bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of sparse Boolean networks with multi-node and self-interactions
Authors: Hurry Christian John , Mozeika Alexander , Annibale Alessia 
Published: September 2022

Abstract
We analyse the equilibrium behaviour and non-equilibrium dynamics of sparse Boolean networks with self-interactions that evolve according to synchronous Glauber dynamics. Equilibrium analysis is achieved via a novel application of the cavity method to the temperature-dependent pseudo-Hamiltonian that characterizes the equilibrium state of systems with parallel dynamics. Similarly, the non-equilibrium dynamics can be analysed by using the dynamical version of the cavity method. It is well known, however, that when self-interactions are present, direct application of the dynamical cavity method is cumbersome, due to the presence of strong memory effects, which prevent explicit analysis of the dynamics beyond a few time steps. To overcome this difficulty, we show that it is possible to map a system of N variables to an equivalent bipartite system of 2N variables, for which the dynamical cavity method can be used under the usual one time approximation scheme. This substantial technical advancement allows for the study of transient and long-time behaviour of systems with self-interactions. Finally, we study the dynamics of systems with multi-node interactions, recently used to model gene-regulatory networks (GRNs), by mapping this to a bipartite system of Boolean variables with two-body interactions. We show that when interactions have a degree of bidirectionality such systems are able to support a multiplicity of diverse attractors, an important requirement for a GRN to sustain multi-cellular life.
A study on in-vitro behaviour of stainless steel 316L subjected to rotational magnetorheological abrasive flow finishing process
Authors: Karthikeyan S , Mohan B , Kathiresan S , Anbuchezhiyan G 
Published: September 2022

Abstract
In Rotational Magnetorheological Abrasive Flow Finishing (R-MRAFF) process, Magnetic Field Intensity (MFI) is the primary factor for the formation of ferrous chains which is responsible for finishing. Changing the pole distance between magnets to achieve a difference in MFI values will alter the strength of the ferrous chains. In this study, three different MFI values such as 0.34, 0.36, and 0.40 Tesla were chosen for finishing on Stainless Steel 316L (SS 316L). Surface wettability, bio-corrosion, and hemocompatibility studies were conducted to investigate the in-vitro behavior of SS 316L. The wettability of the implants changed from hydrophobic (100.92°) to hydrophilic (83.452°) surface as the MFI value increased. Bio-corrosion studies revealed improved corrosion resistance for R-MRAFF process finished samples, with the corrosion rate reduced from 3.693 to 0.967 μm year−1. Hemocompatibility of SS 316L was improved with reduced platelet adhesion when compared to the pristine sample.
Concurrent lines on del Pezzo surfaces of degree one
Authors: van Luijk Ronald , Winter Rosa 
Published: September 2022

Let

X
X

be a del Pezzo surface of degree one over an algebraically closed field, and

K
X

K_X

its canonical divisor. The morphism

φ
\varphi

induced by

|

−
2

K
X

|

|-2K_X|

realizes

X
X

as a double cover of a cone in

P

3

\mathbb {P}^3

, ramified over a smooth sextic curve. The surface

X
X

contains 240 exceptional curves. We prove the following statements. For a point

P
P

on the ramification curve of

φ
\varphi

, at most sixteen exceptional curves contain

P
P

in characteristic

2
2

, and at most ten in all other characteristics. Moreover, for a point

Q
Q

outside the ramification curve, at most twelve exceptional curves contain

Q
Q

in characteristic

3
3

, and at most ten in all other characteristics. We show that these upper bounds are sharp, except possibly in characteristic 5 outside the ramification curve.
Jupytope: computational extraction of structural properties of viral epitopes
Authors: Rashid Shamima , Ng Teng Ann , Kwoh Chee Keong 
Published: September 2022

Abstract
Epitope residues located on viral surface proteins are of immense interest in immunology and related applications such as vaccine development, disease diagnosis and drug design. Most tools rely on sequence-based statistical comparisons, such as information entropy of residue positions in aligned columns to infer location and properties of epitope sites. To facilitate cross-structural comparisons of epitopes on viral surface proteins, a python-based extraction tool implemented with Jupyter notebook is presented (Jupytope). Given a viral antigen structure of interest, a list of known epitope sites and a reference structure, the corresponding epitope structural properties can quickly be obtained. The tool integrates biopython modules for commonly used software such as NACCESS, DSSP as well as residue depth and outputs a list of structure-derived properties such as dihedral angles, solvent accessibility, residue depth and secondary structure that can be saved in several convenient data formats. To ensure correct spatial alignment, Jupytope takes a list of given epitope sites and their corresponding reference structure and aligns them before extracting the desired properties. Examples are demonstrated for epitopes of Influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) viral strains. The extracted properties assist detection of two Influenza subtypes and show potential in distinguishing between four major clades of SARS-CoV2, as compared with randomized labels. The tool will facilitate analytical and predictive works on viral epitopes through the extracted structural information. Jupytope and extracted datasets are available at https://github.com/shamimarashid/Jupytope.
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames
Authors: Zhang Meng , Zhao Jian , Li Chen , Ge Fang , Wu Jing , Jiang Bin , Song Jiangning , Song Xiaofeng 
Published: September 2022

Abstract
Short open reading frames (sORFs) refer to the small nucleic fragments no longer than 303 nt in length that probably encode small peptides. To date, translatable sORFs have been found in both untranslated regions of messenger ribonucleic acids (RNAs; mRNAs) and long non-coding RNAs (lncRNAs), playing vital roles in a myriad of biological processes. As not all sORFs are translated or essentially translatable, it is important to develop a highly accurate computational tool for characterizing the coding potential of sORFs, thereby facilitating discovery of novel functional peptides. In light of this, we designed a series of ensemble models by integrating Efficient-CapsNet and LightGBM, collectively termed csORF-finder, to differentiate the coding sORFs (csORFs) from non-coding sORFs in Homo sapiens, Mus musculus and Drosophila melanogaster, respectively. To improve the performance of csORF-finder, we introduced a novel feature encoding scheme named trinucleotide deviation from expected mean (TDE) and computed all types of in-frame sequence-based features, such as i-framed-3mer, i-framed-CKSNAP and i-framed-TDE. Benchmarking results showed that these features could significantly boost the performance compared to the original 3-mer, CKSNAP and TDE features. Our performance comparisons showed that csORF-finder achieved a superior performance than the state-of-the-art methods for csORF prediction on multi-species and non-ATG initiation independent test datasets. Furthermore, we applied csORF-finder to screen the lncRNA datasets for identifying potential csORFs. The resulting data serve as an important computational repository for further experimental validation. We hope that csORF-finder can be exploited as a powerful platform for high-throughput identification of csORFs and functional characterization of these csORFs encoded peptides.
Integrating multimodal data through interpretable heterogeneous ensembles
Authors: Li Yan Chak , Wang Linhua , Law Jeffrey N , Murali T M , Pandey Gaurav 
Published: September 2022

Abstract

Motivation
Integrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems.

Results
We propose Ensemble Integration (EI) as a novel systematic implementation of the late integration approach. EI infers local predictive models from the individual data modalities using appropriate algorithms and uses heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data and mortality due to coronavirus disease 2019 (COVID-19) from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of a representative EI model for COVID-19 mortality prediction identified several disease-relevant features, such as laboratory test (blood urea nitrogen and calcium) and vital sign measurements (minimum oxygen saturation) and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling.

Availability and implementation
Code and data are available at https://github.com/GauravPandeyLab/ensemble_integration.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
HIF-1α is essential for the augmentation of myometrial contractility during labor
Authors: Wen Bolun , Zheng Zheng , Wang Lele , Qian Xueya , Wang Xiaodi , Chen Yunshan , Bao Junjie , Jiang Yanmin , Ji Kaiyuan , Liu Huishu 
Published: September 2022

Abstract
Uterine contraction is crucial for a successful labor and the prevention of postpartum hemorrhage. It is enhanced by hypoxia; however, its underlying mechanisms are yet to be elucidated. In this study, transcriptomes revealed that hypoxia-inducible factor-1alpha was upregulated in laboring myometrial biopsies, while blockade of hypoxia-inducible factor-1alpha decreased the contractility of the myometrium and myocytes in vitro via small interfering RNA and the inhibitor, 2-methoxyestradiol. Chromatin immunoprecipitation sequencing revealed that hypoxia-inducible factor-1alpha directly binds to the genome of contraction-associated proteins: the promoter of Gja1 and Ptgs2, and the intron of Oxtr. Silencing the hypoxia-inducible factor-1alpha reduced the expression of Ptgs2, Gja1, and Oxtr. Furthermore, blockade of Gja1 or Ptgs2 led to a significant decrease in myometrial contractions in the hypoxic tissue model, whereas atosiban did not remarkably influence contractility. Our study demonstrates that hypoxia-inducible factor-1alpha is essential for promoting myometrial contractility under hypoxia by directly targeting Gja1 and Ptgs2, but not Oxtr. These findings help us to better understand the regulation of myometrial contractions under hypoxia and provide a promising strategy for labor management and postpartum hemorrhage treatment.
Modulating hierarchical learning by high-definition transcranial alternating current stimulation at theta frequency
Authors: Liu Meng , Dong Wenshan , Wu Yiling , Verbeke Pieter , Verguts Tom , Chen Qi 
Published: September 2022

AbstractConsiderable evidence highlights the dorsolateral prefrontal cortex (DLPFC) as a key region for hierarchical (i.e. multilevel) learning. In a previous electroencephalography (EEG) study, we found that the low-level prediction errors were encoded by frontal theta oscillations (4–7 Hz), centered on right DLPFC (rDLPFC). However, the causal relationship between frontal theta oscillations and hierarchical learning remains poorly understood. To investigate this question, in the current study, participants received theta (6 Hz) and sham high-definition transcranial alternating current stimulation (HD-tACS) over the rDLPFC while performing the probabilistic reversal learning task. Behaviorally, theta tACS induced a significant reduction in accuracy for the stable environment, but not for the volatile environment, relative to the sham condition. Computationally, we implemented a combination of a hierarchical Bayesian learning and a decision model. Theta tACS induced a significant increase in low-level (i.e. probability-level) learning rate and uncertainty of low-level estimation relative to sham condition. Instead, the temperature parameter of the decision model, which represents (inverse) decision noise, was not significantly altered due to theta stimulation. These results indicate that theta frequency may modulate the (low-level) learning rate. Furthermore, environmental features (e.g. its stability) may determine whether learning is optimized as a result.
EACVI survey on the multi-modality imaging assessment of the right heart
Authors: Soliman-Aboumarie Hatem , Joshi Shruti S , Cameli Matteo , Michalski Blazej , Manka Robert , Haugaa Kristina , Demirkiran Ahmet , Podlesnikar Tomaz , Jurcut Ruxandra , Muraru Denisa , Badano Luigi P , Dweck Marc R 
Published: September 2022

Abstract

Aims
The European Association of Cardiovascular Imaging (EACVI) Scientific Initiatives Committee performed a global survey to evaluate the use of different cardiac imaging modalities for the evaluation of the right heart.

Methods and results
Delegates from 250 EACVI registered centres were invited to participate in a survey which was also advertised on the EACVI bulletin and on social media. One hundred and thirty-eight respondents from 46 countries across the world responded to the survey. Most respondents worked in tertiary centres (79%) and echocardiography was reported as the commonest imaging modality used to assess the right ventricle (RV). The majority of survey participants (78%) included RV size and function in &gt;90% of their echocardiographic reports. The RV basal diameter obtained from the apical four-chamber view and the tricuspid annular plane systolic excursion were the commonest parameters used for the echocardiographic assessment of RV size and function as reported by 82 and 97% respondents, respectively. Survey participants reported arrhythmogenic cardiomyopathy as the commonest condition (88%) where cardiac magentic resonance (CMR) imaging was used for right heart assessment. Only 52% respondents included RV volumetric and ejection fraction assessments routinely in their CMR reports, while 30% of respondents included these parameters only when RV pathology was suspected. Finally, 73% of the respondents reported pulmonary hypertension as the commonest condition where right heart catheterization was performed.

Conclusion
Echocardiography remains the most frequently used imaging modality for the evaluation of the right heart, while the use of other imaging techniques, most notably CMR, is increasing.
Midterm results of endoscopically assisted first rib resection in the zero position for thoracic outlet syndrome
Authors: Satake Hiroshi , Honma Ryusuke , Nito Toshiya , Naganuma Yasushi , Shibuya Junichiro , Maruyama Masahiro , Uno Tomohiro , Takagi Michiaki 
Published: September 2022

Abstract

OBJECTIVES
We have hypothesized that an endoscopically assisted transaxillary approach in the zero position would be able to improve visualization and allow safe surgery for thoracic outlet syndrome.

METHODS
We performed surgery only for patients with certain objective findings, including blood flow disruption, low blood flow and accelerated blood flow in the subclavian artery demonstrated using Doppler sonography, narrowing of the scalene interval width between the anterior and middle interscalene muscles (interscalene base) or costoclavicular space demonstrated using Duplex ultrasonography or computed tomography angiography. The present study included 45 consecutive patients (50 limbs) who underwent endoscopic transaxillary first rib resection with scalenotomy and brachial plexus neurolysis. We assessed the intraoperative parameters, including the interscalene base, blood loss, operation time, patient satisfaction, preoperative and postoperative Quick Disability of the Arm, Shoulder and Hand and complications.

RESULTS
The mean intraoperatively measured interscalene base width was 6.4 mm. All patients showed improvement after surgery. The outcome was excellent in 40% of cases, good in 48%, fair in 12% and poor in none. Pneumothorax was present in 6%. There were no other complications and no recurrences. Among patients who had been followed up for at least 2 years, the Quick Disability of the Arm, Shoulder and Hand score was significantly improved (42 before surgery vs 12 at final follow-up), especially in athletes relative to non-athletes (0.2 vs 16). The present approach achieved complete relief in 43% of cases overall (91% in athletes and 16% in non-athletes).

CONCLUSIONS
Endoscopically assisted transaxillary first rib resection and brachial plexus neurolysis in the zero position are useful and safe for thoracic outlet syndrome, especially in athletes.
New asymptotic stability results for nonautonomous nonlinear fractional order systems
Authors: Lenka Bichitra Kumar , Bora Swaroop Nandan 
Published: September 2022

Abstract
This paper considers nonautonomous nonlinear fractional order systems where state variables are associated with different fractional orders and lie in the interval $(0, 1]$. Some new comparison theories are proposed for the asymptotic stability analysis of such systems. Illustrative examples are presented, and it is established that some proposed results are effective for the asymptotic analysis of such systems.
Amplitude semblance and its fusion with the third-generation coherence for characterization of fractured-vuggy carbonate reservoirs
Authors: Sui Jingkun , Zeng Qingcai , Yang Zhifang , Zheng Xiaodong , Hu Tianyue 
Published: September 2022

Abstract
In the Tarim Basin, the main hydrocarbon reservoirs of Ordovician carbonate rocks are fractured-vuggy reservoirs, of which the underground river type reservoirs are an important type. Seismic coherence attribute can highlight seismic discontinuity caused by tectonic movements, reservoir boundaries, sedimentary body boundaries or other factors. Thus, it is a widely used key technique in seismic interpretation. There are many algorithms to determine the coherence. Typically, the coherence algorithm based on eigen-structure analysis is the most robust, but is sensitive to waveform differences and insensitive to amplitude differences. This paper proposes an amplitude coherence attribute to measure semblance of root-mean-square (RMS) amplitudes of multiple traces and fuses it with the third-generation coherence (C3) to describe the boundary of underground river. Model test and case study prove that the proposed fused algorithm can effectively identify the amplitude and waveform differences in seismic data.
Q-value estimation of Chang'e
-4 lunar penetrating radar data
Authors: Wang Junyi , Zhao Jingtao , Peng Suping , Cui Rui 
Published: September 2022

Abstract
The geophysical quality Q involved in anelastic energy absorption plays a significant role in the study of subsurface pressure, rock types and temperature distributions. However, with respect to newly collected lunar penetrating radar (LPR) data, scholars mainly focused on related parameters such as the permittivity, density and chemical composition, while the Q-value has rarely been estimated. In this study, we improved the multi-channel quality factor Q estimation method to study shallow underground structures of the Moon, interpret the geological structure and provide reference for the exploration of lunar resources. The improved windowed multi-channel Q estimation method uses multiple spatial coherence-constrained inversion to achieve a stable Q estimation of the whole direction profile in the presence of noise. An example of a numerical simulation of the simple lunar geological model illustrates the feasibility of the proposed method in estimating the Q-value. Partial lunar data collected by Chang'e-4 LPR were used to demonstrate its value with respect to the interpretation of the stratigraphic development history, dislocation and relative permittivity of the Moon.
Dissociated response among multiple metastatic lesions in the patients with metastatic renal cell carcinoma treated with immune checkpoint inhibitors
Authors: Negishi Takahito , Nakagawa Tohru , Nishiyama Naotaka , Kitamura Hiroshi , Okajima Eijiro , Furubayashi Nobuki , Hori Yoshifumi , Kuroiwa Kentarou , Son Yuhyon , Seki Narihito , Tomoda Toshihisa , Nakamura Motonobu 
Published: September 2022

Abstract

Introduction
Metastases from renal cell carcinoma develop in various organs. However, the breadth of discrepancy in response to immune checkpoint inhibitors across tumor sites within the same individual remains unclear.

Patients and methods
We reviewed 50 patients with metastatic renal cell carcinoma who had target lesions at multiple sites and received nivolumab monotherapy (n = 36) or nivolumab plus ipilimumab (n = 14). When the best overall response in tumor burden increased at one site but decreased at other sites, the response was defined as a dissociated response. The response was evaluated according to the Response Evaluation Criteria in Solid Tumors 1.1, and patients who met the definition of dissociated response were categorized as dissociated response. The rate of dissociated response and prognosis were evaluated.

Results
Eight of 36 (22%) and 4 of 14 (29%) patients treated with nivolumab and nivolumab plus ipilimumab were categorized as having dissociated response, respectively. The median overall survival of the patients treated with nivolumab was 20.2 months for those with a partial response, 6.8 months for those with stable disease, and 13.2 months for those with progressive disease, while dissociated response was not reached. There was no significant difference in the median overall survival between patients categorized as having progressive disease and those with dissociates response (P = 0.224).

Conclusion
A certain proportion of patients with metastatic renal cell carcinoma show dissociated response when treated with immune checkpoint inhibitors. The prognosis of patients with dissociated response and progressive disease was not shown to be significantly different.
Exploring the Impact of the COVID-19 Pandemic on Tuberculosis Care and Prevention
Authors: Sahu Suvanand , Wandwalo Eliud , Arinaminpathy Nimalan 
Published: September 2022

Abstract
The COVID-19 pandemic has set back the global tuberculosis (TB) response by several years. In 2020, access to TB prevention and care declined sharply, with TB notifications dropping by 18% compared to 2019. Declines were more pronounced in children, with a 24% drop in 0–14 year-olds and a 28% drop in 0–4 year-olds. As a result, in 2020 the number of deaths due to TB increased to 1.5 million across all ages, reversing a decade-long declining trend. Progress toward the UN High Level Meeting targets for 2022 is at risk, including the targets related to children for TB and drug-resistant TB treatments, and TB preventive therapy. Nonetheless, ending TB by 2030 as envisaged in the Sustainable Development Goals (SDGs) is still possible, but requires increased investments in accelerated case detection, subclinical TB, preventive therapy and an effective vaccine. Investing in TB could prepare the world better for fighting a future airborne pandemic.