bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Stepwise Approach to Surgical Decision-making for Lower Eyelid Ectropion: Insights from a Retrospective Study
Authors: Wang Yinmin , Yang Jun , Yu Shun , Jin Rui , Gu Chuan , Lu Lin 
Published: January 2025

Abstract

Background
Cicatricial lower eyelid ectropion is a serious complication resulting from undesired lower lid blepharoplasty or impaired wound healing. Surgical treatment for ectropion is challenging for oculoplastic surgeons due to the unpredictability of surgical outcome and the difficulty of surgical design.

Objectives
The authors aimed to fully describe the surgical decision-making strategy for cicatricial ectropion, and to potentially enhance treatment outcomes.

Methods
In this study, we conducted a retrospective review of the treatment of 26 patients (30 eyelids) with cicatricial ectropion between 2017 and 2021. We summarized the corresponding decision-making processes before and during surgery. Treatment involved scar tissue release combined with lateral canthal procedures and repair of the skin defect.

Results
During the early postoperative stage, no flap necrosis was observed, and complete surgical healing was achieved within 2 weeks. The ectropion grading scale showed a significant decrease after surgical treatment based on our approach, and most patient symptoms were alleviated. Additionally, the majority of the patients expressed high satisfaction with the aesthetic outcome of the procedure.

Conclusions
This treatment approach significantly enhanced both the appearance and function of the lower lid, which holds considerable promise as an ideal surgical design for cicatricial ectropion.

Level of Evidence: 3 (Therapeutic)
Transcription factor prediction using protein 3D secondary structures
Authors: Liebold Jeanine , Neuhaus Fabian , Geiser Janina , Kurtz Stefan , Baumbach Jan , Newaz Khalique 
Published: January 2025

Abstract

Motivation
Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs. Recently proposed TF prediction methods do not rely on DBDs. Such methods use features of protein sequences to train a machine learning model, and then use the trained model to predict whether a protein is a TF or not. Because the 3-dimensional (3D) structure of a protein captures more information than its sequence, using 3D protein structures will likely allow for more accurate prediction of novel TFs.

Results
We propose a deep learning-based TF prediction method (StrucTFactor), which is the first method to utilize 3D secondary structural information of proteins. We compare StrucTFactor with recent state-of-the-art TF prediction methods based on ∼525 000 proteins across 12 datasets, capturing different aspects of data bias (including sequence redundancy) possibly influencing a method’s performance. We find that StrucTFactor significantly (P-value &lt; 0.001) outperforms the existing TF prediction methods, improving the performance over its closest competitor by up to 17% based on Matthews correlation coefficient.

Availability and implementation
Data and source code are available at https://github.com/lieboldj/StrucTFactor and on our website at https://apps.cosy.bio/StrucTFactor
nipalsMCIA: flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares
Authors: Mattessich Max , Reyna Joaquin , Aron Edel , Ay Ferhat , Kilmer Misha , Kleinstein Steven H , Konstorum Anna 
Published: January 2025

Abstract

Summary
With the increased reliance on multi-omics data for bulk and single-cell analyses, the availability of robust approaches to perform unsupervised learning for clustering, visualization, and feature selection is imperative. We introduce nipalsMCIA, an implementation of multiple co-inertia analysis (MCIA) for joint dimensionality reduction that solves the objective function using an extension to Nonlinear Iterative Partial Least Squares. We applied nipalsMCIA to both bulk and single-cell datasets and observed significant speed-up over other implementations for data with a large sample size and/or feature dimension.

Availability and implementation
nipalsMCIA is available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/nipalsMCIA.html, and includes detailed documentation and application vignettes.
Molecular dynamics simulations of putative primitive proteins including β-aspartic acid residues
Authors: Kato Koichi , Nakayoshi Tomoki , Mizuno Ayato , Yabu Mayuka , Kurimoto Eiji , Oda Akifumi 
Published: January 2025

Abstract
Aspartic acid (Asp) has 2 carboxyl groups, either of which can form an amide bond. However, among the present proteins, only one is involved in a peptide bond, whereas the other is regarded as “side chain,” with only α-Asp identified as a gene-encoded amino acid residue. In this study, molecular dynamics simulations of random peptides were performed to investigate why β-Asp, which may have been present in primitive proteins in the origin of proteins, was excluded from proteinogenic amino acids. [GADV]-peptides, constructed from Gly, Ala, Asp, and Val, were used as putative primitive proteins. Molecular dynamics simulations were performed when β-Asp was used instead of Asp in the [GADV]-peptides and when β-Asp was added to the [GADV]-peptide. The secondary structures of peptides containing β-Asp were less than [GADV]-peptides, and their ability to form a protein-like structure was inferior to that of peptides excluding β-Asp. Thus, the ability to form protein-like structures may have acted as a selection pressure, leading to the elimination of protein synthesis systems utilizing β-Asp from primitive life. When the [GADVB]-peptide, i.e. a β-amino acid β-Ala, was added to the [GADV] amino acid set, the ability to form secondary structures reduced. Therefore, β-amino acids that altered the main chain length were excluded from primitive life, despite β-Ala being relatively abundant on primitive Earth.
Effect of Mg–Nb oxides on hydrogen sorption kinetics of ball-milled MgH2
Authors: Rahman Md Wasikur , Siddiquee Muhammad Nurunnabi , Hossain Mohammad M , Uddin M Jasim 
Published: January 2025

Abstract
Addition of Mg–Nb oxides (e.g. MgNb2O6, Mg4Nb2O9, and Mg3Nb6O11) ameliorates H2 absorption/desorption kinetics of MgH2 as demonstrated in the current article. H2 desorption and absorption rates of the ball-milled MgH2 are evidently temperature-dependent, which points out that the prior rate increases with increasing temperature (593–673 K) and vice versa. Among the tested samples, MgH2 with Mg3Nb6O11 nanoparticles showed superior performance. The Johnson–Mehl–Avrami equation was employed to construct H2 desorption curves as well as find out reaction rate constants at different temperatures. The Arrhenius equation was fitted in the context to estimate the activation energy of the ball-milled MgH2 and MgH2/Mg3Nb6O11 mixtures; for example, the values obtained were 127 and 88 kJ·mol−1, respectively. In addition, a novel experimental setup combining a hydrogen detector with a differential scanning calorimeter was used to confirm the H2 desorption properties of the ball-milled nanoparticles discussed based on the kinetic argument.
Impact of Ag Doping on the Structural, Optical, and Photovoltaic Properties of MAPbI2Br Thin Films
Authors: Hussain Saddam , Khan M I , Atif M , Rodríguez-Rodríguez Margarita , Pellegrini-Cervantes Manuel J 
Published: January 2025

Abstract
Using the spray pyrolysis process, the work shows the production of pristine and 6% Ag-doped methylammonium lead iodide bromide (MAPbI2Br) film. Through X-ray diffraction analysis, it was found that Ag doping led to a significant increase in grain size to 29.64 nm, alongside reductions in dislocation line density to 5.39 x1014 m-2 and d-spacing to 3.18 Å, while maintaining the native cubic crystal structure of MAPbI2Br. This research demonstrates a reduction in deep-level trap states with Ag doping, along with a significant narrowing of the band gap to 1.91 eV in the 6% Ag-doped MAPbI2Br. Moreover, the refractive index and extinction coefficient increased to 2.54 and 2.13, respectively. Regarding solar cell performance, all cells demonstrated encouraging outcomes; still, the 6% Ag-doped cell distinguished itself with a fill factor of 0.82, an open-circuit voltage of 1.07 V, an outstanding short-circuit current density of 11.31 mA/cm², and an efficiency of 10.03%. These results highlight the effectiveness of Ag doping in improving perovskite solar cell technology, marking a notable progress in this field.
Brain functional differences during irony comprehension in adolescents with ASD
Authors: Xu Shilin , Wang Xin , Shen Linling , Yan Xiaohui , Feng Guoyan , Cao Fan 
Published: January 2025

Abstract
Irony comprehension is challenging for both individuals with ASD and poor comprehenders (PCs). We aimed to examine the common and specific mechanisms underlying irony comprehension difficulty in the two populations. Both adolescents with ASD and PC showed lower performance in irony comprehension than an age-matched typical control group (TD). The ASD group also showed deficits in theory of mind (ToM), while the PC group showed impairments in structural language skills. In the brain, the ASD group showed reduced brain activation in the left inferior frontal gyrus (IFG) compared to both the TD and the PC group, suggesting ASD-specific differences, which was further found to be correlated with ToM deficits in ASD. Both the TD and the PC group showed greater activation for the ironic than the literal condition in the bilateral medial prefrontal cortex (mPFC), but the ASD group did not, suggesting ASD-specific difference in irony comprehension. The PC group showed reduced activation in the right cuneus compared to the TD, which was correlated with the language comprehension score, suggesting different mechanisms than ASD. Our findings provide insights about the neurocognitive mechanisms underlying impaired irony comprehension in ASD and PC.
Hayek and Schmitt on the ‘depoliticization’ of the economy
Authors: Nientiedt Daniel 
Published: January 2025

Abstract
Both Friedrich Hayek and Carl Schmitt criticize the role played by economic interest groups in modern democracies. This paper points out that their descriptions of how such groups attempt to obtain favourable treatment from the state (‘rent seeking’) are highly similar. The paper then discusses their proposed solutions. Schmitt’s solution, referred to as ‘depoliticization’, involves the establishment of an authoritarian state together with a corporatist economic system. Hayek, by contrast, argues in favour of constitutionally limiting the ability of politicians to grant privileges to economic groups. The paper further asks whether, as claimed in the literature, Hayek’s solution is similar to Schmitt’s in that both attempt to shield the free market economy from democratic oversight. It is reasoned that Hayek’s solution is not undemocratic (unless one defines democracy as pure majoritarianism), while Schmitt’s solution is not conducive to free markets.
Deconditioning in quiescent Crohn’s disease patients with heightened fatigue perception
Authors: McGing Jordan J , Serres Sébastien , Nicholas Rosemary , Gupta Ayushman , Radford Shellie J , Nixon Aline V , Mallinson Joanne , Bradley Christopher , Bawden Stephen , Francis Susan T , Greenhaff Paul L , Moran Gordon W 
Published: January 2025

Abstract

Background and Objective
Inflammatory bowel disease (IBD) fatigue aetiology is poorly understood. This study quantified body composition and physical function alongside proton magnetic resonance imaging (1H MRI) and spectroscopy (31P MRS) measures of organ structure and function in quiescent Crohn’s disease patients (CD) and healthy volunteers (HVs), to identify a physiological basis for IBD fatigue.

Methods
Body composition was determined using dual-energy X-ray absorptiometry and 1H MRI. Knee extensor isometric strength and isokinetic fatigue were measured using dynamometry. 1H MRI was used to quantify cardiac output, cerebral blood flow (gmCBF), and brain oxygen extraction fraction (OEF) at rest, and during supine, steady-state exercise, and recovery. 31P MRS was used to quantify post-exercise muscle phosphocreatine (PCr) resynthesis.

Results
Sixteen CD and 12 HV (age, sex, and BMI matched) were recruited. Fatigue perception was greater (13.9 ± 1 vs 8.3 ± 0.9, P = .001), and daily step count was less (5482 ± 684 vs 8168 ± 1123, P = .04) in CD. During steady-state exercise, gmCBF was less in CD (653 ± 30 vs 823 ± 40 mL/min, P = .003). Cardiac output and brain OEF were no different. Post-exercise PCr resynthesis was less in CD (17.2 ± 2.0 vs 25.3 ± 2.4 mM·min−1, P = .02). Body composition, isometric strength, and isokinetic fatigability were no different.

Conclusions
CD self-reported increased fatigue perception and exhibited a slower rate of post-exercise PCr resynthesis compared to HV. This occurred independently of changes in body composition, muscle strength, and fatigability. IBD fatigue may be linked to peripheral muscle deconditioning and lower gmCBF during submaximal exercise.
A Binary IV Model for Persuasion: Profiling Persuasion Types among Compliers
Authors: Yu Zeyang 
Published: January 2025

Abstract
In an empirical study of persuasion, researchers often use a binary instrument to encourage individuals to consume information and take some action. We show that, with a binary Imbens-Angrist instrumental variable model and the monotone treatment response assumption, it is possible to identify the joint distribution of potential outcomes among compliers. This is necessary to identify the percentage of mobilised voters and their statistical characteristic defined by the moments of the joint distribution of treatment and covariates. Specifically, we develop a method that enables researchers to identify the statistical characteristic of persuasion types: always-voters, never-voters, and mobilised voters among compliers. These findings extend the kappa weighting results in Abadie (2003). We also provide a sharp test for the two sets of identification assumptions. The test boils down to testing whether there exists a nonnegative solution to a possibly under-determined system of linear equations with known coefficients. An application based on on Green et al. (2003) is provided.
Deep learning model for identifying acute heart failure patients using electrocardiography in the emergency room
Authors: Moon Jose , Kim Jong-Ho , Hong Soon Jun , Yu Cheol Woong , Kim Yong Hyun , Kim Eung Ju , Cha Jung-Joon , Joo Hyung Joon 
Published: January 2025

Abstract

Aims
Acute heart failure (AHF) poses significant diagnostic challenges in the emergency room (ER) because of its varied clinical presentation and limitations of traditional diagnostic methods. This study aimed to develop and evaluate a deep learning model using electrocardiogram (ECG) data to enhance AHF identification in the ER.

Methods and results
In this retrospective cohort study, we analysed the ECG data of 19 285 patients who visited ERs of three hospitals between 2016 and 2020; 9119 with available left ventricular ejection fraction and N-terminal prohormone of brain natriuretic peptide level data and who were diagnosed with AHF were included in the study. We extracted morphological and clinical parameters from ECG data to train and validate four machine learning models: baseline linear regression and more advanced models including XGBoost, Light GBM, and CatBoost. The CatBoost algorithm outperformed other models, showing superior area under the receiver operating characteristic and area under the precision–recall curve diagnostic accuracy across both internal (0.89 ± 0.01 and 0.89 ± 0.01) and external (0.90 and 0.89) validation data sets, respectively. The model demonstrated high accuracy, precision, recall, and f1 score, indicating robust performance in AHF identification.

Conclusion
The developed machine learning model significantly enhanced AHF detection in the ER using conventional 12-lead ECGs combined with clinical data. These findings suggest that ECGs, a common tool in the ER, can effectively help screen for AHF.
From gastroenteritis to myocarditis: a case series of Campylobacter-mediated cardiac involvement
Authors: Craveiro Costa Ricardo , Ribeiro Estevens Maria , Correia Marta , Cristóvão Cláudia , Saraiva Martins Duarte , Castro Faria Hugo 
Published: January 2025

Abstract

Background
While viruses remain the leading cause of infectious myocarditis, improved diagnostic methods have highlighted the role of bacteria as a possible cause. We report two cases of myocarditis as a complication of Campylobacter jejuni infection.

Case summaries
Patient A, a 17-year-old Caucasian male with a history of asthma, presented to the emergency department (ED) after experiencing fever and nausea for four days, followed by 1 day of diarrhoea and chest discomfort. Laboratory evaluation revealed elevated troponin levels. Transthoracic echocardiography showed left ventricular enlargement and apical dyskinesia. C. jejuni was identified in stool cultures. Cardiac magnetic resonance imaging confirmed the diagnosis of myocarditis. The patient was treated with furosemide and enalapril, with improvement of symptoms. Patient B, a previously healthy 14-year-old Caucasian male, presented to the ED with retrosternal chest pain lasting 2 h. He also reported a 3-day history of fever, nausea, and diarrhoea. Electrocardiography showed widespread PR-segment depression and concave ST-segment elevation. Laboratory testing revealed elevated Troponin I levels, and C. jejuni was identified in stool cultures. Cardiac magnetic resonance imaging findings were consistent with acute myocarditis. The patient was treated with ibuprofen and azithromycin, leading to resolution of symptoms. Eight months later, he returned with recurrent chest pain and dry cough. Cardiac magnetic resonance imaging at this time showed T1 and T2 criteria consistent with recurrent myocarditis.

Discussion
Although rare, clinicians should be aware of the potential cardiac involvement in patients with Campylobacter gastroenteritis, paying special attention to myocarditis symptoms like chest pain or shortness of breath, especially in areas with elevated Campylobacter infection rates.
A case report of a rare cardiac anomaly associated with Ellis–van Creveld syndrome: common atrium, partial atrioventricular septal defect, and hypoplastic left ventricle
Authors: Kido Takashi , Toba Shuhei , Yamasaki Takato , Asada Dai , Tsumura Sanae 
Published: January 2025

Abstract

Background
A partial atrioventricular septal defect (AVSD) with a hypoplastic left ventricle and common atrium is a rare combination of cardiac anomalies that can be associated with Ellis–van Creveld (EVC) syndrome.

Case summary
A female neonate with EVC syndrome was diagnosed with an unbalanced AVSD and hypoplastic left ventricle. Pulmonary artery banding and ductus ligation were performed at 23 days after birth. The postoperative course was complicated by moderate atrioventricular valve (AVV) regurgitation and low cardiac output. On postoperative Day 6, emergent extracorporeal membrane oxygenation (ECMO) was performed to treat acute circulatory failure. Under suspicion of systemic ventricular outflow tract obstruction, the Damus–Kaye–Stansel procedure with a systemic-to-pulmonary artery shunt and AVV plasty were performed. Intraoperatively, no ventricular septal defect was found. The right and left AVV orifices were found to be separated. Postoperatively, the patient could not be weaned from cardiopulmonary bypass and continued to receive ECMO support. Eight days postoperatively, a right ventricle-to-pulmonary artery shunt and division of the systemic-to-pulmonary artery shunt were performed to increase the pulmonary blood flow. On postoperative Day 5, the ECMO was successfully removed under continuous infusion of adrenalin, but the patient died of severe renal failure 4 days later. The parents consented to autopsy. The heart was permanently preserved by perfusion–distention fixation and wax infiltration.

Discussion
We reported a rare combination of cardiac defects of common atrium, partial AVSD, and hypoplastic left ventricle associated with EVC syndrome. Accurately diagnosing the presence of ventricular septal defect is essential part in determining surgical treatment strategy.
High implantation of a balloon-expandable valve above the left ventricular outflow calcification improves the prosthetic valve function without increasing complications: a case series
Authors: Onishi Kyohei , Mizutani Kazuki , Soejima Naoko , Fujita Kosuke , Yasuda Masakazu , Ueno Masafumi , Sakaguchi Genichi , Nakazawa Gaku 
Published: January 2025

Abstract

Background
The initial outcomes of transcatheter aortic valve replacement in patients with left ventricular outflow tract calcification are poor. Furthermore, balloon-expandable transcatheter aortic valve replacement is associated with an increased risk of annular rupture, and self-expandable transcatheter aortic valve replacement is associated with worse post-operative residual paravalvular leakage grades. Therefore, developing an optimal method for transcatheter aortic valve replacement for patients with left ventricular outflow tract calcification is desirable.

Case summary
We present two cases of successful balloon-expandable transcatheter aortic valve replacement, wherein the transcatheter heart valve was implanted above the left ventricular outflow tract calcification to avoid annular rupture and paravalvular leakage, and one case each of balloon-expandable and self-expandable transcatheter aortic valve replacements, wherein the transcatheter heart valve was implanted at a normal height. Although annular rupture did not occur in any of the cases, more-than-mild paravalvular leakage persisted post-operatively in cases where the transcatheter heart valve was placed at a normal height.

Discussion
Annular rupture is more likely to occur in areas with high calcification at the joint than in noncalcified areas. Furthermore, the greater the calcification in the landing zone of the transcatheter heart valve, the more the paravalvular leakage persists. Therefore, high implantation of transcatheter heart valves above the left ventricular outflow tract calcification can be an effective method to avoid annular rupture and paravalvular leakage.
Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off
Authors: Diakaki Makrina , Andreo Jimenez Beatriz , de Lange Ezra , Butterbach Patrick , van der Heijden Liesbeth , Köhl Jürgen , de Boer Wietse , Postma Joeke 
Published: January 2025

Abstract
Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.