bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of BWT variants for string collections
Authors: Cenzato Davide , Lipták Zsuzsanna 
Published: May 2024

Abstract

Motivation
In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows–Wheeler transform (BWT) in string processing, a number of dedicated tools have been developed for computing the BWT of string collections. While the focus has been on improving efficiency, both in space and time, the exact definition of the BWT used has not been at the center of attention. As we show in this paper, the different tools in use often compute non-equivalent BWT variants: the resulting transforms can differ from each other significantly, including the number r of runs, a central parameter of the BWT. Moreover, with many tools, the transform depends on the input order of the collection. In other words, on the same dataset, the same tool may output different transforms if the dataset is given in a different order.

Results
We studied 18 dedicated tools for computing the BWT of string collections and were able to identify 6 different BWT variants computed by these tools. We review the differences between these BWT variants, both from a theoretical and from a practical point of view, comparing them on eight real-life biological datasets with different characteristics. We find that the differences can be extensive, depending on the datasets, and are largest on collections of many similar short sequences. The parameter r, the number of runs of the BWT, also shows notable variation between the different BWT variants; on our datasets, it varied by a multiplicative factor of up to 4.2.

Availability and implementation
Source code and scripts to replicate the results and download the data used in the article are available at https://github.com/davidecenzato/BWT-variants-for-string-collections.
Pulse pressure modifies the association between diastolic blood pressure and decrease in kidney function: the Japan Specific Health Checkups Study
Authors: Tamaki Hiroyuki , Eriguchi Masahiro , Yoshida Hisako , Uemura Takayuki , Tasaki Hikari , Nishimoto Masatoshi , Kosugi Takaaki , Samejima Ken-ichi , Iseki Kunitoshi , Fujimoto Shouichi , Konta Tsuneo , Moriyama Toshiki , Yamagata Kunihiro , Narita Ichiei , Kasahara Masato , Shibagaki Yugo , Kondo Masahide , Asahi Koichi , Watanabe Tsuyoshi , Tsuruya Kazuhiko 
Published: May 2024

ABSTRACT

Background
Unlike systolic blood pressure (SBP), the prognostic value of diastolic blood pressure (DBP) in kidney function has not been established. We hypothesized that pulse pressure (PP), which is associated with arteriosclerosis, would affect the prognostic value of DBP.

Methods
This longitudinal study used data from the Japan Specific Health Checkups Study was conducted between 2008 and 2014. The participants were stratified into three PP subgroups (low PP ≤39, normal PP 40–59 and high PP ≥60 mmHg). The exposures of interest were SBP and DBP, and the association between SBP/DBP and kidney outcomes (30% decline in the estimated glomerular filtration rate from baseline) was examined in each PP subgroup using a Cox proportional hazards model.

Results
Among 725 022 participants, 20 414 (2.8%) developed kidney outcomes during a median follow-up period of 34.6 months. Higher SBP was consistently associated with a higher incidence of kidney outcome in all PP subgroups. Although DBP had a positive linear association with the incidence of kidney outcome in low- and normal-PP subgroups, both lower (≤60 mmHg) and higher (≥101 mmHg) DBP were associated with a higher incidence of kidney outcome in the high-PP subgroup, with a U-shaped curve. Hazard ratios (95% confidence intervals) of ≤60 mmHg (reference: 61–80 mmHg in normal-PP subgroup) and ≥101 mmHg were 1.26 (1.15–1.38) and 1.86 (1.62–2.14), respectively.

Conclusions
In this large population-based cohort, DBP was differently associated with kidney outcome by PP level; lower DBP was significantly associated with a higher incidence of kidney outcome in the high-PP subgroup but not in the low- and normal-PP subgroups.
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis
Authors: Wu Tao , Hou Yaopan , Xin Guanghao , Niu Jingyan , Peng Shanshan , Xu Fanfan , Li Ying , Chen Yuling , Yu Yifangfei , Zhang Huixue , Kong Xiaotong , Cao Yuze , Ning Shangwei , Wang Lihua , Hao Junwei 
Published: May 2024

Abstract
Multiple sclerosis (MS) is the most common inflammatory demyelinating disease of the central nervous system. ‘Omics’ technologies (genomics, transcriptomics, proteomics) and associated drug information have begun reshaping our understanding of multiple sclerosis. However, these data are scattered across numerous references, making them challenging to fully utilize. We manually mined and compiled these data within the Multiple Sclerosis Gene Database (MSGD) database, intending to continue updating it in the future. We screened 5485 publications and constructed the current version of MSGD. MSGD comprises 6255 entries, including 3274 variant entries, 1175 RNA entries, 418 protein entries, 313 knockout entries, 612 drug entries and 463 high-throughput entries. Each entry contains detailed information, such as species, disease type, detailed gene descriptions (such as official gene symbols), and original references. MSGD is freely accessible and provides a user-friendly web interface. Users can easily search for genes of interest, view their expression patterns and detailed information, manage gene sets and submit new MS-gene associations through the platform. The primary principle behind MSGD’s design is to provide an exploratory platform, aiming to minimize filtration and interpretation barriers while ensuring highly accessible presentation of data. This initiative is expected to significantly assist researchers in deciphering gene mechanisms and improving the prevention, diagnosis and treatment of MS.
Database URL: http://bio-bigdata.hrbmu.edu.cn/MSGD
Extensive coronary artery thrombosis in a paediatric patient with Kawasaki disease: a case report
Authors: Kasap Tilbe , Voges Inga , Rinne Katy , Langguth Patrick 
Published: May 2024

Abstract

Background
Kawasaki disease (KD) is a paediatric multi-system vasculitis. Mainly, the coronary arteries become affected due to acute inflammation and formation of coronary artery aneurysms (CAAs) may occur. As the size of the CAA increases, so does the risk of clinical complications and serious cardiac outcomes. These patients may experience life-threatening thrombotic coronary artery occlusion and myocardial ischaemia unless antiplatelet and anticoagulation therapy is not initiated in a timely manner.1

Case summary
This case report presents a 12-year-old patient with KD who developed CAAs in two coronary arteries despite initial administration of intravenous immunoglobulins and acetylsalicylic acid, followed by extensive thrombosis of both coronary arteries, although antithrombotic therapy was started after the diagnosis of CAAs.

Discussion
Our case is notable because of the severity of the clinical manifestation despite the administration of antiplatelet agents and anticoagulants. It could be speculated that the development of coronary thrombosis in this case might be strongly correlated with the late initiation of oral anticoagulation. The high-quality images of the affected coronary arteries in such a young patient could be of educational value.
Early structural valve deterioration of balloon expandable transcatheter aortic valve leaflets due to intrinsic and extrinsic nodular calcifications in a haemodialysis patient: a case report
Authors: Onishi Kyohei , Mizutani Kazuki , Sato Yu , Nakazawa Gaku 
Published: May 2024

Abstract

Background
Several reports have shown that transcatheter aortic valves are comparable in durability to surgical aortic valves. However, early structural valve deterioration (SVD) is rarely reported to occur, especially in haemodialysis patients.

Case summary
We present a case of rapidly progressive bioprosthetic aortic valve stenosis in a patient with end-stage renal disease secondary to diabetic nephropathy in an 83-year-old female admitted due to progressive dyspnoea and orthopnoea. A 23 mm sized SAPIEN3 bioprosthetic aortic valve showed normal function for the first year after transcatheter aortic valve implantation (TAVI), but then rapidly developed stenosis and required acute hospitalization for heart failure a year and a half after surgery. Emergent surgical aortic valve replacement with a 19 mm On-X valve (CryoLife, Kennesaw, GA, USA) was performed. Pathological examination of the explanted SAPIEN 3 valve demonstrated severely degenerated bioprosthetic pericardial leaflets with severe intrinsic and extrinsic nodular calcifications, which could limit the leaflet motion.

Discussion
There is a lack of reports on the long-term procedural outcomes of TAVI in haemodialysis patients. The development of SVD in patients undergoing dialysis is multifactorial and has yet to be fully elucidated. In the presented case, the removed TAVI valve had severe extrinsic calcified nodules alongside a fibrin thrombus. Considering these pathological findings, antithrombotic therapy to prevent fibrin thrombus from adhering to the TAVI valve may be important to avoid early SVD.
Cost-effectiveness analysis of a cardio-oncology rehabilitation framework compared to an exercise intervention for cancer survivors with high cardiovascular risk
Authors: Viamonte Sofia G , Tavares Aida , Alves Alberto J , Joaquim Ana , Vilela Eduardo , Capela Andreia , Costa Ana João , Duarte Barbara , Rato Nuno Dias , Afreixo Vera , Fontes Carvalho Ricardo , Santos Mário , Ribeiro Fernando 
Published: May 2024

Abstract

Aims
A cardio-oncology rehabilitation model among cancer survivors showed superior results compared with those of a community-based exercise intervention. However, questions remain about its cost-effectiveness. This study aims to assess the cost-effectiveness of a centre-based cardiac rehabilitation (CBCR) programme when compared to usual care encompassing a community-based exercise training (CBET), among cancer survivors with high cardiovascular risk.

Methods and results
The CORE study was a single-centre, prospective, randomized controlled trial; 80 adult cancer survivors with previous exposure to cardiotoxic cancer treatment and/or with previous cardiovascular disease were assigned (1:1 ratio) to an 8-week CBCR or CBET, twice/week. Cost-effectiveness was a pre-specified secondary endpoint. Outcomes included healthcare resource use and costs, quality-adjusted life-years (QALYs), and cost-effectiveness; the incremental cost-effectiveness ratio (ICER) was computed from a societal perspective. A total of 75 patients completed the study (CBCR n = 38; CBET n = 37). The CBCR group had a significantly higher cost per patient (477.76 ± 39.08€) compared to the CBET group (339.32 ± 53.88€), with a significant between-group difference of 138.44€ [95% confidence interval (CI), 116.82–160.05€, P &lt; 0.01]. A between-group difference of 0.100 points in QALYs was observed, favouring CBCR (95% CI, −0.163 to −0.037, P = 0.002). When CBCR was compared with CBET, the ICER was €1383.24 per QALY gained; at a willingness-to-pay threshold of €5000 per QALY, the probability of CBCR being cost-effective was 99.9% (95% CI, 99.4–100.0).

Conclusion
The CORE trial shows that CBCR is a cost-effective intervention in the management of cancer survivors with high cardiovascular risk, reinforcing the potential benefits of this multidisciplinary approach in supportive care of this specific subset of cancer patients.

Registration
ClinicalTrials.gov: NCT05132998
Atrial fibrillation is perpetuated by human heart secretome in ex-vivo langendorff-perfused hearts
Authors: Boegner M , Bock M , Huettemeister J , Jeising T , Schallopp L , Eggert-Doktor D , Falk V , Hindricks G , Gerds-Li J H , Hohendanner F 
Published: May 2024

Abstract

Introduction
Atrial fibrillation (AF) confers high morbidity and mortality, yet parts of the underlying pathophysiology remain elusive. Left atrial (LA) pressure is altered by the presence of AF and vice-versa. The cardiac secretome might be influenced by LA pressure and potentially alters the susceptibility of the atria to AF. We investigated the effect of the human cardiac secretome on atrial electrophysiology in a translational ex-vivo setting.

Methods
We obtained venous (coronary sinus) serum samples during AF and in sinus rhythm (SR) in patients hospitalized for pulmonary vein isolation (PVI). Moreover, LA tissue was collected from patients undergoing cardiac surgery and coronary sinus serum samples were collected before (CTRL) and after intraoperative volume challenge (VC). Single cardiomyocytes were isolated from human LA tissue and Ca2+ dependent excitation-contraction coupling (ECC) was studied using confocal line-scan imaging with CTRL or VC. Moreover, a modified Langendorff-Setup with the ability to monitor and control intra-cardiac pressure was utilized to perfuse mouse hearts with AF and SR serum. A multielectrode array (MEA) was placed on the epicardial aspect of the left atrium to measure electrical signals in a spatiotemporal fashion. External bipolar burst pacing protocols were applied to test AF inducibility.

Results
Ca2+ dependent ECC (i.e. Ca2+ amplitude and release) in human cardiomyocytes was unaltered with exposure to VC serum. Upon introducing a modified version of the Langendorff setup with the ability of linear pressure adjustment, a burst pacing protocol to test for AF inducibility was successfully implemented in mice atria. Atria perfused with human AF serum showed significantly increased AF inducibility as compared to SR serum. Moreover, both, total AF duration as well as number of AF episodes (i.e. AF burden) were increased in AF vs. SR serum upon several different pacing protocols.

Conclusion
Cardiac secretome during increased LA pressure had no significant effect on Ca2+ dependent ECC in human cardiomyocytes. However, secretome during AF conferred pro-arrhythmogenic properties as compared to SR, further strengthening the concept of "AF begets AF". Ongoing experiments test the hypothesis of potential differences in the multi-level omics profile of AF serum as the underlying mechanism.
The circadian pattern of atrial fibrillation onset
Authors: Van Den Broek M , Gottlieb L A , Vermeer J R , Overeem S , Dekker L R C 
Published: May 2024

Abstract

Background/Introduction
Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia affecting 2% of the population. Within the broad spectrum of AF symptomatology, there is a particular subset of patients that show a predominant or even exclusive nocturnal onset of paroxysmal AF.

Purpose
The aim of this study is to assess the timing of onset of AF in the 24-hour cycle and to assess whether a circadian rhythm is present in the onset of AF.

Methods
The MEDLINE, EMBASE, and CENTRAL databases, searched from inception to September 2023, provided 18 studies detailing the onset of AF in a 24-hour cycle. Patients had either paroxysmal or persistent AF. Studies performed in ICU populations (n=3) were omitted due to different triggers for AF. Time of AF onset was determined either by Cardiac Implantable Electronic Device (CIED) (n=5), Holter (n=7) or minute history taking (n=3).
The presence and statistical significance of a 24-hour periodicity is tested using the cosinor analysis: Y(t)= A ⋅ sin(2πft + α) + β where the amplitude, frequency, phase and error (A, f, α and β, respectively) are computed by single harmonic regression using a nonlinear least-squares method. Goodness of fit is estimated using R2, the statistical significance of the model is tested using a zero-amplitude test.

Results
The 15 studies included 2.080 patients with 11.886 onsets of AF. The blue bars in Figure 1 represent the total of AF onsets from all studies per hour. The pattern of onset AF can be approximated well by a single sine function (Onset(t)= 95.7915 ⋅ sin((2π ⋅ 0.0417 ⋅ t) – 1.8386) + 510.5500, R2 0.77, P = 0.03) with a 24-hour period, clearly establishing the 24-hour rhythmicity in the onset of AF (Figure 1, red line). Hours with significantly more onset of AF compared to the mean, assessed by residual Chi2 testing, are exclusively nocturnal (22.00-7.00, indicated by a moon symbol in Figure 1) while hours with significantly less onset are exclusively during daytime (7.00-22.00, indicated by a sun symbol in Figure 1).

Conclusion
Despite the potential limitations due to the methods used, such as arrhythmia discrimination in CIED-studies and asymptomatic episodes in case of history taking, the overall picture of predominance of nocturnal AF onset is clearly established. Multiple pathophysiological mechanisms might underlie this circadian pattern and nocturnal predominance, like obstructive sleep apnea and increased vagal tone, which should be subject of further research.time of onset of AF over a 24h period
Dietary sodium intake and atrial myopathy
Authors: Johnson L S , Lundeberg J E , Mcintyre W F , Conen D , Healey J S , Platonov P , Arnlov J , Engstrom G 
Published: May 2024

Abstract

Background
Diagnostic markers associated with atrial cardiomyopathy, a precursor state to atrial fibrillation (AF), include premature atrial complex (PACs) frequency, left atrial volume index (LAVi) and p-wave indices. Life-style factors associated with atrial myopathy markers are insufficiently studied. Sodium intake is a modifiable risk factor for hypertension, cardiovascular disease and AF.

Purpose
We aimed to study the association between sodium intake and atrial myopathy markers in the population-based multicenter Swedish CArdioPulmonary bioImage Study.

Methods
We included 5,309 randomly invited 50–65-year-olds at the Malmö (n=1,125,) and Uppsala sites (n=4,184) without AF who had contributed a 24hECG and a fasting morning urine sample, from which daily sodium intake was estimated using the Kawasaki formula. At the Malmö site resting ECGs from which P-wave indices could be measured were available in 1,066 individuals, and LAVi was available in a random subsample (n=357). The association between sodium intake and atrial myopathy markers was modeled adjusted for age, sex, body mass index, smoking, systolic blood pressure, antihypertensive treatment, coronary artery disease, and heart failure using negative binomial regression for PAC frequency, linear regression for P-wave duration and LAVi and logistic regression for P-wave terminal force in V1, all using sodium intake as a continuous variable and strata at &lt;2, 2.0-2.99g, 3.0-3.99g, 4.0-4.99g and ≥5 g/day, with 3.0-3.99 as the reference category. We also modeled the association between sodium intake and PACs using restricted cubic splines.

Results
The mean age was 58.1 (±4.1) years, and 52.7% were female. The mean estimated sodium intake was 3.3 (±1.4) g/day. Mean 24h PAC count was 27, 4.7% had ≥500 PACs. High sodium intakes were associated with increased PAC frequency, of 14% (95% confidence interval (CI 1-29% p=0.03)) for 4.0-4.99g/day and 25% (95%CI 8-45%, p=0.002) for intakes ≥5.0g/day, compared to sodium intakes of 3.0-3.99 g/day. There was no significant association between low sodium intakes (&lt;3.0 g/day) and PACs, Figure 1. Sodium intakes of 4.0-4.99 g/day were associated with increased P-wave duration, ß-coefficient 2.4 (95%CI 0.3-4.1, p=0.03), compared to 3.0-3.99g/day, but there was no association between sodium intakes and LAVi, or P-wave terminal force in V1, either as a continuous variable or in strata.

Conclusion
High dietary sodium intake is associated with PAC frequency, a known prediction of AF and stroke. Whether reduced sodium diets could reduce PAC frequency, and whether that would impact AF and stroke risk needs further study.Sodium intake and PAC frequency
Quality of life when switching from a vitamin K antagonist to non-vitamin K antagonist oral anticoagulation in frail older patients with atrial fibrillation
Authors: Van Doorn S , Joosten L P T , Kohlen B T G , Nierman M C , Koek H L , Hemels M E W , Huisman M V , Kruip M , Faber L M , Wiersma N M , Buding W F , Adriaansen H J , Rutten F H , Geersing G J 
Published: May 2024

Abstract

Background
Many older patients with atrial fibrillation (AF) are frail, putting them at high risk of adverse outcomes including mortality, hospitalization, functional decline, and dependency on others. In this special population, management strategies – such as anticoagulation for stroke prevention – need special consideration. To what extent the type of anticoagulation influences the quality of life (QoL) in frail patients with AF is unclear.

Purpose
To assess QoL in frail older patients with AF switching from a vitamin K antagonist (VKA) to a non-VKA oral anticoagulant (NOAC), as compared to patients continuing a VKA.

Methods
We used data from the FRAIL-AF trial that randomized frail older AF patients between continuing VKA treatment or switching to any NOAC. At baseline, after six months and twelve months of follow-up, QoL was assessed using the EQ-5D-5L questionnaire. For every timepoint, the mean EQ-5D-5L score was calculated with corresponding 95% confidence intervals (CI), missing data were imputed using ten-fold multiple imputation. Absolute differences in EQ-5D-5L score were calculated between patients switching to a NOAC and patients continuing with a VKA, with corresponding 95% CI. The distribution of the scores on each domain of the EQ-5D-5L was compared using a chi-square test.

Results
In total 661 patients continued VKA treatment, and 663 switched to a NOAC. The median age was 82.2 years (interquartile range (IQR) 78.7 – 86.5), 61.3% were male. Major bleeding or clinically relevant non-major bleeding occurred in 101 patients (17.8 per 100 person-years) switching to NOAC therapy, and 62 patients (10.5 events per 100 person-years) continuing with a VKA (hazard ratio 1.69, 95% confidence interval 1.23 – 2.32). Mortality occurred in 44 and 46 patients, respectively. In 25 patients data was missing. Table 1 shows the mean EQ-5D-5L scores at baseline, at 6 months follow-up and at 12 months follow-up. Scores were similar between patients switching to NOAC treatment or continuing with a VKA and did not change significantly during 12 months follow-up. Table 2 shows the distribution of the scores on all domains of the EQ-5D-5L, with no significant differences between groups.

Conclusion
Switching from a VKA to a NOAC in frail older patients with AF was associated with an increased risk of bleeding, yet without any effect on overall and different domains of QoL.