bluuebunny/crossref_metadata_2025 huggingface dataset:
ARGONAUTE10 controls cell fate specification and formative cell divisions in the Arabidopsis root
Authors: El Arbi Nabila , Schürholz Ann-Kathrin , Handl Marlene U , Schiffner Alexei , Hidalgo Prados Inés , Schnurbusch Liese , Wenzl Christian , Zhao Xin’Ai , Zeng Jian , Lohmann Jan U , Wolf Sebastian
Published: April 2024

A key question in plant biology is how oriented cell divisions are integrated with patterning mechanisms to generate organs with adequate cell type allocation. In the root vasculature, a gradient of miRNA165/6 controls the abundance of HD-ZIP III transcription factors, which in turn control cell fate and spatially restrict vascular cell proliferation to specific cells. Here, we show that vascular development requires the presence of ARGONAUTE10, which is thought to sequester miRNA165/6 and protect HD-ZIP III transcripts from degradation. Our results suggest that the miR165/6-AGO10-HDZIP III module acts by buffering cytokinin responses and restricting xylem differentiation. Mutants of AGO10 show faster growth rates and strongly enhanced survival under severe drought conditions. However, this superior performance is offset by markedly increased variation and phenotypic plasticity in sub-optimal carbon supply conditions. Thus, AGO10 is required for the control of formative cell division and coordination of robust cell fate specification of the vasculature, while altering its expression provides a means to adjust phenotypic plasticity.
Sulfur-doped porous carbon sheets embedded with rich iron sites for 1O2 dominated peroxymonosulfate activation
Authors: Song Yadan , Liu Yalong , Li Yangju , Hu Haipeng , Huang Kexin , Zhang Zhe , Li Zhongxian , Cao Wanning , Jiang Kai , Wu Dapeng
Published: April 2024

Porous carbon films co-doped with iron, nitrogen, and sulfur were synthesized via a one-step pyrolysis process, which have multiple active sites and can produce bulk 1O2 through PMS activation, which is effective in phenol degradation.
Memory effect in ferroelectric polyvinylidene fluoride (PVDF) films via spin crossover probes
Authors: Koo Yong Sung , Galan-Mascaros Jose Ramon
Published: April 2024

A composite film combining a ferroelectric organic polymer with a spin crossover coordination polymer exhibits memory effect in their ferroelectric properties, with the appearance of thermal hysteresis in electric polarization and coercivity.
Heterointerface regulation of covalent organic framework-anchored graphene via a solvent-free strategy for high-performance supercapacitor and hybrid capacitive deionization electrodes
Authors: Xu Liming , Liu Yong , Xuan Xiaoyang , Xu Xingtao , Li Yuquan , Lu Ting , Pan Likun
Published: March 2024

A 2D redox-active pyrazine-based COF was solvent-free anchored on graphene for heterointerface regulation, displaying exciting energy storage and desalination performances.
Iodomethane in C1 chemistry: application in palladium-catalyzed [2 + 2 + 1] annulation
Authors: Zhang Jin-Ke , Fang Yu-Chen , Chen Jia-He , Shan Jing , Bai Mei , Huang Qiang , Chen Yong-Zheng , Han Wen-Yong
Published: April 2024

A variety of chromone-containing polycyclic compounds were smoothly forged in up to 93% yield via palladium-catalyzed [2 + 2 + 1] annulation of 3-iodochromones, bridged olefins, and iodomethane, in which iodomethane was used as the methylene source.
Synthesis and characterization of a CsPbCl3 perovskite doped with Nd3+: structural, optical, and energy transfer properties
Authors: Stefanski Mariusz , Bondzior Bartosz , Basinski Adam , Ptak Maciej , Lou Bibo , Ma Chong-Geng
Published: April 2024

The levels of Nd3+ in CsPbCl3 lie below the top of the host's VB. Consequently, Nd3+ luminescence is not observed.
Spiro-centre substitution effects in the intramolecular spin–spin interactions of spirobiacridine diradicals
Authors: Ogawa Shinichi , Kanetomo Takuya , Enomoto Masaya
Published: April 2024

Spirodiradicals with the Si and Ge spiro atoms exhibit a S = 1 state. The magnetic interaction in the Si derivative was found to be lower than that in the Ge derivative, implying a negative effect on σ*(Si–Cα)–π* hyperconjugation.
Hydrogenolysis of furfuryl alcohol over CuCeMgAl mixed metal oxide catalysts derived from layered double hydroxides
Authors: Wang Zhihui , Li Wenbo , Fu Xinyao , Zhang Chen , Zhang Wei , Huang Long , Li Cuiqing
Published: April 2024

LDH-derived CuCeMgAl mixed metal oxide catalysts were synthesized. Ce addition promoted Cu dispersion and improved catalyst basicity, resulting in high activity in furfuryl alcohol hydrogenolysis and high selectivity toward 1,2-pentanediol.
Analysis of Stress Distribution and Displacement Based on the Miniscrew Positions of the Palatal Slope Bone-borne Expander: A Finite Element Study
Authors: Leeisaramas Chakree , Chantarapanich Nattapon , Inglam Samroeng , Insee Kanlaya
Published: March 2024

Objectives This study aimed to investigate the stress distribution pattern of the palatal slope bone-borne expander on the maxillary area according to a different anteroposterior position of anchored miniscrews using finite element analysis.

Materials and Methods Nasomaxillary stereolithography files with three different anteroposterior anchored miniscrew positions of the palatal slope bone-borne expander were determined as model A, B, and C. Each model consists of four supported miniscrews. Model A: two anterior miniscrews were located between the maxillary canine and the first premolar, and two posteriors between the second premolar and the first molar. Model B: two anteriors were between the lateral incisor and the canine, and two posteriors were the same as in model A. Model C: two anteriors were the same as in model A, and two posteriors were distal to the first molar. One turn of expander screws was applied. Maximum principal stress, equivalent elastic strain, equivalent von Mises stress, and transverse displacement were evaluated.

Results The maximum principal stress was mostly found at the bone-miniscrew interface. Model A exhibited an intersecting area of stress between the supported miniscrews. The highest value of principal stress was in model B, while model C showed a uniform distribution pattern. The elastic strain pattern was similar to the principal stress in all models. The highest value of equivalent von Mises stress was located on the expander screw. The largest amount of transverse displacement of teeth was in model A, while model C exhibited a more consistent transverse displacement than other models. Vertical displacement of posterior teeth was also noticed.

Conclusion Based on the result, it revealed that the various anteroposterior miniscrew placements of the palatal slope bone-borne expander had various patterns of stress distribution and resulted in various outcomes. It may be inferred that model A's miniscrew location was advantageous for obtaining expansion quantities, but model C's miniscrew position was advantageous for maintaining consistent biomechanics.
Potency of Hyperbaric Oxygen Therapy on Oral Candidiasis Diabetes Mellitus
Authors: Parisihni Kristanti , Mulawarmanti Dian , Widowati Kharinna
Published: March 2024

Objectives This study aimed to determine the potency of hyperbaric oxygen therapy (HBOT) to the blood glucose level, amount of lymphocytes, and the expression of antibody anti-Candida in oral candidiasis diabetes mellitus.

Materials and Methods Thirty Wistar rats were divided into five groups: K1 normal-control group, while K2, P1, P2, and P3 were diabetes induced by streptozotocin 50 mg/kg body weight. Oral candidiasis was induced by inoculation 0.1 mL Candida albicans ATCC 10321 on dorsum of the tongue. P1 was given nystatin oral suspension, P2 was treated by HBOT 2.4 ATA, 3 × 30 minutes each with a 5-minute interval, and P3 was treated by the combination of nystatin and HBOT. All the treatments were performed for 5 consecutive days. Fasting blood glucose level was examined on glucometer strips, lymphocyte was examined from complete blood count, and the expression of antibody anti-Candida was examined on immunohistochemistry staining

Statistical Analysis Data analyzed by a one-way analysis of variance and least significant difference test with the result of p-value less than 0.05 was considered to be statistically signiﬁcant.

Results HBOT reduced blood glucose level (p > 0.05) increased the amount of lymphocyte (p < 0.05). All treatments reduced the expression of antibody anti-Candida (p < 0.05) with the best result on combination of HBOT with nystatin.

Conclusion HBOT decreased the blood glucose level, increased the amount of lymphocytes, and reduced the expression of antibody anti-Candida in oral candidiasis diabetes mellitus.
Factors Influencing Health Care Professionals' Perceptions of Frequent Drug–Drug Interaction Alerts
Authors: Biady Yasmine , Lee Teresa , Pham Lily , Patanwala Asad , Poon Simon , Ritchie Angus , Burke Rosemary , Penm Jonathan
Published: March 2024

Background Drug–drug interactions (DDIs) remain a highly prevalent issue for patients in both community and hospital settings. Electronic medication management systems have implemented DDI alerts to mitigate DDI-related harm from occurring.

Objectives The primary aim of this study was to explore factors that influence health care professionals' (hospital doctors, hospital pharmacists, general practitioners, and community pharmacists) perceptions and action taken by them in response to DDI alerts.

Methods A qualitative study was conducted using semi-structured interviews between early January and late February 2021. The top 20 most frequently triggered DDI alerts previously identified were used as examples of alert prompts shown to participants.

Results A total of 20 participants were recruited. General practitioners (n = 4) were most likely to consider DDI alerts to be clinically relevant and important, and hospital doctors (n = 4) were most likely to consider these alerts not being clinically relevant nor important. Three main factors were identified to influence health care professionals' perceptions of DDI alerts, which included clinical relevance, visual presentation, and content of alerts.

Conclusion Health care professionals' perceptions of DDI alerts are influenced by multiple factors and considerations are required to create tailored alerts for users and their clinical contexts. Improvement in DDI alerts should be a priority to improve patient medication safety and health outcomes.
In-Hospital Pulmonary Arterial Embolism after Catheter Ablation of Over 45,000 Cardiac Arrhythmias: Individualized Case Analysis of Multicentric Data
Authors: Doldi Florian , Geßler Nele , Anwar Omar , Kahle Ann-Kathrin , Scherschel Katharina , Rath Benjamin , Köbe Julia , Lange Philipp Sebastian , Frommeyer Gerrit , Metzner Andreas , Meyer Christian , Willems Stephan , Kuck Karl-Heinz , Eckardt Lars
Published: March 2024

Objective and Background Data on incidence of in-hospital pulmonary embolisms (PE) after catheter ablation (CA) are scarce. To gain further insights, we sought to provide new findings through case-based analyses of administrative data.

Methods Incidences of PE after CA of supraventricular tachycardias (SVT), atrial fibrillation (AF), atrial flutter (AFlu), and ventricular tachycardias (VT) in three German tertiary centers between 2005 and 2020 were determined and coded by the G-DRG (German Diagnosis Related Groups System) and OPS (German Operation and Procedure Classification) systems. An administrative search was performed with a consecutive case-based analysis.

Results Overall, 47,344 ablations were analyzed (10,037 SVT; 28,048 AF; 6,252 AFlu; 3,007 VT). PE occurred in 14 (0.03%) predominantly female (n = 9; 64.3%) patients with a mean age of 55.3 ± 16.9 years, body mass index 26.2 ± 5.1 kg/m2, and left ventricular ejection fraction of 56 ± 13.6%. PE incidences were 0.05% (n = 5) for SVT, 0.02% (n = 5) for AF, and 0.13% (n = 4) for VT ablations. No patient suffered PE after AFlu ablation. Five patients (35.7%) with PE after CA had no prior indication for oral anticoagulation (OAC). Preprocedural international normalized ratio in PE patients was 1.2 ± 0.5. Most patients with PE following CA presented with symptoms the day after the procedure (n = 9) after intraprocedural heparin application of 12,943.2 ± 5,415.5 IU. PE treatment included anticoagulation with either phenprocoumon (n = 5) or non-vitamin K-dependent OAC (n = 9). Two patients with PE died after VT/AF ablation, respectively. The remaining patients were discharged without sequels.

Conclusion Over a 15-year period, incidence of PE after ablation is low, particularly low in patients with ablation for AF/AFlu. This is most likely due to stricter anticoagulation management in these patients compared with those receiving SVT/VT ablation procedures and could argue for continuation of OAC prior to ablation. Optimizing periprocedural anticoagulation management should be subject of further prospective trials.
Measuring Indonesian young consumers’ halal purchase intention of foreign-branded food products
Authors: Pradana Mahir , Rubiyanti Nurafni , Marimon Frederic
Published: March 2024

This article is among the few focusing on halal young consumer behavior in Indonesia. The focus is to examine the topic of halal food product purchase intention. Here, we focus specifically on Muslim teenagers in Indonesia to explore whether they still hold on to the halal principle that most Muslims adhere to when consuming food. This research examine their halal awareness based on theory of planned behavior (TPB) theory and compare it to the previous publications so far. To reach this objective, we used quantitative methodology. Our data was acquired from 161 Indonesian young Muslim consumers. Furthermore, the variance-based structural equation modeling and Theory of Planned Behavior (TPB) research model were utilized. Our findings demonstrate that subjective norm and attitude are significant determinants of halal food buying intent. However, perceived behavioral control has not been established as a purchase intention component. Finally, this study provides additional research on halal consumer behavior, focusing on the empirical findings of young Indonesian consumers, especially seen from TPB perspective.
Theoretical study of proton-coupled electron transfer reaction in metal-hydride complexes
Authors: Liu Xiaoyun , Dan Xiaohan , Shi Qiang
Published: April 2024

Metal-hydride (M-H) complexes are crucial for a variety of catalytic reactions. There have been indications of concerted proton-coupled electron transfer (PCET) reaction recently in several studies involving tungsten hydride complexes covalently connected to pyridyl groups. In this piece of work, we use the density functional theory and nonadiabatic rate theory to study concerted PCET reactions in weakly hydrogen bonded systems. Two dimensional potential energy surfaces of the metal-hydride complexes are first constructed. Wave functions and vibrational energy levels are then obtained, which are used to analyze the transition between each pair of vibronic states and to obtain the total rate constant. It is demonstrated that, because of the hydrogen donor-acceptor distance thermal fluctuations, the concerted PCET reaction and the total reaction rate constant can be significantly enhanced even in the case of weak hydrogen bonding between the proton donor and acceptor.
Spectroscopic identification and bonding properties of HNCOCa+: A matrix isolation and computational study
Authors: Jiang Xin , Sun Beibei , Wang Guanjun , Wang Lina , Zeng Xiaoqing , Zhou Mingfei
Published: April 2024

Metal (iso)cyanides dominate the molecular inventory of metal-bearing species in the interstellar medium. Their oxide counterparts, metal (iso)cyanates, have potential as interstellar molecules and have received significant attention. However, cationic complexes HNCOM+ as precursors to metal (iso)cyanates are rarely studied. Herein, we investigated HNCOCa+ by exploiting infrared spectrometry with isotopic substitutions and quantum chemical calculations. For comparison, the light and heavy alkaline earth metal cationic complexes HNCOBe+ and HNCOBa+ were also explored. HNCOCa+ and HNCOBe+ rather than HNCOBa+ can be experimentally generated by the reactions of metal cations with HNCO. The observed antisymmetric and symmetric NCO stretching vibrations in HNCOCa+ (2362.6 and 1330.4 cm−1) are higher than those in free HNCO (2268.5 and 1320.3 cm−1) but lower than those in HNCOBe+ (2426.4 and 1355.2 cm−1). These shifts can be explained by the charge polarization within the NCO fragment in HNCOBe+ and HN-COCa+. Bonding analysis suggests that HNCO–Be+ bond favors covalent character (54%) while HNCO–Ca+ bond has higher electrostatic character (57%). The dominant electrostatic interaction (64%) in HNCO–Ba+ bond results in the low bond energy, which might account for its absence in experiments.
Vertical and horizontal links in constructional networks
Authors: Ungerer Tobias
Published: April 2024

Recent models of constructional networks combine vertical links between schemas and their subtypes with horizontal
links between constructions at the same level of abstraction. It remains unclear, however, whether vertical and horizontal
analyses express distinct information about the network, or whether one can be reformulated in terms of the other. In this paper,
it is argued that vertical and horizontal links do not encode distinct cognitive mechanisms but that they are notational variants
for representing a common notion of constructional similarity. The practical advantages of each notation are outlined, and some
potential objections to the present account are addressed.
Prospects of detecting deviations to Kerr geometry with radiation reaction effects in EMRIs
Authors: Chowdhuri Abhishek , Bhattacharyya Arpan , Kumar Shailesh
Published: April 2024

Direct detection of gravitational waves and binary black hole mergers have proven to be
remarkable investigations of general relativity. In order to have a definitive answer as to
whether the black hole spacetime under test is the Kerr or non-Kerr, one requires accurate mapping
of the metric. Since EMRIs are perfect candidates for space-based detectors, Laser Interferometer
Space Antenna (LISA) observations will serve a crucial purpose in mapping the spacetime metric. In
this article, we consider such a study with the Johannsen spacetime that captures the deviations
from the Kerr black hole and further discuss their detection prospects. We analytically derive the
leading order post-Newtonian corrections in the average loss of energy and angular momentum fluxes
generated by a stellar-mass object exhibiting eccentric equatorial motion in the Johannsen
background. We further study the orbital evolution of the inspiralling object within the adiabatic
approximation. We lastly provide the possible detectability of deviations from the Kerr black hole
by estimating gravitational wave dephasing and highlight the crucial role of LISA observations.
A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction
Authors: Kumar Halder Anup , Agarwal Abhishek , Jodkowska Karolina , Plewczynski Dariusz
Published: March 2024

Genomic data analysis has witnessed a surge in complexity and volume, primarily driven by the advent of high-throughput technologies. In particular, studying chromatin loops and structures has become pivotal in understanding gene regulation and genome organization. This systematic investigation explores the realm of specialized bioinformatics pipelines designed specifically for the analysis of chromatin loops and structures. Our investigation incorporates two protein (CTCF and Cohesin) factor-specific loop interaction datasets from six distinct pipelines, amassing a comprehensive collection of 36 diverse datasets. Through a meticulous review of existing literature, we offer a holistic perspective on the methodologies, tools and algorithms underpinning the analysis of this multifaceted genomic feature. We illuminate the vast array of approaches deployed, encompassing pivotal aspects such as data preparation pipeline, preprocessing, statistical features and modelling techniques. Beyond this, we rigorously assess the strengths and limitations inherent in these bioinformatics pipelines, shedding light on the interplay between data quality and the performance of deep learning models, ultimately advancing our comprehension of genomic intricacies.
scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics
Authors: Zheng Chuanyang , Wang Yixuan , Cheng Yuqi , Wang Xuesong , Wei Hongxin , King Irwin , Li Yu
Published: March 2024

Single-cell RNA sequencing has achieved massive success in biological research fields. Discovering novel cell types from single-cell transcriptomics has been demonstrated to be essential in the field of biomedicine, yet is time-consuming and needs prior knowledge. With the unprecedented boom in cell atlases, auto-annotation tools have become more prevalent due to their speed, accuracy and user-friendly features. However, existing tools have mostly focused on general cell-type annotation and have not adequately addressed the challenge of discovering novel rare cell types. In this work, we introduce scNovel, a powerful deep learning-based neural network that specifically focuses on novel rare cell discovery. By testing our model on diverse datasets with different scales, protocols and degrees of imbalance, we demonstrate that scNovel significantly outperforms previous state-of-the-art novel cell detection models, reaching the most AUROC performance(the only one method whose averaged AUROC results are above 94%, up to 16.26% more comparing to the second-best method). We validate scNovel’s performance on a million-scale dataset to illustrate the scalability of scNovel further. Applying scNovel on a clinical COVID-19 dataset, three potential novel subtypes of Macrophages are identified, where the COVID-related differential genes are also detected to have consistent expression patterns through deeper analysis. We believe that our proposed pipeline will be an important tool for high-throughput clinical data in a wide range of applications.
A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts
Authors: Pan Jie , Zhang Zhen , Li Ying , Yu Jiaoyang , You Zhuhong , Li Chenyu , Wang Shixu , Zhu Minghui , Ren Fengzhi , Zhang Xuexia , Sun Yanmei , Wang Shiwei
Published: March 2024

Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.
Benchmarking digital PCR partition classification methods with empirical and simulated duplex data
Authors: Chen Yao , De Spiegelaere Ward , Trypsteen Wim , Gleerup David , Vandesompele Jo , Lievens Antoon , Vynck Matthijs , Thas Olivier
Published: March 2024

Digital PCR (dPCR) is a highly accurate technique for the quantification of target nucleic acid(s). It has shown great potential in clinical applications, like tumor liquid biopsy and validation of biomarkers. Accurate classification of partitions based on end-point fluorescence intensities is crucial to avoid biased estimators of the concentration of the target molecules. We have evaluated many clustering methods, from general-purpose methods to specific methods for dPCR and flowcytometry, on both simulated and real-life data. Clustering method performance was evaluated by simulating various scenarios. Based on our extensive comparison of clustering methods, we describe the limits of these methods, and formulate guidelines for choosing an appropriate method. In addition, we have developed a novel method for simulating realistic dPCR data. The method is based on a mixture distribution of a Poisson point process and a skew-$t$ distribution, which enables the generation of irregularities of cluster shapes and randomness of partitions between clusters (‘rain’) as commonly observed in dPCR data. Users can fine-tune the model parameters and generate labeled datasets, using their own data as a template. Besides, the database of experimental dPCR data augmented with the labeled simulated data can serve as training and testing data for new clustering methods. The simulation method is available as an R Shiny app.
FAIR Header Reference genome: a TRUSTworthy standard
Authors: Wright Adam , Wilkinson Mark D , Mungall Christopher , Cain Scott , Richards Stephen , Sternberg Paul , Provin Ellen , Jacobs Jonathan L , Geib Scott , Raciti Daniela , Yook Karen , Stein Lincoln , Molik David C
Published: March 2024

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR’s design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity
Authors: Thrift William John , Perera Jason , Cohen Sivan , Lounsbury Nicolas W , Gurung Hem R , Rose Christopher M , Chen Jieming , Jhunjhunwala Suchit , Liu Kai
Published: March 2024

Antigen presentation on MHC class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an anti-drug response. Significant progress has been made in pMHCII presentation modeling due to the collection of large-scale pMHC mass spectrometry datasets (ligandomes) and advances in machine learning. Here, we develop graph-pMHC, a graph neural network approach to predict pMHCII presentation. We derive adjacency matrices for pMHCII using Alphafold2-multimer and address the peptide–MHC binding groove alignment problem with a simple graph enumeration strategy. We demonstrate that graph-pMHC dramatically outperforms methods with suboptimal inductive biases, such as the multilayer-perceptron-based NetMHCIIpan-4.0 (+20.17% absolute average precision). Finally, we create an antibody drug immunogenicity dataset from clinical trial data and develop a method for measuring anti-antibody immunogenicity risk using pMHCII presentation models. Our model increases receiver operating characteristic curve (ROC)-area under the ROC curve (AUC) by 2.57% compared to just filtering peptides by hits in OASis alone for predicting antibody drug immunogenicity.
DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage
Authors: Li Yiming , Zhang Haoling , Chen Yuxin , Shen Yue , Ping Zhi
Published: March 2024

DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been developed to ensure accurate information retrieval, but they will decrease storage density or increase computing complexity. Here, we apply the Bloom Filter, a space-efficient probabilistic data structure, to DNA storage to achieve the anti-error, or anti-contamination function. This method only needs the original correct DNA sequences (referred to as target sequences) to produce a corresponding data structure, which will filter out almost all the incorrect sequences (referred to as non-target sequences) during sequencing data analysis. Experimental results demonstrate the universal and efficient filtering capabilities of our method. Furthermore, we employ the Counting Bloom Filter to achieve the file version control function, which significantly reduces synthesis costs when modifying DNA-form files. To achieve cost-efficient file version control function, a modified system based on yin–yang codec is developed.
The effect of parathyroid hormone lowering by etelcalcetide therapy on calcification propensity and calciprotein particles in hemodialysis patients
Authors: Thiem Ursula , Lenz Jakob , Haller Maria C , Pasch Andreas , Smith Edward R , Cejka Daniel
Published: March 2024

Background

This study investigated whether parathyroid hormone (PTH) lowering with etelcalcetide, and the consequent effects on mineral and bone metabolism, could improve serum calcification propensity (T50 time) and decrease calciprotein particle (CPP) load in hemodialysis patients with secondary hyperparathyroidism.

Methods

In this single-arm, prospective, dose-escalation proof-of-principle study, hemodialysis patients received etelcalcetide at 2.5 mg/dialysis session with increments of 2.5 mg every 4 weeks to a maximum dose of 15 mg three times a week or until a pre-specified safety endpoint was reached, followed by an 8-week wash-out phase.

Results

Out of 36 patients recruited (81% male, 62 ± 13 years), 16 patients completed the study per protocol with a mean maximum tolerated dose of etelcalcetide of 9.5 ± 2.9 mg/dialysis session. With escalating doses of etelcalcetide, PTH and serum calcium levels significantly decreased (P < 0.0001). While there was no significant change in T50 times or serum phosphate levels, etelcalcetide did yield significant and consistent reductions in serum levels of endogenous calciprotein monomers [−35.4 (−44.4 to −26.5)%, P < 0.0001], primary [−22.4 (−34.5 to −10.3)%, P < 0.01] and secondary CPP [−29.1 (−45.7 to −12.4)%, P < 0.01], an effect that was reversed after therapy withdrawal. Serum levels of osteoclastic markers significantly decreased with escalating doses of etelcalcetide, while levels of the osteoblastic marker remained stable.

Conclusions

Lowering of PTH with etelcalcetide did not result in statistically significant changes in T50. By contrast, homogenous reductions in serum levels of calciprotein monomers, primary and secondary CPP were observed.
Inflammatory-mediated atrial cardiomyopathy diagnosed using multimodality imaging and successfully treated with prednisolone: a case report
Authors: Larsen Birgitte Carbuhn , Al-Badri Kadhem Helo Abbas , Mellemkjær Søren , Bærentzen Steen , Oxlund Christina Stolzenburg , Pryds Kasper
Published: March 2024

Background

Atrial fibrillation is a common cardiac arrhythmia and often develops secondary to structural cardiac changes. Both the occurrence of atrial fibrillation and/or structural changes of the heart may lead to development of atrial cardiomyopathy and heart failure (HF). However, isolated atrial cardiomyopathy caused by focal atrial thickening is a rare condition, previously only described in case reports as a result of different aetiologies all linked to inflammation.

Case summary

A patient with inflammatory-mediated atrial cardiomyopathy causing atrial fibrillation and acute decompensated HF presented as isolated left atrial wall thickening on transoesophageal echocardiography. The diagnosis was confirmed using multimodality imaging with transthoracic and transoesophageal echocardiography, cardiac magnetic resonance imaging, positron emissions tomography/computer tomography scanning and intracardiac echocardiography-guided endomyocardial biopsy. Despite no specific histological aetiology, the observed atrial cardiomyopathy might be associated with type 1 diabetes mellitus. The patient in the present case was successfully treated with prednisolone.

Discussion

Diabetes mellitus is an important risk factor for developing atrial fibrillation and diabetic cardiomyopathy, due to reduced levels of anti-inflammatory and increased levels of proinflammatory cytokines causing cardiac inflammatory structural remodelling. The regression of the atrial thickening might be due to prednisolone’s anti-inflammatory effects and thereby ability to suppress atrial remodelling and reduce the occurrence of atrial fibrillation. However, the effect of prednisolone might only affect the non-manifested inflammatory-mediated atrial remodelling. Due to the rare occurrence of isolated atrial cardiomyopathy a multiple imaging approach during the diagnostic process and follow-ups are essential to determine the aetiology and effect of the treatment.
Estimating the timber value of a forest property using geographically balanced samples and unoccupied aerial vehicle data
Authors: Räty Janne , Heikkinen Juha , Kukkonen Mikko , Mehtätalo Lauri , Kangas Annika , Packalen Petteri
Published: March 2024

A common task in forestry is to determine the value of a forest property, and timber is the most valuable component of that property. Remotely sensed data collected by an unoccupied aerial vehicle (UAV) are suited for this purpose as most forest properties are of a size that permits the efficient collection of UAV data. These UAV data, when linked to a probability sample of field plots, enable the model-assisted (MA) estimation of the timber value and its associated uncertainty. Our objective was to estimate the value of timber (€/ha) in a 40-ha forest property in Finland. We used a systematic sample of field plots (n = 160) and 3D image point cloud data collected by an UAV. First, we studied the effects of spatial autocorrelation on the variance estimates associated with the timber value estimates produced using a field data-based simple expansion (EXP) estimator. The variance estimators compared were simple random sampling, Matérn, and a variant of the Grafström–Schelin estimator. Second, we compared the efficiencies of the EXP and MA estimators under different sampling intensities. The sampling intensity was varied by subsampling the systematic sample of 160 field plots. In the case of the EXP estimator, the simple random sampling variance estimator produced the largest variance estimates, whereas the Matérn estimator produced smaller variance estimates than the Grafström–Schelin estimator. The MA estimator was more efficient than the EXP estimator, which suggested that the reduction of sampling intensity from 160 to 60 plots is possible without deterioration in precision. The results suggest that the use of UAV data improves the precision of timber value estimates compared to the use of field data only. In practice, the proposed application improves the cost-efficiency of the design-based appraisal of a forest property because expensive field workload can be reduced by means of UAV data.
Can we obtain reliable seismic b-values for real-time catalogues?
Authors: Li Linxuan , Luo Gang
Published: March 2024

The seismic b-value in Gutenberg–Richter law is an important parameter in earthquake science research and earthquake risk assessment. People have tried to use b-values for short-term earthquake forecasts, and this requires the premise of estimating reliable b-values for real-time seismic catalogues. However, estimating b-values for real-time catalogues, which are usually of poor qualities, is usually faced with many difficulties and problems. In this study, through a series of numerical tests, we investigate the performance of three methods, including the commonly used maximum-likelihood estimation method and two relatively new b-value estimation methods, namely the b-positive and K–M slope methods, on calculating b-values for real-time seismic catalogues. We also apply these three methods to both observed seismic catalogues (the seismic sequence in the Costa Marchigiana, Italy, and a high-resolution early aftershock sequence of the 2023 two Mw ∼7.8 earthquakes in Türkiye) and synthetic real-time seismic catalogues. The results in this study show that it seems difficult to obtain accurate b-values for real-time earthquake catalogues by each of these three methods, but the combination of these methods may give a better judgment—if all three methods suggest that the change in b-value is significant, the probability of making a correct decision is very high. Facing the uncertainty of b-value estimation that always exists, we advocate exploring the effectiveness of standard b-value estimation strategies in practical applications.
Genome-wide transcriptome analysis reveals key regulatory networks and genes involved in the determination of seed hardness in vegetable soybean
Authors: Wang Congcong , Lin Jianyu , Bu Yuanpeng , Sun Ruidong , Lu Yang , Gai JunYi , Xing Han , Guo Na , Zhao Jinming
Published: April 2024

Seed hardness is an important quality trait of vegetable soybean. To determine the factors underlying seed hardness, two landraces with contrasting seed hardness, Niumaohuang (low seed hardness) and Pixiansilicao (high seed hardness), were selected from 216 soybean accessions originating from 26 provinces in China. The contents of the main components in vegetable soybean seeds such as water, soluble sugar, starch, protein and oil were measured, and transcriptome analyses performed during five stages of seed developmental. Transcriptome analysis indicates that during the middle and late stages of seed development, a large number of genes involved in the synthesis or degradation of starch, storage protein, and fatty acids were differentially expressed, leading to differences in the accumulation of stored substances during seed maturation among Niumaohuang and Pixiansilicao. The activity of cell proliferation and the formation of cell walls in the middle and late stages of seed development may also affect the hardness of seeds to a certain extent. In addition, weighted gene co-expression network analysis (WGCNA) was undertaken to identify co-expressed gene modules and hub genes that regulate seed hardness. Overexpression of a candidate seed hardness regulatory hub gene, GmSWEET2, resulted in increased seed hardness. In this study, the important role of GmSWEET2 in regulating the hardness of vegetable soybean seeds was verified and numerous potential key regulators controlling seed hardness and the proportion of seed components were identified, laying the groundwork for improving the texture of vegetable soybean.
A materialist reconsideration of international peace practice and its human and non-human constituents
Authors: Lakitsch Maximilian
Published: April 2024

The international community's sobering track record of sustainably reducing the number of armed conflicts worldwide, as well as the increasing involvement of non-human complexities in times of climate crisis suggest that current approaches to foster peace are too narrow and inflexible. So far, demands and calls for more flexible and adaptive peace practice made by policy-makers and researchers have not led to a related paradigm shift. In order to contribute to such a change of practice, this article advances a speculative analytical attempt that seeks to conceptually uncover new modes of engaging with the world for the purpose of peace. It builds on Baruch Spinoza's materialism and describes peace as intimately interrelated with the issue of political community. Following Spinoza, the article reconsiders the imaginary of political community as something that is constantly being rearticulated by a contingent complexity of human and non-human actors, and thus transcends the geographic scope of its formal borders as well as its epistemic scope across power hierarchies. Finally, the article introduces the human–non-human multitude as political subject that is able to detect and interpret the constituents of a political community, and therefore to maintain and sustain peace.
Optimal scheduling of integrated energy systems considering wind power uncertainty
Authors: Chang Yufang , Zhou Xinyi , Huang Wencong , Zhai Guisheng
Published: March 2024

To reduce the impact of high wind power penetration rate on integrated energy systems, a wind power scenario generation method based on polynomial regression is proposed and an optimization scheduling model is constructed accordingly. First, a probability distribution model for wind power is constructed. Then, scenario generation is performed through Latin hypercube sampling and typical scenarios are obtained using the synchronous back propagation elimination method. Finally, the optimal output of each piece of equipment in the system is obtained with the lowest overall cost as the optimization objective. The simulation results validate the effectiveness and low-carbon nature of this method, while reducing costs.
Research on the trade-in modes for electric vehicle power batteries under deposit and fund policies
Authors: Tang Jinhuan , Sheng Zhuo , Zhao Dan
Published: March 2024

Recycling power batteries has gained attention as electric vehicles (EVs) develop rapidly. Government deposit and fund policies encourage battery recycling and cascade utilization. Thus, we construct six trade-in modes for battery supplier, EV manufacturer, and external recycler as recycle entity under deposit and fund policies. Supply chain member profits, battery recycling rate, environmental impact, and social welfare are compared between modes. The results are as follows: (1) Deposit policy has a greater battery recycling rate and lower environmental impact than fund policy, so the best trade-in mode is with the EV manufacturer as recycling entity; (2) Battery supplier and EV manufacturer gain more from the fund policy when recycling themselves, whereas external recycler prefers the deposit policy; (3) Battery supplier recycling under ‘high deposit-high subsidy’ is more likely to promote social welfare, while EV manufacturer recycling under ‘high deposit-low subsidy’ will help the government balance revenue and expenditure.
Short-term photovoltaic output power prediction based on similar day and optimized BP neural network
Authors: Ye Gaoxiang , Yang Jie , Xia Fangzhou , Shao Feifan , Xu Jingyou , Yang Zili , Peng Wenyan , Zheng Zijian
Published: March 2024

The photovoltaic (PV) output power is affected by the ambient temperature, seasons, weather and other factors, which makes the PV output power very unstable. Therefore, accurate prediction of the PV output power is highly beneficial. This paper is dedicated to finding a simple and reliable PV short-term output power prediction method. First, we choose four key parameters, season, solar irradiance, temperature and relative humidity, to predict PV output power by using the similar day theory, which is mainly because the above four parameters are decisive for PV output power, although more parameters being taken into account will make the prediction accuracy higher, but it brings along with it an increase in the complexity; secondly, we choose the backpropagation (BP) neural network because it is very suitable for the PV output power prediction due to its excellent learning ability; finally, we optimize the standard BP neural network in loss functions, activation functions and optimizers to further improve its prediction accuracy. We validate the proposed method in different seasons and under other weather conditions. The results show that the proposed method has better prediction results, the optimized BP neural network has better performance compared with the standard BP neural network, and the standard deviation of the prediction is improved from ~1382, ~1571, ~1457, ~989 to ~903, ~792, ~333 and ~409.
Pentagram Rigidity for Centrally Symmetric Octagons
Authors: Evan Schwartz Richard
Published: April 2024

In this paper I will establish a special case of a conjecture that intertwines the deep diagonal pentagram maps and Poncelet polygons. The special case is that of the $3$-diagonal map acting on affine equivalence classes of centrally symmetric octagons. The proof involves establishing that the map is Arnold-Liouville integrable in this case, and then exploring the Lagrangian surface foliation in detail.
Arithmetic Trialitarian Hyperbolic Lattices Are Not Locally Extended Residually Finite
Authors: Bogachev Nikolay , Slavich Leone , Sun Hongbin
Published: April 2024

A group is LERF (locally extended residually finite) if all its finitely generated subgroups are separable. We prove that the trialitarian arithmetic lattices in $\mathbf{PSO}_{7,1}(\mathbb{R})$ are not LERF. This result, together with previous work by the third author, implies that no arithmetic lattice in $\mathbf{PO}_{n,1}(\mathbb{R})$, $n>3$, is LERF.
Recent advances regarding the potential roles of invariant natural killer T cells in cardiovascular diseases with immunological and inflammatory backgrounds
Authors: Iwabuchi Kazuya , Satoh Masashi , Yoshino Kazuhisa , Ishimori Naoki
Published: March 2024

Invariant natural killer T (iNKT) cells, which bear αβ-type T-cell antigen-receptors (TCRs), recognize glycolipid antigens in a cluster of differentiation 1d (CD1d)-restricted manner. Regarding these cells, the unique modes of thymic selection and maturation elucidate innateness, irrespective of them also being members of the adaptive immune system as a T-cell. iNKT cells develop and differentiate into NKT1 [interferon γ (IFN-γ)-producing], NKT2 [interleukin 4 (IL-4)/IL-13-producing], or NKT17 (IL-17-producing) subsets in the thymus. After egress, NKT10 (IL-10-producing), follicular helper NKT (NKTfh; IL-21-producing), and regulatory NKT (NKTreg) subsets emerge following stimulation in the periphery. Moreover, iNKT cells have been shown to possess several physiological or pathological roles. iNKT cells exhibit dual alleviating or aggravating roles in experimentally induced immune and/or inflammatory diseases in mice. These findings indicate that the modulation of iNKT cells can be employed for therapeutic use or prevention of human diseases. In this review, we discuss the potential roles of iNKT cells in the development of immune/inflammatory diseases of the cardiovascular system, with emphasis on atherosclerosis, aortic aneurysms, and cardiac remodeling.