bluuebunny/crossref_metadata_2025_split huggingface dataset:
EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data
Authors: Li Sijie , Li Yuxi , Sun Yu , Li Yaru , Chen Xiaoyang , Tang Songming , Chen Shengquan 
Published: April 2024

Abstract

Summary
Recent technical advancements in single-cell chromatin accessibility sequencing (scCAS) have brought new insights to the characterization of epigenetic heterogeneity. As single-cell genomics experiments scale up to hundreds of thousands of cells, the demand for computational resources for downstream analysis grows intractably large and exceeds the capabilities of most researchers. Here, we propose EpiCarousel, a tailored Python package based on lazy loading, parallel processing, and community detection for memory- and time-efficient identification of metacells, i.e. the emergence of homogenous cells, in large-scale scCAS data. Through comprehensive experiments on five datasets of various protocols, sample sizes, dimensions, number of cell types, and degrees of cell-type imbalance, EpiCarousel outperformed baseline methods in systematic evaluation of memory usage, computational time, and multiple downstream analyses including cell type identification. Moreover, EpiCarousel executes preprocessing and downstream cell clustering on the atlas-level dataset with 707 043 cells and 1 154 611 peaks within 2 h consuming &lt;75 GB of RAM and provides superior performance for characterizing cell heterogeneity than state-of-the-art methods.

Availability and implementation
The EpiCarousel software is well-documented and freely available at https://github.com/biox-nku/epicarousel. It can be seamlessly interoperated with extensive scCAS analysis toolkits.
Meta-analysis of transjugular intrahepatic portosystemic shunt creation with or without intravascular ultrasound guidance
Authors: Yu Qian , Ahmed Osman , Gutti Subhash , Iyer Deepak , Kwak Daniel , Ahmed Syed Samaduddin , Said Adam , Angle J Fritz , Navuluri Rakesh , Lorenz Jonathan M , Patel Mikin 
Published: April 2024

Abstract

Objective
To conduct a meta-analysis to assess the efficacy of intravascular ultrasound (IVUS) during transjugular intrahepatic portosystemic shunt (TIPS) creation.

Methods
MEDLINE and Embase databases were queried until July 2022 for comparative studies reporting procedure metrics for TIPS creation with or without IVUS guidance. Meta-analysis was performed with random-effects modelling for total procedural time, time to portal venous access, fluoroscopy time, iodinated contrast volume use, air kerma, dose area product, and number of needle passes. Intraoperative procedure-related complications were also reviewed.

Results
Of 95 unique records initially identified, 6 were eligible for inclusion. A total of 194 and 240 patients underwent TIPS with and without IVUS guidance. Pooled analyses indicated that IVUS guidance was associated with reduced total procedure time (SMD −0.76 [95% CI −1.02, −0.50] P &lt; .001), time to portal venous access (SMD −0.41 [95% CI −0.67, −0.15] P = .002), fluoroscopy time (SMD, −0.54 [95% CI −1.02, −0.07]; P = .002), contrast volume use (SMD, −0.89 [95% CI −1.16, −0.63]; P &lt; .001), air kerma (SMD, −0.75 [95% CI −1.11, −0.38]; P &lt; .001) and dose area product (SMD, −0.98 [95% CI −1.77, −0.20]; P = .013). A total of 4.2 and 7.8 needle passes were required in the IVUS and non-IVUS group, respectively (SMD, −0.60 [95% CI −1.42, 0.21]; P = .134). Pooled complication rates were 15.2% (12/79) and 21.4% (28/131), respectively.

Conclusion
IVUS guidance during TIPS creation improves procedural metrics including procedural time, contrast usage, and radiation exposure.

Advances in Knowledge
(1) The use of IVUS during TIPS is associated with shorter procedural time, lower contrast usage, and radiation exposure. (2)The use of IVUS is not associated with higher complication rates.
Safety and efficacy of cryoablation of soft-tissue tumours: a systematic review
Authors: Bodard Sylvain , Marcelin Clement , Kastler Adrian , Dimopoulos Platon M , Petre Elena N , Frandon Julien , Razakamanantsoa Leo , Cornelis Francois H 
Published: April 2024

Abstract

Objectives
To assess the safety and efficacy of percutaneous cryoablation (CA) of soft-tissue tumours [desmoid tumours (DTs), vascular malformations (VMs), and abdominal wall endometriosis (AWE)].

Methods
This systematic review of studies published before January 2024 encompassed a detailed analysis of CA techniques and technical aspects for the treatment of soft-tissue tumours. Data concerning CA efficacy, complication rates, and other relevant metrics were extracted and included for analysis.

Results
The analysis included 27 studies totalling 554 CA procedures. For DT (13 studies, 393 sessions), CA showed an average pain reduction of 79 ± 17% (range: 57-100) and a lesion volume decrease of 71.5 ± 9.8% (range: 44-97). VM (4 studies, 58 sessions) had a 100% technical success rate and an average pain reduction of 72 ± 25% (range: 63-85). The average pain reduction for AWE (6 studies, 103 sessions) was 82 ± 13% (range: 62-100). Overall, the complication rate for CA was low, with minor adverse events (AEs) in about 20% of patients and major events in less than 5% of patients.

Conclusions
Showing substantial efficacy in pain reduction and lesion volume decrease, as well as low incidence of severe AE, CA presents as a highly effective and safe alternative for the treatment of soft-tissue tumours.

Advances in knowledge
CA is effective and safe in treating soft-tissue tumours, particularly DT, VM, and AWE.
Neurocomputational model of compulsivity: deviating from an uncertain goal-directed system
Authors: Kim Taekwan , Lee Sang Wan , Lho Silvia Kyungjin , Moon Sun-Young , Kim Minah , Kwon Jun Soo 
Published: April 2024

Abstract
Despite a theory that an imbalance in goal-directed versus habitual systems serve as building blocks of compulsions, research has yet to delineate how this occurs during arbitration between the two systems in obsessive-compulsive disorder. Inspired by a brain model in which the inferior frontal cortex selectively gates the putamen to guide goal-directed or habitual actions, this study aimed to examine whether disruptions in the arbitration process via the fronto-striatal circuit would underlie imbalanced decision-making and compulsions in patients.
Thirty patients with obsessive-compulsive disorder [mean (standard deviation) age = 26.93 (6.23) years, 12 females (40%)] and 30 healthy controls [mean (standard deviation) age = 24.97 (4.72) years, 17 females (57%)] underwent functional MRI scans while performing the two-step Markov decision task, which was designed to dissociate goal-directed behaviour from habitual behaviour. We employed a neurocomputational model to account for an uncertainty-based arbitration process, in which a prefrontal arbitrator (i.e. inferior frontal gyrus) allocates behavioural control to a more reliable strategy by selectively gating the putamen. We analysed group differences in the neural estimates of uncertainty of each strategy. We also compared the psychophysiological interaction effects of system preference (goal-directed versus habitual) on fronto-striatal coupling between groups. We examined the correlation between compulsivity score and the neural activity and connectivity involved in the arbitration process.
The computational model captured the subjects’ preferences between the strategies. Compared with healthy controls, patients had a stronger preference for the habitual system (t = −2.88, P = 0.006), which was attributed to a more uncertain goal-directed system (t = 2.72, P = 0.009). Before the allocation of controls, patients exhibited hypoactivity in the inferior frontal gyrus compared with healthy controls when this region tracked the inverse of uncertainty (i.e. reliability) of goal-directed behaviour (P = 0.001, family-wise error rate corrected). When reorienting behaviours to reach specific goals, patients exhibited weaker right ipsilateral ventrolateral prefronto-putamen coupling than healthy controls (P = 0.001, family-wise error rate corrected). This hypoconnectivity was correlated with more severe compulsivity (r = −0.57, P = 0.002).
Our findings suggest that the attenuated top-down control of the putamen by the prefrontal arbitrator underlies compulsivity in obsessive-compulsive disorder. Enhancing fronto-striatal connectivity may be a potential neurotherapeutic approach for compulsivity and adaptive decision-making.
Catalyzing communities of research rigour champions
Authors: Brumback Audrey C , Ngiam William X Q , Lapato Dana M , Allison David B , Daniels Christin L , Dougherty Michael , Hazlett Haley F , Kerr Kara L , Pusek Susan , Rethlefsen Melissa L , Schrag Naomi ,   NINDS workshop Catalyzing Communities of Research Rigor Champions, Abrams Mathew , Adams Eryn , Allison David B , Alperin Juan Pablo , Bosch Gundula , Brumback Audrey , Centola Damon , Coolen Lique , Clyburne-Sherin April , Croker Jennifer , Crüwell Sophia , Daniels Christin , DeBolt Michaela , Dirnagl Ulrich , Dougherty Michael , Errington Timothy , Franko Maryrose , Hatch Anna , Jordan Kari , Kerr Kara , Kilicoglu Halil , Kording Konrad , Lapato Dana , Lee Carole , Lowenberg Daniella , Lundwall Rebecca , MacLeod Malcolm , Maldonaldo-Vlaar Carmen , Munafo Marcus , Nelson Alexandra , Nelson Nicole , Ngiam William , Nusser Sarah , Peng Roger , Polka Jessica , Poldrack Russell , Puri Ishwar , Pusek Susan , Raamana Pradeep Reedy , Reinagel Pamela , Rethlefsen Melissa , Ritt Jason , Ross Joseph , Salt Karen , Schrag Naomi , Steckler Thomas , Weissgerber Tracey , Whyte Alonzo , Williams Jason , Ye Hao 
Published: April 2024

Abstract
The biomedical sciences must maintain and enhance a research culture that prioritizes rigour and transparency. The US National Institute of Neurological Disorders and Stroke convened a workshop entitled ‘Catalyzing Communities of Research Rigor Champions’ that brought together a diverse group of leaders in promoting research rigour and transparency (identified as ‘rigour champions’) to discuss strategies, barriers and resources for catalyzing technical, cultural and educational changes in the biomedical sciences. This article summarizes 2 days of panels and discussions and provides an overview of critical barriers to research rigour, perspectives behind reform initiatives and considerations for stakeholders across science. Additionally, we describe applications of network science to foster, maintain and expand cultural changes related to scientific rigour and opportunities to embed rigourous practices into didactic courses, training experiences and degree programme requirements. We hope this piece provides a primer for the wider research community on current discussions and actions and inspires individuals to build, join or expand collaborative networks within their own institutions that prioritize rigourous research practices.
Structural connectivity at term equivalent age and language in preterm children at 2 years corrected
Authors: Barnes-Davis Maria E , Williamson Brady J , Kline Julia E , Kline-Fath Beth M , Tkach Jean , He Lili , Yuan Weihong , Parikh Nehal A 
Published: April 2024

Abstract
We previously reported interhemispheric structural hyperconnectivity bypassing the corpus callosum in children born extremely preterm (&lt;28 weeks) versus term children. This increased connectivity was positively associated with language performance at 4–6 years of age in our prior work. In the present study, we aim to investigate whether this extracallosal connectivity develops in extremely preterm infants at term equivalent age by leveraging a prospective cohort study of 350 very and extremely preterm infants followed longitudinally in the Cincinnati Infant Neurodevelopment Early Prediction Study. For this secondary analysis, we included only children born extremely preterm and without significant brain injury (n = 95). We use higher-order diffusion modelling to assess the degree to which extracallosal pathways are present in extremely preterm infants and predictive of later language scores at 22–26 months corrected age. We compare results obtained from two higher-order diffusion models: generalized q-sampling imaging and constrained spherical deconvolution. Advanced MRI was obtained at term equivalent age (39–44 weeks post-menstrual age). For structural connectometry analysis, we assessed the level of correlation between white matter connectivity at the whole-brain level at term equivalent age and language scores at 2 years corrected age, controlling for post-menstrual age, sex, brain abnormality score and social risk. For our constrained spherical deconvolution analyses, we performed connectivity-based fixel enhancement, using probabilistic tractography to inform statistical testing of the hypothesis that fibre metrics at term equivalent age relate to language scores at 2 years corrected age after adjusting for covariates. Ninety-five infants were extremely preterm with no significant brain injury. Of these, 53 had complete neurodevelopmental and imaging data sets that passed quality control. In the connectometry analyses adjusted for covariates and multiple comparisons (P &lt; 0.05), the following tracks were inversely correlated with language: bilateral cerebellar white matter and middle cerebellar peduncles, bilateral corticospinal tracks, posterior commissure and the posterior inferior fronto-occipital fasciculus. No tracks from the constrained spherical deconvolution/connectivity-based fixel enhancement analyses remained significant after correction for multiple comparisons. Our findings provide critical information about the ontogeny of structural brain networks supporting language in extremely preterm children. Greater connectivity in more posterior tracks that include the cerebellum and connections to the regions of the temporal lobes at term equivalent age appears to be disadvantageous for language development.
Inferior parietal cortex represents relational structures for explicit transitive inference
Authors: Xu Biman , Wu Jing , Xiao Haoyun , Münte Thomas F , Ye Zheng 
Published: April 2024

Abstract
The human brain is distinguished by its ability to perform explicit logical reasoning like transitive inference. This study investigated the functional role of the inferior parietal cortex in transitive inference with functional MRI. Participants viewed premises describing abstract relations among items. They accurately recalled the relationship between old pairs of items, effectively inferred the relationship between new pairs of items, and discriminated between true and false relationships for new pairs. First, the inferior parietal cortex, but not the hippocampus or lateral prefrontal cortex, was associated with transitive inference. The inferior parietal activity and functional connectivity were modulated by inference (new versus old pairs) and discrimination (true versus false pairs). Moreover, the new/old and true/false pairs were decodable from the inferior parietal representation. Second, the inferior parietal cortex represented an integrated relational structure (ordered and directed series). The inferior parietal activity was modulated by serial position (larger end versus center pairs). The inferior parietal representation was modulated by symbolic distance (adjacent versus distant pairs) and direction (preceding versus following pairs). It suggests that the inferior parietal cortex may flexibly integrate observed relations into a relational structure and use the relational structure to infer unobserved relations and discriminate between true and false relations.
First-in-human clinical series of a novel conformable large-lattice pulsed field ablation catheter for pulmonary vein isolation
Authors: Reddy Vivek Y , Anter Elad , Peichl Petr , Rackauskas Gediminas , Petru Jan , Funasako Moritoshi , Koruth Jacob S , Marinskis Germanas , Turagam Mohit , Aidietis Audrius , Kautzner Josef , Natale Andrea , Neuzil Petr 
Published: April 2024

Abstract

Aims
Pulsed field ablation (PFA) has significant advantages over conventional thermal ablation of atrial fibrillation (AF). This first-in-human, single-arm trial to treat paroxysmal AF (PAF) assessed the efficiency, safety, pulmonary vein isolation (PVI) durability and one-year clinical effectiveness of an 8 Fr, large-lattice, conformable single-shot PFA catheter together with a dedicated electroanatomical mapping system.

Methods and results
After rendering the PV anatomy, the PFA catheter delivered monopolar, biphasic pulse trains (5–6 s per application; ∼4 applications per PV). Three waveforms were tested: PULSE1, PULSE2, and PULSE3. Follow-up included ECGs, Holters at 6 and 12 months, and symptomatic and scheduled transtelephonic monitoring. The primary and secondary efficacy endpoints were acute PVI and post-blanking atrial arrhythmia recurrence, respectively. Invasive remapping was conducted ∼75 days post-ablation. At three centres, PVI was performed by five operators in 85 patients using PULSE1 (n = 30), PULSE2 (n = 20), and PULSE3 (n = 35). Acute PVI was achieved in 100% of PVs using 3.9 ± 1.4 PFA applications per PV. Overall procedure, transpired ablation, PFA catheter dwell and fluoroscopy times were 56.5 ± 21.6, 10.0 ± 6.0, 19.1 ± 9.3, and 5.7 ± 3.9 min, respectively. No pre-defined primary safety events occurred. Upon remapping, PVI durability was 90% and 99% on a per-vein basis for the total and PULSE3 cohort, respectively. The Kaplan–Meier estimate of one-year freedom from atrial arrhythmias was 81.8% (95% CI 70.2–89.2%) for the total, and 100% (95% CI 80.6–100%) for the PULSE3 cohort.

Conclusion
Pulmonary vein isolation (PVI) utilizing a conformable single-shot PFA catheter to treat PAF was efficient, safe, and effective, with durable lesions demonstrated upon remapping.
Incidence of phrenic nerve injury during pulmonary vein isolation using different cryoballoons: data from a large prospective ablation registry
Authors: Tachibana Shinichi , Miyazaki Shinsuke , Nitta Junichi , Shirai Yasuhiro , Nagata Yasutoshi , Sagawa Yuichiro , Sekiguchi Yukio , Inamura Yukihiro , Sasaki Takeshi , Yamauchi Yasuteru , Inaba Osamu , Ono Yuichi , Suzuki Makoto , Suzuki Atsushi , Iwai Shinsuke , Okada Hiroyuki , Mizukami Akira , Azegami Koji , Hachiya Hitoshi , Handa Keita , Goto Kentaro , Nishimura Takuro , Hirao Kenzo , Takahashi Atsushi , Sasano Tetsuo 
Published: April 2024

Abstract

Aims
Phrenic nerve injury (PNI) is the most common complication during cryoballoon ablation. Currently, two cryoballoon systems are available, yet the difference is unclear. We sought to compare the acute procedural efficacy and safety of the two cryoballoons.

Methods
This prospective observational study consisted of 2,555 consecutive atrial fibrillation (AF) patients undergoing pulmonary vein isolation (PVI) using either conventional (Arctic Front Advance) (AFA-CB) or novel cryoballoons (POLARx) (POLARx-CB) at 19 centers between January 2022 and October 2023.

Results
Among 2,555 patients (68.8 ± 10.9 years, 1,740 men, paroxysmal AF[PAF] 1,670 patients), PVIs were performed by the AFA-CB and POLARx-CB in 1,358 and 1,197 patients, respectively. Touch-up ablation was required in 299(11.7%) patients. The touch-up rate was significantly lower for POLARx-CB than AFA-CB (9.5% vs. 13.6%, p = 0.002), especially for right inferior PVs (RIPVs). The touch-up rate was significantly lower for PAF than non-PAF (8.8% vs. 17.2%, P &lt; 0.001) and was similar between the two cryoballoons in non-PAF patients. Right PNI occurred in 64(2.5%) patients and 22(0.9%) were symptomatic. It occurred during the right superior PV (RSPV) ablation in 39(1.5%) patients. The incidence was significantly higher for POLARx-CB than AFA-CB (3.8% vs. 1.3%, P &lt; 0.001) as was the incidence of symptomatic PNI (1.7% vs. 0.1%, P &lt; 0.001). The difference was significant during RSPV (2.5% vs. 0.7%, P &lt; 0.001) but not RIPV ablation. The PNI recovered more quickly for the AFA-CB than POLARx-CB.

Conclusions
Our study demonstrated a significantly higher incidence of right PNI and lower touch-up rate for the POLARx-CB than AFA-CB in the real-world clinical practice.
Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis
Authors: De Jode Aurélien , Faria Rui , Formenti Giulio , Sims Ying , Smith Timothy P , Tracey Alan , Wood Jonathan M D , Zagrodzka Zuzanna B , Johannesson Kerstin , Butlin Roger K , Leder Erica H 
Published: April 2024

Abstract
The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35 Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44 kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.
A fully scalable homogenization method to upscale 3-D elastic media
Authors: Cao J , Brossier R , Capdeville Y , Métivier L , Sambolian S 
Published: April 2024

SUMMARY
Modelling seismic wavefields in complex 3-D elastic media is the key in many fields of Earth Science: seismology, seismic imaging, seismic hazard assessment and earthquake source mechanism reconstruction. This modelling operation can incur significant computational cost, and its accuracy depends on the ability to take into account the scales of the subsurface heterogeneities varying. The theory of homogenization describes how the small-scale heterogeneities interact with the seismic waves and allows to upscale elastic media consistently with the wave equation. In this study, an efficient and scalable numerical homogenization tool is developed, relying on the similarity between the equations describing the propagation of elastic waves and the homogenization process. By exploiting the optimized implementation of an elastic modelling kernel based on a spectral-element discretization and domain decomposition, a fully scalable homogenization process, working directly on the spectral-element mesh, is presented. Numerical experiments on the entire SEAM II foothill model and a 3-D version of the Marmousi II model illustrate the efficiency and flexibility of this approach. A reduction of two orders of magnitude in terms of absolute computational cost is observed on the elastic wave modelling of the entire SEAM II model at a controlled accuracy.