficult to predict.
Host learning selects for the coevolution of greater egg mimicry and narrower antiparasitic egg-rejection thresholds
Authors: Xu Kuangyi , Servedio Maria R , Winnicki Sarah K , Moskat Csaba , Hoover Jeffrey P , Turner Abbigail M , Hauber Mark E 
Published: September 2023

Abstract
Egg rejection is an effective and widespread antiparasitic defense to eliminate foreign eggs from the nests of hosts of brood parasitic birds. Several lines of observational and critical experimental evidence support a role for learning by hosts in the recognition of parasitic versus own eggs; specifically, individual hosts that have had prior or current experience with brood parasitism are more likely to reject foreign eggs. Here we confirm experimentally the role of prior experience in altering subsequent egg-rejection decisions in the American robin Turdus migratorius, a free-living host species of an obligate brood parasite, the brown-headed cowbird Molothrus ater. We then model the coevolutionary trajectory of both the extent of mimicry of host eggs by parasitic eggs and the host’s egg rejection thresholds in response to an increasing role of learning in egg recognition. Critically, with more learning, we see the evolution of both narrower (more discriminating) rejection thresholds in hosts and greater egg mimicry in parasites. Increasing host clutch size (number of eggs/nest) and increasing parasite load (parasitism rate) also have narrowing effects on the egg-rejection threshold. Together, these results suggest that learning from prior experience with egg rejection may play an important role in the coevolution of egg-mimetic lineages of brood parasites and the refined egg rejection defenses of hosts.
Source-encoded waveform inversion in the Northern Hemisphere
Authors: Cui Congyue , Bachmann Etienne , Peter Daniel , Liu Zhaolun , Tromp Jeroen 
Published: September 2023

SUMMARY
We use source-encoded waveform inversion to image Earth’s Northern Hemisphere. The encoding method is based on measurements of Laplace coefficients of stationary wavefields. By assigning to each event a unique frequency, we compute Fréchet derivatives for all events simultaneously based on one ‘super’ forward and one ‘super’ adjoint simulation for a small fraction of the computational cost of classical waveform inversion with the same data set. No cross-talk noise is introduced in the process, and the method does not require all events to be recorded by all stations. Starting from global model GLAD_M25, we performed 100 conjugate gradient iterations using a data set consisting of 786 earthquakes recorded by 9846 stations. Synthetic inversion tests show that we achieve good convergence based on this data set, and we see a consistent misfit reduction during the inversion. The new model, named SE100, has much higher spatial resolution than GLAD_M25, revealing details of the Yellowstone and Iceland hotspots, subduction beneath the Western United States and the upper mantle structure beneath the Arctic Ocean.
Development and validation of the Health Literacy Scale for community-dwelling older adults in Taiwan
Authors: Kuo Shu-Hsin , Liang Ming-Hao 
Published: September 2023

Abstract
Health literacy is a crucial factor in determining one’s health outcomes. Individuals with high health literacy possess the ability to access, comprehend, evaluate, and utilize health information to maintain, enhance, and advocate for good health. This study aimed to develop and validate a tool called the Health Literacy Questionnaire for Older Adults (HLQ-OA) specifically designed to assess the health literacy of community-dwelling older adults in Taiwan. The development of the HLQ-OA occurred in two phases. Firstly, a systematic literature review was conducted, followed by the evaluation of content validity and face validity through expert and older adult assessments. Subsequently, a cross-sectional study was carried out, involving a convenient sample of 481 older adults from community-dwelling long-term care stations. The final version of the HLQ-OA comprised 16 items that assessed four competencies associated with accessing, understanding, appraising, and applying health-related information. The HLQ-OA demonstrated excellent internal consistency, with an overall Cronbach’s α coefficient of 0.94. Additionally, the model fit indices indicated an acceptable fit: RMSEA = 0.046, GFI = 0.909, CFI = 0.945, TLI = 0.939. Furthermore, a high correlation was observed between the HLQ-OA and the HL-SF12 (r = 0.832). These findings support the reliability and validity of the HLQ-OA as a tool for assessing the health literacy of older adults. In conclusion, the HLQ-OA is a reliable and valid instrument that can be effectively utilized to measure the health literacy levels of older adults.
Why we need weather forecast analogues for marine ecosystems
Authors: Link J S , Thur S , Matlock G , Grasso M 
Published: September 2023

Abstract
Marine ecosystems face many consequential pressures. Yet, we lack an integrative and predictive capacity to understand how marine ecosystems will respond to the cumulative impacts of these pressures, including climate change. It is not enough to detect responses after the fact; it has become imperative to know in advance where major biological resources or hazards will occur, when they will peak, and how that will impact economic performance. Although forecasts exist for some components of marine ecosystems, these are disparate and suffer from a lack of coordination. There is a need for coordinated, cross-ecosystem scale, integrated, marine ecosystem predictions and synthesis products. The value proposition relative to the blue economy is quite high, positively influencing billions if not trillions of marine sector dollars.