bluuebunny/crossref_metadata_2025_split huggingface dataset:
Permutation entropy of indexed ensembles: quantifying thermalization dynamics
Authors: Aragoneses Andrés , Kapulkin Arie , Pattanayak Arjendu K 
Published: May 2023

Abstract
We introduce ‘PI-Entropy’

Π
(

ρ
˜

)

(the Permutation entropy of an Indexed ensemble) to quantify mixing due to complex dynamics for an ensemble ρ of different initial states evolving under identical dynamics. We find that

Π
(

ρ
˜

)

acts as an excellent proxy for the thermodynamic entropy

S
(
ρ
)

but is much more computationally efficient. We study 1-D and 2D iterative maps and find that

Π
(

ρ
˜

)

dynamics distinguish a variety of system time scales and track global loss of information as the ensemble relaxes to equilibrium. There is a universal S-shaped relaxation to equilibrium for generally chaotic systems, and this relaxation is characterized by a shuffling timescale that correlates with the system’s Lyapunov exponent. For the Chirikov Standard Map, a system with a mixed phase space where the chaos grows with nonlinear kick strength K, we find that for high K,

Π
(

ρ
˜

)

behaves like the uniformly hyperbolic 2D Cat Map. For low K we see periodic behavior with a relaxation envelope resembling those of the chaotic regime, but with frequencies that depend on the size and location of the initial ensemble in the mixed phase space as well as K. We discuss how

Π
(

ρ
˜

)

adapts to experimental work and its general utility in quantifying how complex systems change from a low entropy to a high entropy state.
Large parametric amplification in kinetic inductance dominant resonators based on 3 nm-thick epitaxial superconductors
Authors: Chien Wei-Chen , Chang Yu-Han , Lu Cheng Xin , Ting Yen-Yu , Wu Cen-Shawn , Lin Sheng-Di , Kuo Watson 
Published: May 2023

Abstract
Ultra-thin superconducting aluminum films of 3-nm grown on sapphire by molecule-beam epitaxy show excellent superconductivity and large kinetic inductance. This results in a record high Kerr non-linearity of 33 kHz and 3.62 MHz per photon in notch-type and transmission-type resonators, respectively. 4-wave mixing leverages this non-linearity to achieve 12 dB parametric amplification in transmission type resonator, making the ultra-thin film ideal for photon detection and amplification applications.
Proteomic and Clinicopathologic Assessment of Penile Amyloidosis: A Single Institutional Review of 12 Cases
Authors: Tekin Burak , Gilani Sarwat I , Dasari Surendra , Theis Jason D , Rech Karen L , Dao Linda N , Cubilla Antonio L , Herrera Hernandez Loren P , Jimenez Rafael E , Cheville John C , Dispenzieri Angela , Howard Matthew T , McPhail Ellen D , Erickson Lori A , Guo Ruifeng , Gupta Sounak 
Published: May 2023

Abstract

Objectives
There is a paucity of data on penile amyloidosis. We aimed to assess the frequency of different amyloid types in surgical specimens from the penis involved by amyloidosis and correlate relevant clinicopathologic parameters with proteomic findings.

Methods
Since 2008, our reference laboratory has performed liquid chromatography/tandem mass spectrometry (LC-MS/MS) for amyloid typing. The institutional pathology archive and reference laboratory database were queried to retrospectively identify all penile surgical pathology specimens with LC-MS/MS results between January 1, 2008, and November 23, 2022. Archived H&E-stained and Congo red–stained sections were re-reviewed.

Results
Twelve cases of penile amyloidosis were identified, which represented 0.35% (n = 3,456) of penile surgical specimens. AL-type amyloid was most frequent (n = 7), followed by keratin-type amyloid (n = 3) and ATTR (transthyretin)–type amyloid (n = 2). AL-type amyloid cases often showed diffuse dermal/lamina propria deposition, whereas all keratin-type amyloid cases were localized to the superficial dermis. Two cases with keratin-type amyloid had concomitant cutaneous findings (penile intraepithelial neoplasia and condyloma).

Conclusions
This series, the largest to date, demonstrates that penile amyloidosis has a heterogeneous proteomic landscape. To the best of our knowledge, this is the first study describing ATTR (transthyretin)–type penile amyloid.
Size-selective harvesting impacts learning and decision-making in zebrafish, Danio rerio
Authors: Roy Tamal , Rohr Tabea , Arlinghaus Robert 
Published: May 2023

Abstract
Size-selective harvesting common to fisheries is known to evolutionarily alter life history and behavioral traits in exploited fish populations. Changes in these traits may, in turn, modify learning and decision-making abilities through energetic trade-offs with brain investment that can vary across development or via correlations with personality traits. We examined the hypothesis of size-selection induced alteration of learning performance in three selection lines of zebrafish (Danio rerio) generated through intensive harvesting for large, small and random body-size for five generations followed by no further selection for ten generations that allowed examining evolutionarily fixed outcomes. We tested associative learning ability throughout ontogeny in fish groups using a color-discrimination paradigm with a food reward, and the propensity to make group decisions in an associative task. All selection lines showed significant associative abilities that improved across ontogeny. The large-harvested line fish showed a significantly slower associative learning speed as subadults and adults than the controls. We found no evidence of memory decay as a function of size-selection. Decision-making speed did not vary across lines, but the large-harvested line made faster decisions during the probe trial. Collectively, our results show that large size-selective harvesting evolutionarily alters associative and decision-making abilities in zebrafish, which could affect resource acquisition and survival in exploited fish populations.
MetaMOPE: a web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics
Authors: Tsai Dong-Ming , Chang Ching-Yao , Lin Shih-Ming , Kuo Tien-Chueh , Wang San-Yuan , Chen Guan-Yuan , Kuo Ching-Hua , Tseng Yufeng Jane 
Published: May 2023

Abstract

Motivation
Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used in metabolomics studies, while HILIC LC-MS is particularly suited for polar metabolites. Determining an optimized mobile phase and developing a proper liquid chromatography method tend to be laborious, time-consuming and empirical.

Results
We developed a containerized web tool providing a workflow to quickly determine the optimized mobile phase by batch-evaluating chromatography peaks for metabolomics LC-MS studies. A mass chromatographic quality value, an asymmetric factor, and the local maximum intensity of the extracted ion chromatogram were calculated to determine the number of peaks and peak retention time. The optimal mobile phase can be quickly determined by selecting the mobile phase that produces the largest number of resolved peaks. Moreover, the workflow enables one to automatically process the repeats by evaluating chromatography peaks and determining the retention time of large standards. This workflow was validated with 20 chemical standards and successfully constructed a reference library of 571 metabolites for the HILIC LC-MS platform.

Availability and implementation
MetaMOPE is freely available at https://metamope.cmdm.tw. Source code and installation instructions are available on GitHub: https://github.com/CMDM-Lab/MetaMOPE.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
tiny-count: a counting tool for hierarchical classification and quantification of small RNA-seq reads with single-nucleotide precision
Authors: Tate Alex J , Brown Kristen C , Montgomery Taiowa A 
Published: May 2023

Abstract

Summary
tiny-count is a highly flexible counting tool that allows for hierarchical classification and quantification of small RNA reads from high-throughput sequencing data. Selection rules can be used to filter reads by 5′ nucleotide, length, position of alignments in relation to reference features, and by the number of mismatches to reference sequences. tiny-count can quantify reads aligned to a genome or directly to small RNA or transcript sequences. With tiny-count, users can quantify a single class of small RNAs or multiple classes in parallel. tiny-count can resolve distinct classes of small RNAs, for example, piRNAs and siRNAs, produced from the same locus. It can distinguish small RNA variants, such as miRNAs and isomiRs, with single-nucleotide precision. tRNA, rRNA, and other RNA fragments can also be quantified. tiny-count can be run alone or as part of tinyRNA, a workflow that provides a basic all-in-one command line-based solution for small RNA-seq data analysis, with documentation and statistics generated at each step for accurate and reproducible results.

Availability and implementation
tiny-count and other tinyRNA tools are implemented in Python, C++, Cython, and R, and the workflow is coordinated with CWL. tiny-count and tinyRNA are free and open-source software distributed under the GPLv3 license. tiny-count can be installed via Bioconda (https://anaconda.org/bioconda/tiny-count) and both tiny-count and tinyRNA documentation and software downloads are available at https://github.com/MontgomeryLab/tinyRNA. Reference data, including genome and feature information, for certain species can be found at https://www.MontgomeryLab.org.
Laparoscopic lavage for Hinchey III perforated diverticulitis: factors for treatment failure in two randomized clinical trials
Authors: Azhar Najia , Lambrichts Daniël , Lange Johan , Yaqub Sheraz , Øresland Tom , Schultz Johannes , Bemelman Willem , Buchwald Pamela 
Published: May 2023

Abstract

Background
The Scandinavian Diverticulitis (SCANDIV) trial and the LOLA arm of the LADIES trial randomized patients with Hinchey III perforated diverticulitis to laparoscopic peritoneal lavage or sigmoid resection. The aim of this analysis was to identify risk factors for treatment failure in patients with Hinchey III perforated diverticulitis.

Methods
This was a post hoc analysis of the SCANDIV trial and LOLA arm. Treatment failure was defined as morbidity requiring general anaesthesia (Clavien–Dindo grade IIIb or higher) within 90 days. Age, sex, BMI, ASA fitness grade, smoking status, previous episodes of diverticulitis, previous abdominal surgery, time to surgery, and surgical competence were all tested in univariable and multivariable logistic regression analyses using an interaction variable.

Results
The pooled analysis included 222 patients randomized to laparoscopic lavage and primary resection (116 and 106 patients respectively). Univariable analysis found ASA grade to be associated with advanced morbidity in both groups, and the following factors in the laparoscopic lavage group: smoking, corticosteroid use, and BMI. Significant factors for laparoscopic lavage morbidity in multivariable analysis were smoking (OR 7.05, 95 per cent c.i. 2.07 to 23.98; P = 0.002) and corticosteroid use (OR 6.02, 1.54 to 23.51; P = 0.010).

Conclusion
Active smoking status and corticosteroid use were risk factors for laparoscopic lavage treatment failure (advanced morbidity) in patients with perforated diverticulitis.
Pericardial effusions: perspective of the acute cardiac care physician
Authors: Jain C Charles , Reddy Yogesh N V 
Published: May 2023

Abstract
Pericardial effusions can result in acute haemodynamic compromise and require rapid intervention. Understanding pericardial restraint is essential to determine the approach to newly identified pericardial effusions in the intensive care unit. As pericardial effusions stretch the pericardium, the pericardial compliance reserve is eventually exhausted, with an exponential rise in compressive pericardial pressure. The severity of pericardial pressure increase depends on both the rapidity and volume of pericardial fluid accumulation. This increase in pericardial pressure is reflected in an increase in measured left- and right-sided ‘filling’ pressures, but paradoxically left ventricular end-diastolic volume (the true left ventricular preload) is decreased. This uncoupling of filling pressures and preload is the hallmark of pericardial restraint. When this occurs acutely from a pericardial effusion, rapid recognition and pericardiocentesis can be lifesaving. In this review, we will discuss the haemodynamics and pathophysiology of acute pericardial effusions, provide a physiological guide to determine the need for pericardiocentesis in acute care, and discuss important caveats to management.
Can Acta Jure Gestionis Be Attributable to the State? A Restrictive Doctrine of State Responsibility
Authors: Okada Yohei 
Published: May 2023

Abstract
The distinction between acta jure imperii and jure gestionis, while playing a pivotal role in the law of state immunity, appears alien to the law of state responsibility. However, recent practice has shown conceptual overlaps between these different areas of international law. The sovereign/commercial dichotomy has informed the attribution of parastatal entities’ conduct to a state under Article 5 of the International Law Commission’s Articles on Responsibility of States for Internationally Wrongful Acts (ARSIWA). More precisely, acta jure gestionis have been excluded from the scope of attributable conduct. Against this backdrop, this study investigates whether, and to what extent, the distinction between acta jure imperii and jure gestionis dictates the interpretation and application of Article 5 of ARSIWA. We conclude that the distinction does have relevance in this context, although Article 5 was not designed to preclude the attributability of commercial acts. However, its obscure wording has allowed subsequent practice to overly narrow the scope of attributable conduct. This study, critically analysing a restrictive doctrine of state responsibility, aims to provide a more accurate and desirable conception of the rule and a clear and detailed guideline on when the commercial act of parastatal entities can be attributable to the state.
Aridity modulates biogeographic distribution and community assembly of cyanobacterial morphotypes in drylands
Authors: Guo Xiaoyu , Li Hua , Huo Da , Hu Chunxiang , Li Renhui , Zhang Silong , Song Lirong 
Published: May 2023

Abstract
The patterns of biogeographic distribution and assembly processes of microbiota are of vital importance for understanding ecological adaptation and functioning maintenance. However, the role of morphological characteristics in microbial assembly is still poorly ascertained. Here, by integrating high-throughput sequencing and robust extrapolation of traits, we investigated taxonomic and phylogenetic turnovers of various cyanobacterial morphotypes in biocrusts to evaluate the contributions of deterministic and stochastic processes across a large scale of drylands in northwestern China. The results showed that the non-heterocystous filamentous category dominated biocrusts in the arid ecosystem and exhibited strong tolerance against environmental fluctuations. Despite the significant distance-decay relationship of β-diversity detected in all categories, both species composition and phylogenetic turnover rates of coccoid cyanobacteria were higher than non-heterocystous filamentous and heterocystous morphotypes. Moreover, the assembly of cyanobacteria was driven by different ecological processes that the entire community and non-heterocystous filamentous morphotype were governed by deterministic processes, while stochasticity prevailed in heterocystous and coccoid cyanobacteria. Nonetheless, aridity can modulate the balance between determinism and stochasticity and prompt a shifting threshold among morphotypes. Our findings provide a unique perspective to understanding the critical role of microbial morphology in community assembly and facilitate the prediction of biodiversity loss under climate change.
A case of Budd–Chiari syndrome combined with drainage of the inferior vena cava into the left atrium
Authors: Shen Yue , Wu Qingsong , Xiao Jun , Chen Liangwan 
Published: May 2023

Abstract
Abnormal drainage of the inferior vena cava to the left atrium and Budd–Chiari syndrome are different congenital malformations. The combination of these 2 disorders is very rare. We report a case of a 35-year-old woman with anomalous inferior vena cava drainage into the left atrium resulting in delayed hypoxic symptoms after interventional therapy for Budd–Chiari syndrome 17 years ago. We speculate that an abnormality of the Eustachian valve is the cause of these 2 disorders. After surgical treatment, the patient's oxygen saturation returned to normal.
Optimized preoperative planning of double outlet right ventricle patients by 3D printing and virtual reality: a pilot study
Authors: Peek Jette J , Bakhuis Wouter , Sadeghi Amir H , Veen Kevin M , Roest Arno A W , Bruining Nico , van Walsum Theo , Hazekamp Mark G , Bogers Ad J J C 
Published: May 2023

Abstract

OBJECTIVES
In complex double outlet right ventricle (DORV) patients, the optimal surgical approach may be difficult to assess based on conventional 2-dimensional (2D) ultrasound (US) and computed tomography (CT) imaging. The aim of this study is to assess the added value of 3-dimensional (3D) printed and 3D virtual reality (3D-VR) models of the heart used for surgical planning in DORV patients, supplementary to the gold standard 2D imaging modalities.

METHODS
Five patients with different DORV subtypes and high-quality CT scans were selected retrospectively. 3D prints and 3D-VR models were created. Twelve congenital cardiac surgeons and paediatric cardiologists, from 3 different hospitals, were shown 2D-CT first, after which they assessed the 3D print and 3D-VR models in random order. After each imaging method, a questionnaire was filled in on the visibility of essential structures and the surgical plan.

RESULTS
Spatial relationships were generally better visualized using 3D methods (3D printing/3D-VR) than in 2D. The feasibility of ventricular septum defect patch closure could be determined best using 3D-VR reconstructions (3D-VR 92%, 3D print 66% and US/CT 46%, P &lt; 0.01). The percentage of proposed surgical plans corresponding to the performed surgical approach was 66% for plans based on US/CT, 78% for plans based on 3D printing and 80% for plans based on 3D-VR visualization.

CONCLUSIONS
This study shows that both 3D printing and 3D-VR have additional value for cardiac surgeons and cardiologists over 2D imaging, because of better visualization of spatial relationships. As a result, the proposed surgical plans based on the 3D visualizations matched the actual performed surgery to a greater extent.
Key considerations for designing, conducting and analysing a cluster randomized trial
Authors: Hemming Karla , Taljaard Monica 
Published: May 2023

AbstractNot only do cluster randomized trials require a larger sample size than individually randomized trials, they also face many additional complexities. The potential for contamination is the most commonly used justification for using cluster randomization, but the risk of contamination should be carefully weighed against the more serious problem of questionable scientific validity in settings with post-randomization identification or recruitment of participants unblinded to the treatment allocation. In this paper we provide some simple guidelines to help researchers conduct cluster trials in a way that minimizes potential biases and maximizes statistical efficiency. The overarching theme of this guidance is that methods that apply to individually randomized trials rarely apply to cluster randomized trials. We recommend that cluster randomization be only used when necessary—balancing the benefits of cluster randomization with its increased risks of bias and increased sample size. Researchers should also randomize at the lowest possible level—balancing the risks of contamination with ensuring an adequate number of randomization units—as well as exploring other options for statistically efficient designs. Clustering should always be allowed for in the sample size calculation; and the use of restricted randomization (and adjustment in the analysis for covariates used in the randomization) should be considered. Where possible, participants should be recruited before randomizing clusters and, when recruiting (or identifying) participants post-randomization, recruiters should be masked to the allocation. In the analysis, the target of inference should align with the research question, and adjustment for clustering and small sample corrections should be used when the trial includes less than about 40 clusters.
Citrobacter freundii resistant to novel β-lactamase inhibitor combinations and cefiderocol, co-producing class A, B and D carbapenemases encoded by transferable plasmids
Authors: Riccobono Eleonora , Salvetti Sara , Coppi Marco , Montenora Iolanda , Di Pilato Vincenzo , Rossolini Gian Maria 
Published: May 2023

Abstract

Objectives
To characterize a carbapenem-resistant Citrobacter freundii (Cf-Emp) co-producing class A, B and D carbapenemases, resistant to novel β-lactamase inhibitor combinations (BLICs) and cefiderocol.

Methods
Carbapenemase production was tested by an immunochromatography assay. Antibiotic susceptibility testing (AST) was performed by broth microdilution. WGS was performed using short- and long-read sequencing. Transfer of carbapenemase-encoding plasmids was assessed by conjugation experiments.

Results
Cf-Emp was isolated on selective medium for carbapenem-resistant Enterobacterales from the surveillance rectal swab taken at hospital admission from a patient of Moroccan origin. Cf-Emp produced three different carbapenemases, including KPC-2, OXA-181 and VIM-1, and was resistant to all β-lactams including carbapenems, novel BLICs (ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam) and cefiderocol. MIC of aztreonam/avibactam was 0.25 mg/L. The strain belonged to ST22, one of the C. freundii lineages of global diffusion, known to be associated with carbapenemase production. Each carbapenemase gene was located aboard a different plasmid (named pCf-KPC, pCf-OXA and pCf-VIM, respectively), which also carried other clinically relevant resistance genes, such as armA (pCf-KPC), blaSHV-12 (pCf-VIM) and qnrS1 (pCf-OXA). Transferability to Escherichia coli J53 by conjugation was observed for all plasmids.

Conclusions
The finding of enterobacterial strains carrying multiple carbapenemase genes on transferable plasmids is alarming, because similar strains could provide an important reservoir for disseminating these clinically relevant resistance determinants.