bluuebunny/crossref_metadata_2025 huggingface dataset:
Active forgetting requires Sickie function in a dedicated dopamine circuit inDrosophila
Authors: Zhang Xiaofan , Sabandal John Martin , Tsaprailis George , Davis Ronald L.
Published: September 2022

Forgetting is an essential component of the brain’s memory management system, providing a balance to memory formation processes by removing unused or unwanted memories, or by suppressing their expression. However, the molecular, cellular, and circuit mechanisms underlying forgetting are poorly understood. Here we show that the memory suppressor gene,sickie, functions in a single dopamine neuron (DAn) by supporting the process of active forgetting inDrosophila. RNAi knockdown (KD) ofsickieimpairs forgetting by reducing the Ca2+influx and DA release from the DAn that promotes forgetting. Coimmunoprecipitation/mass spectrometry analyses identified cytoskeletal and presynaptic active zone (AZ) proteins as candidates that physically interact with Sickie, and a focused RNAi screen of the candidates showed that Bruchpilot (Brp)—a presynaptic AZ protein that regulates calcium channel clustering and neurotransmitter release—impairs active forgetting likesickieKD. In addition, overexpression ofbrprescued the impaired forgetting ofsickieKD, providing evidence that they function in the same process. Moreover, we show thatsickieKD in the DAn reduces the abundance and size of AZ markers but increases their number, suggesting that Sickie controls DAn activity for forgetting by modulating the presynaptic AZ structure. Our results identify a molecular and circuit mechanism for normal levels of active forgetting and reveal a surprising role of Sickie in maintaining presynaptic AZ structure for neurotransmitter release.
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome
Authors: Rahman Sanim , Hoffmann Niklas A. , Worden Evan J. , Smith Marissa L. , Namitz Kevin E. W. , Knutson Bruce A. , Cosgrove Michael S. , Wolberger Cynthia
Published: September 2022

The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase,
W
DR5,
R
bBp5,
A
sh2L, and
D
PY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.
Formation of Modern Chinese speech-quotativenǐ shuō‘you say’ and feedback-seekingnǐ shuō‘you tell me’
Authors: Long Haiping , Wang Xianhui , Wang Lei
Published: September 2022

In Modern Chinese, four construction types involvingnǐ shuōmay be distinguished. In this study, it is argued that the prosodically unseparated speech-quotativenǐ shuō(S1) develops from the prosodically separated speech-quotationnǐ shuō(S3) through a hypothesized complementation pathway which makes thenǐ shuōpredicate the matrix clause of the following content clause. Prosodically unseparated feedback-seekingnǐ shuō(S2), in contrast, develops from a prosodically separated feedback-seekingnǐ shuō(S4) via a hypothesized conjoining pathway which involves the loss of a prosodic gap between the feedback-seekingnǐ shuōpredicate and the clause that it occurs with. Contrary to the common assumption in the literature, S2 does not develop from S1. Meaning difference influences the selection of each of the two pathways, and in the source construction when an S3 or S4 is prosodically separated from the clause it occurs with, it is not the matrix clause of the latter. The account given in this study may also be used to explain the formation of English parenthetical predicateyou say.
Understanding the effect of nitrosylation on dynamics of human epidermal growth factor: a µs simulation study
Authors: Razzokov Jamoliddin , Fazliev Sunnatullo , Erkinova Dinora , Mamatkulov Shavkat , Chen Zhitong
Published: September 2022

Advancements in plasma science, such as the development cold atmospheric plasmas made it possible to easily generate reactive oxygen and nitrogen species (RONS) and apply them onto biological media at ambient conditions. Studying the interactions of RONS with biomolecules is a central topic of plasma medicine. One of the main targets of plasma medicine is to take control over signaling proteins such as human epidermal growth factor (hEGF) which is important protein in cancer treatment and wound healing. The oxidative damage of RONS on various proteins, including hEGF, was investigated using molecular dynamics (MD) simulations. However, another effect of RONS—nitrosative damage—is left unexplored. Plasma treatment can induce substantial damage via nitrosylation by reactive nitrogen species. Thus, elucidating effects of nitrosylation on protein structures is crucial, especially in plasma medicine. Here, we perform MD simulations to explore the effect of nitrosylation on the conformation of hEGF. We carried out MD simulations with different degrees of modifications of hEGF structures to mimic short and long plasma exposure times. Our results show that the nitrosylation induces conformational changes in hEGF and the breakage of disulfide bonds which might modulate binding of hEGF with its receptor. But the structural stability of hEGF remains almost unchallenged to the nitrosative damage, even to the disruption of disulfide bonds. The results assist plasma medicine applications in cancer treatment and wound healing by modulating plasma treatment time and chemical compositions of plasma-generated RONS to mediate effective oxidation of biological environment and develop optimal treatment protocols.
Low energy effective theory for axion strings
Authors: Dine Michael
Published: September 2022

We consider aspects of the low energy (classical) effective field theory description of
global cosmic strings. In the non-relativistic limit, we study the extent to which these are
described by the combination of the Nambu-Gotto and Kalb-Ramond actions. While in a formal sense
this is the case for infinitely long strings, for more realistic situations, the collective
coordinates of the system do not provide a complete description for more than brief intervals; as
time evolves it becomes necessary to include low momentum goldstone excitations as well.
Entropy of quantum Markov states on Cayley trees
Authors: Souissi Abdessatar , Mukhamedov Farrukh
Published: September 2022

In this paper, we continue the investigation of quantum Markov states (QMSs) and define their mean entropies. Such entropies are explicitly computed under certain conditions. The present work takes a huge leap forward at tackling one of the most important open problems in quantum probability, which concerns the calculations of mean entropies of quantum Markov fields. Moreover, it opens up a new perspective for the generalization of many interesting results related to the one-dimensional QMSs and quantum Markov chains to multi-dimensional cases.
Refraction, diffraction and energy losses studies using Arduino and Raspberry Pi
Authors: Janek M
Published: September 2022

The major purpose of this paper is to present laboratory measurements for a physics foundation course that meet the needs of the physics department. Furthermore, for obvious reasons, measures should be low-cost. Arduino and Raspberry Pi are low cost and open-source platforms that include both hardware and software that can be beneficial in a physics laboratory. Because of its inexpensive cost, wide range of sensors and transducers, ease of use, and open nature, they are the optimal tool for engaging students in active and cooperative learning. Measurements based on mentioned platforms related to refraction and diffraction processes, as well as to hysteresis losses measurement, are presented.
Amplification and interaction of two optical waves with third harmonic spectral delay
Authors: Kasapeteva Z , Dakova D , Kovachev K , Kovachev L
Published: September 2022

In the present paper the parametric interaction between two optical waves, which are propagating in few-mode optical fibers, is investigated. This occurs under the influence of the processes of third harmonic generation, self-phase modulation and cross-phase modulation. The generation of third-harmonic or THz generation in femtosecond region is described by a system of two coupled nonlinear differential equations. A new analytical solution of this system, which characterizes the periodic energy exchange between the two waves, is found. Depending on the wavenumber mismatch Δk, the obtained result can be used for studying different optical processes of generation of signal wave in nonlinear dispersive media. The mentioned effects are strongly related to modern optical sensors, parametric amplifiers and communication systems.
Laser ring structures in step-index fibers
Authors: Slavchev V , Dakova A , Gocheva N , Bozhikoliev I , Kovachev K , Biswas A
Published: September 2022

The formation and propagation of optical ring structures, given by a system of amplitude equations for the components of the electric field is investigated. The calculations are made in approximation of second-order linear dispersion and self-phase modulation. New class analytical solutions, characterizing the generation and evolution of laser ring structures in optical waveguides with step-index profile and anomalous dispersion, are described in the present work. The stability of these optical formations is a result of the specific combination of nonlinearity, diffraction and angular distribution. Laser vortices have an amplitude type of singularity which appears as depolarization of the vector field in the light radiation spot.
RSSI study of wireless Internet of Things technologies
Authors: Dinev D , Haka A
Published: September 2022

The Internet of Things (IoT) idea now entails a dispersed collection of different sensor networks with several functions that collect data, which is then analysed and used in applications such as smart cities. These networks are capable of transmitting massive volumes of data in a relatively efficient, yet unsecure wireless environment. These applications will only succeed if is developed a dependable a low-cost real-time method for pinpointing accurate location. Power consumption is another consideration for indoor localisation. Recent wireless technologies like ZigBee, Bluetooth Low Energy (BLE) and Long Range (LoRa), use less resources, making them ideal for interior positioning. When IoT devices are utilised, these technologies are compared in terms of precision of localisation and power consumption. Tracking the Received Signal Strength Indicator (RSSI) values can be used to locate mobile sensor nodes for low-power IoT networks. The RSSI values of sensor nodes in the BLE, ZigBee and LoRa networks for IoT were explore in this study.
Simplified model of process to design the two stages gasification system for reuse of municipal waste
Authors: Šetinc Marko
Published: September 2022

Municipal waste largely consists of carbon, hydrogen and oxygen. Other elements are represented in smaller proportions. Mostly, this type of waste ends up in the incinerator or landfill. Re-use is limited due to the contamination of the raw material. On paper, the model is presented that enables step by step conversion of waste into synthesis gas, which is a raw material for methanol production and production of other hydrocarbons, through the gasification system. This method allows endless re-use of material, with part of the raw material being converted into energy, carbon dioxide and water. On paper, the design of the model and the efficiency of the process is presented.
Analysis of indoor environment perceptions in the smart building
Authors: Krawczyk N , Wojciechowska P
Published: September 2022

Thermal comfort is of fundamental importance for people staying in a closed environment. The article focuses on research on thermal comfort in a smart building. The study was performed using two methods. The first method with the Testo 400 microclimate meter, the second method with anonymous questionnaires. The microclimate meter made it possible to measure air parameters (including temperature, humidity, speed, CO2 concentration). The anonymous poll included questions about the thermal sensations vote, thermal preferences, thermal acceptability vote, air humidity and humidity preferences vote. Students from Poland, faculty of Environmental, Geomatic and Energy Engineering, participated in the study. The research showed that the respondents preferred lower thermal conditions with the temperature range from 22.4 °C to 25.1 °C. The percentage of the students who found the conditions as unsatisfactory - has exceeded the permitted 10% range.
Optimization of the operation of Drăgan-Iad hydropower development using Flower Pollination Algorithm
Authors: Tică E-I , Neagoe A , Popa F , Popa B
Published: September 2022

For the operation of a large hydropower development, it was imagined as optimization problem to realize an annual planned energy generation with monthly imposed fractions. It was conceived a model based on a flower pollination algorithm. Simulations were done for mean hydrological year, with imposed minimal and maximal volumes, for five initial volumes in the reservoir and in two hypotheses related to the imposed annual energy. For imposing realization of the designed energy, for the initial volume into the reservoir set to three lowest values, the planned energy is not realized because the volume into reservoir reaches the minimum allowable volume at the end of the year. For larger volumes at the beginning of the year, the planned annual energy is realized. For the planned annual energy imposed at a lower value, for the three lowest volumes into the reservoir at the beginning of the year the planned energy is realized, and for the other two larger values the program realizes a larger energy generation because, during the year, the volume into the reservoir reach the maximum allowable volume and it was compulsory to operate the hydropower plant to lower the volume. The overall conclusion of the paper is that FPA is very efficient for solving this type of optimization problem applied to a large hydropower development.
Combined electrochemical treatment coupled to anaerobic digestion effluents
Authors: Marmanis D , Emmanouil C , Thysiadou A , Fantidis J G , Kokkinos N , Diamantis V
Published: September 2022

Electrochemical treatment is an effective method to improve physicochemical characteristics of effluents and to minimize the environmental footprint of anaerobic digestion facilities. In the present research an anaerobic digester effluent was subjected to post-treatment, using electro-oxidation or electrocoagulation processes for significant reduction of Chemical oxygen demand and ammonia. A combined electro-oxidation and electrocoagulation treatment was also performed. Results show satisfactory decrease of both Chemical oxygen demand and ammonium nitrogen, which however were relative to the method applied, the time duration and the current intensity. A combined use of both methods may be the best solution for the post-treatment of this high burden effluent. All the presented values have occurred from experiments in the Chemistry Department of the International Hellenic University.
Verification of the Fanger model with field experimental data
Authors: Stokowiec K , Kotrys-Działak D , Jastrzębska P
Published: September 2022

Thermal comfort is one of the main aspect of human life due to the period of time each of us spends inside of the enclosed room on one hand as well as the health issues connected with the sick building syndrome on the other. Presently, the international standards are based on the Fanger model with calculations of proper indexes according to the inside air parameters as well as characteristics for room users. The paper presents the verification of Fanger model with experimental data obtained from research conducted in 6 classrooms of an intelligent, educational building. The measurements were acquired by means of Testo 400 meter where air parameters such as temperature or humidity were collected. For other evidence the questionnaire was prepared, where respondents presented their thermal sensation together with the information of their clothes present thermal insulation. The results proved that the Fanger model is not precise, since the findings calculated with the international standard differ from those obtained from the questionnaires.
Study of the electromechanical load of the motor-reducer group for a double drum drive of a belt conveyor
Authors: Dzhustrov K , Iliev Zh
Published: September 2022

The article presents a study of the electro-mechanical loading of the motor-reducer group for driving a belt conveyor. The current of the two drive motors has been measured following an emergency replacement of the reducer gear and the hydraulic clutch of the first drive unit. The traction forces in the belting generated by the two driving drums have been established. A comparison is made of the current records from this study and those from the enterprise information system. Thermal imaging photos have been taken of the two reducers and the hydraulic clutches of the drive units. The electromechanical state of the motor-reducer groups is analyzed and conclusions are drawn regarding the operation of the belt conveyor.
Influence degree of skin-effect for overhead line conductors
Authors: Sukhichev M , Skochko E
Published: September 2022

This paper analyzes the skin-effect influence on ACSR conductors for overhead lines. The analysis is based on numerical models: one cylinder, and two coaxial cylinders, and cylinders layers. The authors compare all models with each other, as well as with the well-known analytical solution, and direct current mode. All numerical models were verified by comparison with the analytical solution. The results show the one cylinder model get incorrect results for ACSR conductors. Moreover, the maximum error about 40% is given by conductors with a medium cross-sectional area, such as the ”AC 240/39” conductor by GOST 839-2019. The two coaxial cylinders model gives better results but about 10% less than the cylinders layers model, since it does not consider the electric field penetration between wires of a conductor. As a result, the authors conclude that the skin effect has a great influence for all ACSR conductors.
Dynamical symmetry algebras of two superintegrable two-dimensional systems
Authors: Marquette I , Quesne C
Published: September 2022

A complete classification of 2D quadratically superintegrable systems with scalar potential on two-dimensional conformally flat spaces has been performed over the years and 58 models, divided into 12 equivalence classes, have been obtained. We will re-examine two pseudo-Hermitian quantum systems E
8 and E
10 from such a classification by a new approach based on extra sets of ladder operators. They correspond in fact to two of those equivalence classes. Those extra ladder operators are exploited to obtain the generating spectrum algebra and the dynamical symmetry one. We will relate the generators of the dynamical symmetry algebra to the Hamiltonian, thus demonstrating that the latter can be written in an algebraic form. We will also link them to the integrals of motion providing the superintegrability property. This demonstrates how the underlying dynamical symmetry algebra allows to write the integrals in terms of its generators and therefore explains the symmetries. Furthermore, we will exploit those algebraic constructions to generate extended sets of states and give the action of the ladder operators on them. We will present polynomials of the Hamiltonian and the integrals of motion that vanish on some of those states, then demonstrating that the sets of states not only contain eigenstates, but also generalized states which are beyond the well-known eigenstates of diagonalizable Hamiltonians and satisfy more complicated polynomial identities. Our approach provides a natural framework for such states.
Dynamics of sparse Boolean networks with multi-node and self-interactions
Authors: Hurry Christian John , Mozeika Alexander , Annibale Alessia
Published: September 2022

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

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

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

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

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

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

Considerable 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

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 >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

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

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

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

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

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

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.
SELF-ADMINISTRATION OR PRACTITIONER ADMINISTRATION? THE SCOPE OF FUTURE GERMAN ASSISTED DYING LEGISLATION
Authors: Braun Kerstin
Published: September 2022

In 2020, the German Federal Constitutional Court declared unconstitutional and void a 2015 criminal law penalising suicide assistance in a recurring fashion and called into existence a right to a self-determined death, including the use of suicide services, where available. Due to subsequent legislative inaction, no holistic assisted dying legislation offering protection for vulnerable individuals is currently in place in Germany. Calls have been made for law reform in this area. This article contemplates the possible scope of a future assisted dying framework in Germany. It does so by focusing on the method of administration and analyses whether such a framework should be limited to allowing eligible persons to self-administer relevant lethal medications, which have been prescribed to them by a medical practitioner or whether, and to what extent, practitioners should be able to administer relevant lethal substances to patients. This is comparatively analysed while also keeping in mind any stipulations made by the German Constitutional Court in its 2020 judgment on the requirements of future assisted dying legislation. The article concludes that an assisted dying framework allowing a free choice between self and practitioner administration in Germany best complies with the guidance provided by the Constitutional Court.
Ion acceleration in Mars’ twisted magnetotail
Authors: Curry Shannon M , Tatum P , Mitchell D , Luhmann J G , McFadden J , Ruhunusiri S , DiBraccio G , Ramstad R , Xu S
Published: September 2022

Mars lacks a global magnetic field and instead has a unique, ‘hybrid’ magnetosphere composed of crustal magnetic fields, which are stronger in the Southern hemisphere than the Northern hemisphere. These crustal fields are believed to drive a twist in the magnetotail at Mars. This is important because heavy ions escape from this induced magnetotail, which is a major source of atmospheric erosion. We present analysis of heavy ions produced in Mars’ upper atmosphere that are transported downtail along the twisted current sheet and observed by the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission. We identified O+, O$_2\, ^+$, and CO$_2\, ^+$ being accelerated to different energies at a range of distances downtail and found that heavy ions in the 10–50 eV energy population have the highest flux. We present tail slices of ion fluxes for different interplanetary magnetic field (IMF) configurations based on the BY component of the IMF and find that the different configurations affect the degree of tail twist and the transport of heavy ions in the induced magnetotail lobes. We find that the total escape rate for O+, O$_2\, ^+$, and CO$_2\, ^+$ is 5.5e24 s-1, with 50% escaping between 2–200 eV.