bluuebunny/crossref_metadata_2025 huggingface dataset:
Anchor boxes adaptive optimization algorithm for maritime object detection in video surveillance
Authors: Zheng Jiachun , Zhao Shijia , Xu Zhiping , Zhang Lei , Liu Jiantao
Published: December 2023

With the development of the marine economy, video surveillance has become an important technical guarantee in the fields of marine engineering, marine public safety, marine supervision, and maritime traffic safety. In video surveillance, maritime object detection (MOD) is one of the most important core technologies. Affected by the size of maritime objects, distance, day and night weather, and changes in sea conditions, MOD faces challenges such as false detection, missed detection, slow detection speed, and low accuracy. However, the existing object detection algorithms usually adopt predefined anchor boxes to search and locate for objects of interest, making it difficult to adapt to maritime objects’ complex features, including the varying scale and large aspect ratio difference. Therefore, this paper proposes a maritime object detection algorithm based on the improved convolutional neural network (CNN). Firstly, a differential-evolutionary-based K-means (DK-means) anchor box clustering algorithm is proposed to obtain adaptive anchor boxes to satisfy the maritime object characteristics. Secondly, an adaptive spatial feature fusion (ASFF) module is added in the neck network to enhance multi-scale feature fusion. Finally, focal loss and efficient intersection over union (IoU) loss are adopted to replace the original loss function to improve the network convergence speed. The experimental results on the Singapore maritime dataset show that our proposed algorithm improves the average precision by 7.1%, achieving 72.7%, with a detection speed of 113 frames per second, compared with You Only Look Once v5 small (YOLOv5s). Moreover, compared to other counterparts, it can achieve a better speed–accuracy balance, which is superior and feasible for the complex maritime environment.
Quantitative provenance study of sediments in the coastal tidal flats of central Jiangsu based on grain-size End-Member analysis
Authors: Li Yanxia , Zhao Yifei , Xu Wenjian , Liu Nian , Xu Min
Published: December 2023

The coastal mudflats in central Jiangsu Province are influenced by the sediment supply from the Yangtze River and the abandoned Yellow River. However, the sources of sediment in this area have yet to be confirmed, and quantitative studies have been limited. In this study, we addressed this gap by obtaining sediment core samples with lengths of approximately 100 cm from Dongtai and Sheyang, respectively, on the central coast of Jiangsu Province in 2018. The sediment sources were identified and quantitatively evaluated using a grain-size end-member(EM) model. The findings revealed that (1) Sheyang was decomposed into five EMs, with EMs 1-3 originating from the abandoned Yellow River, EM 4 originating from the Yangtze River and the North Jiangsu radial sand ridges (NJRSR), and EM 5 originating from the NJRSR. Over a century scale, the abandoned Yellow River contributed 73.91% to sediment deposition in Sheyang, while the Yangtze River and the NJRSR contributed 26.09%. (2) Dongtai was decomposed into six EMs, with EMs 1-4 originating from the abandoned Yellow River, EM 5 originating from the Yangtze River, and EM 6 originating from the Yangtze River and the NJRSR. Over a century scale, the abandoned Yellow River contributed 70.55% to sediment deposition in Dongtai, and the Yangtze River and the NJRSR contributed 29.45%. (3) On a temporal scale, the contribution of the abandoned Yellow River to sediment deposition on the central mudflats of Jiangsu Province showed an increasing trend. Spatially, the contribution of the abandoned Yellow River to sediment deposition decreased from north to south. (4) There were significant changes in the sediment sources of Sheyang and Dongtai at the depths of 56 cm and 60 cm, respectively, which both experiencing an increased sediment supply from the abandoned Yellow River. In Dongtai, the sediment on the southern side had increased contributions from the abandoned Yellow River due to a reduction in the sediment supply from the Yangtze River. In Sheyang, the sediment on the northern side had increased contributions from the abandoned Yellow River due to the introduction of Spartina alterniflora, despite no actual changes in the sediment sources.
Comparative transcriptome analysis of SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-229E identifying potential IFN/ISGs targets for inhibiting virus replication
Authors: Liu Yuzhuang , Lu Tianyi , Li Cuidan , Wang Xiaotong , Chen Fei , Yue Liya , Jiang Chunlai
Published: December 2023

Introduction

Since its outbreak in December 2019, SARS-CoV-2 has spread rapidly across the world, posing significant threats and challenges to global public health. SARS-CoV-2, together with SARS-CoV and MERS-CoV, is a highly pathogenic coronavirus that contributes to fatal pneumonia. Understanding the similarities and differences at the transcriptome level between SARS-CoV-2, SARS-CoV, as well as MERS-CoV is critical for developing effective strategies against these viruses.

Methods

In this article, we comparatively analyzed publicly available transcriptome data of human cell lines infected with highly pathogenic SARS-CoV-2, SARS-CoV, MERS-CoV, and lowly pathogenic HCoV-229E. The host gene expression profiles during human coronavirus (HCoV) infections were generated, and the pathways and biological functions involved in immune responses, antiviral efficacy, and organ damage were intensively elucidated.

Results

Our results indicated that SARS-CoV-2 induced a stronger immune response versus the other two highly pathogenic HCoVs. Specifically, SARS-CoV-2 induced robust type I and type III IFN responses, marked by higher upregulation of type I and type III IFNs, as well as numerous interferon-stimulated genes (ISGs). Further Ingenuity Pathway Analysis (IPA) revealed the important role of ISGs for impeding SARS-CoV-2 infection, and the interferon/ISGs could be potential targets for therapeutic interventions. Moreover, our results uncovered that SARS-CoV-2 infection was linked to an enhanced risk of multi-organ toxicity in contrast to the other two highly pathogenic HCoVs.

Discussion

These findings provided valuable insights into the pathogenic mechanism of SARS-CoV-2, which showed a similar pathological feature but a lower fatality rate compared to SARS-CoV and MERS-CoV.
Mitochondrial genome sequence of the protist Ancyromonas sigmoides Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec
Authors: Gastineau Romain , Harðardóttir Sara , Guilmette Caroline , Lemieux Claude , Turmel Monique , Otis Christian , Boyle Brian , Levesque Roger C. , Gauthier Jeff , Potvin Marianne , Lovejoy Connie
Published: December 2023

Introduction

There is little information on evolutionarily ancient eukaryotes, which are often referred to as basal eukaryotes, in Arctic waters. Despite earlier studies being conducted in the Russian White Sea, only few have been reported.

Methods

Following a shotgun sequence survey of diatom cultures from Sugluk Inlet off the Hudson Strait in Northern Québec, we obtained the complete mitochondrial genome and the operon of nuclear ribosomal RNA genes from a strain that matches that of Ancyromonas sigmoides (Kent, 1881).

Results

The sequence of the mitogenome retrieved was 41,889 bp in length and encoded 38 protein-coding genes, 5 non-conserved open-reading frames, and 2 rRNA and 24 tRNA genes. The mitogenome has retained sdh2 and sdh3, two genes of the succinate dehydrogenase complex, which are sometimes found among basal eukaryotes but seemingly missing among the Malawimonadidae, a lineage sister to Ancyromonadida in some phylogenies. The phylogeny inferred from the 18S rRNA gene associated A. sigmoides from Sugluk Inlet with several other strains originating from the Arctic. The study also unveiled the presence of a metagenomic sequence ascribed to bacteria in GenBank, but it was clearly a mitochondrial genome with a gene content highly similar to that of A. sigmoides, including the non-conserved open-reading frames.

Discussion

After re-annotation, a phylogeny was inferred from mitochondrial protein sequences, and it strongly associated A. sigmoides with the misidentified organism, with the two being possibly conspecific or sibling species as they are more similar to one another than to species of the genus Malawimonas. Overall our phylogeny showed that the ice associated ancryomonads were clearly distinct from more southerly strains.
Harnessing fungal endophytes for natural management: a biocontrol perspective
Authors: Bhardwaj Mansavi , Kailoo Swadha , Khan Rabiya Tabbassum , Khan Sofia Sharief , Rasool Shafaq
Published: December 2023

In the ever-evolving realm of agriculture, the convoluted interaction between plants and microorganisms have assumed paramount significance. Fungal endophytes, once perceived as mere bystanders within plant tissues, have now emerged as dynamic defenders of plant health. This comprehensive review delves into the captivating world of fungal endophytes and their multifaceted biocontrol mechanisms. Exploring their unique ability to coexist with their plant hosts, fungal endophytes have unlocked a treasure trove of biological weaponry to fend off pathogens and enhance plant resilience. From the synthesis of bioactive secondary metabolites to intricate signaling pathways these silent allies are masters of biological warfare. The world of fungal endophytes is quite fascinating as they engage in a delicate dance with the plant immune system, orchestrating a symphony of defense that challenges traditional notions of plant-pathogen interactions. The journey through the various mechanisms employed by these enigmatic endophytes to combat diseases, will lead to revelational understanding of sustainable agriculture. The review delves into cutting-edge research and promising prospects, shedding light on how fungal endophytes hold the key to biocontrol and the reduction of chemical inputs in agriculture. Their ecological significance, potential for bioprospecting and avenues for future research are also explored. This exploration of the biocontrol mechanisms of fungal endophytes promise not only to enrich our comprehension of plant-microbe relationships but also, to shape the future of sustainable and ecofriendly agricultural practices. In this intricate web of life, fungal endophytes are indeed the unsung heroes, silently guarding our crops and illuminating a path towards a greener, healthier tomorrow.
Impact of bacteriocin-producing strains on bacterial community composition in a simplified human intestinal microbiota
Authors: Ríos Colombo Natalia S. , Perez-Ibarreche Mariana , Draper Lorraine A. , O’Connor Paula M. , Field Des , Ross R. Paul , Hill Colin
Published: December 2023

Bacteriocins are antimicrobial peptides that have been studied for decades as food bio-preservatives or as alternatives to antibiotics. They also have potential as modulators of the gut microbiome, which has been linked to human health. However, it is difficult to predict a priori how bacteriocins will impact complex microbial communities through direct and indirect effects. Here we assess the effect of different bacteriocin-producing strains on a Simplified Human Intestinal Microbiota (SIHUMI) model, using a set of bacteriocin-producing strains (Bac+) and otherwise isogenic non-producers (Bac−). Bacteriocins from different classes and with different activity spectra were selected, including lantibiotics such as lacticin 3147 and nisin A, and pediocin-like bacteriocins such as pediocin PA-1 among other peptides. SIHUMI is a bacterial consortium of seven diverse human gut species that assembles to a predictable final composition in a particular growth medium. Each member can be individually tracked by qPCR. Bac+ and Bac− strains were superimposed on the SIHUMI system, and samples were taken at intervals up to 48 h. The genome copy number of each SIHUMI member was evaluated using specific primers. We establish that the composition of the community changes in response to the presence of either broad- or narrow-spectrum bacteriocin producers and confirm that there are significant off-target effects. These effects were analyzed considering antagonistic inter-species interactions within the SIHUMI community, providing a comprehensive insight into the possible mechanisms by which complex communities can be shaped by bacteriocins.
Distinct evolution of ST11 KL64 Klebsiella pneumoniae in Taiwan
Authors: Li Yia-Ting , Wang Yao-Chen , Chen Chih-Ming , Tang Hui-Ling , Chen Bo-Han , Teng Ru-Hsiou , Chiou Chien-Shun , Lu Min-Chi , Lai Yi-Chyi
Published: December 2023

Carbapenem-resistant ST11_KL64 Klebsiella pneumoniae emerged as a significant public health concern in Taiwan, peaking between 2013 and 2015, with the majority of isolates exhibiting OXA-48 as the sole carbapenemase. In this study, we employed whole-genome sequencing to investigate the molecular underpinnings of ST11_KL64 isolates collected from 2013 to 2021. Phylogenomic analysis revealed a notable genetic divergence between the ST11_KL64 strains in Taiwan and those in China, suggesting an independent evolutionary trajectory. Our findings indicated that the ST11_KL64_Taiwan lineage originated from the ST11_KL64 lineage in Brazil, with recombination events leading to the integration of ICEKp11 and a 27-kb fragment at the tRNAASN sites, shaping its unique genomic landscape. To further elucidate this unique sublineage, we examined the plasmid contents. In contrast to ST11_KL64_Brazil strains, which predominantly carried blaKPC-2, ST11_KL64_Taiwan strains exhibited the acquisition of an epidemic blaOXA-48-carrying IncL plasmid. Additionally, ST11_KL64_Taiwan strains consistently harbored a multi-drug resistance IncC plasmid, along with a collection of gene clusters that conferred resistance to heavy metals and the phage shock protein system via various Inc-type plasmids. Although few, there were still rare ST11_KL64_Taiwan strains that have evolved into hypervirulent CRKP through the horizontal acquisition of pLVPK variants. Comprehensive characterization of the high-risk ST11_KL64 lineage in Taiwan not only sheds light on its epidemic success but also provides essential data for ongoing surveillance efforts aimed at tracking the spread and evolution of ST11_KL64 across different geographical regions. Understanding the molecular underpinnings of CRKP evolution is crucial for developing effective strategies to combat its emergence and dissemination.
Unveiling microbial biomarkers of ruminant methane emission through machine learning
Authors: Peng Chengyao , May Ali , Abeel Thomas
Published: December 2023

Background

Enteric methane from cow burps, which results from microbial fermentation of high-fiber feed in the rumen, is a significant contributor to greenhouse gas emissions. A promising strategy to address this problem is microbiome-based precision feed, which involves identifying key microorganisms for methane production. While machine learning algorithms have shown success in associating human gut microbiome with various human diseases, there have been limited efforts to employ these algorithms to establish microbial biomarkers for methane emissions in ruminants.

Methods

In this study, we aim to identify potential methane biomarkers for methane emission from ruminants by employing regression algorithms commonly used in human microbiome studies, coupled with different feature selection methods. To achieve this, we analyzed the microbiome compositions and identified possible confounding metadata variables in two large public datasets of Holstein cows. Using both the microbiome features and identified metadata variables, we trained different regressors to predict methane emission. With the optimized models, permutation tests were used to determine feature importance to find informative microbial features.

Results

Among the regression algorithms tested, random forest regression outperformed others and allowed the identification of several crucial microbial taxa for methane emission as members of the native rumen microbiome, including the genera Piromyces, Succinivibrionaceae UCG-002, and Acetobacter. Additionally, our results revealed that certain herd locations and feed composition markers, such as the lipid intake and neutral-detergent fiber intake, are also predictive features for methane emissions.

Conclusion

We demonstrated that machine learning, particularly regression algorithms, can effectively predict cow methane emissions and identify relevant rumen microorganisms. Our findings offer valuable insights for the development of microbiome-based precision feed strategies aiming at reducing methane emissions.
Selective oxytocin receptor activation prevents prefrontal circuit dysfunction and social behavioral alterations in response to chronic prefrontal cortex activation in male rats
Authors: Janz Philipp , Knoflach Frederic , Bleicher Konrad , Belli Sara , Biemans Barbara , Schnider Patrick , Ebeling Martin , Grundschober Christophe , Benekareddy Madhurima
Published: December 2023

Introduction

Social behavioral changes are a hallmark of several neurodevelopmental and neuropsychiatric conditions, nevertheless the underlying neural substrates of such dysfunction remain poorly understood. Building evidence points to the prefrontal cortex (PFC) as one of the key brain regions that orchestrates social behavior. We used this concept with the aim to develop a translational rat model of social-circuit dysfunction, the chronic PFC activation model (CPA).

Methods

Chemogenetic designer receptor hM3Dq was used to induce chronic activation of the PFC over 10 days, and the behavioral and electrophysiological signatures of prolonged PFC hyperactivity were evaluated. To test the sensitivity of this model to pharmacological interventions on longer timescales, and validate its translational potential, the rats were treated with our novel highly selective oxytocin receptor (OXTR) agonist RO6958375, which is not activating the related vasopressin V1a receptor.

Results

CPA rats showed reduced sociability in the three-chamber sociability test, and a concomitant decrease in neuronal excitability and synaptic transmission within the PFC as measured by electrophysiological recordings in acute slice preparation. Sub-chronic treatment with a low dose of the novel OXTR agonist following CPA interferes with the emergence of PFC circuit dysfunction, abnormal social behavior and specific transcriptomic changes.

Discussion

These results demonstrate that sustained PFC hyperactivity modifies circuit characteristics and social behaviors in ways that can be modulated by selective OXTR activation and that this model may be used to understand the circuit recruitment of prosocial therapies in drug discovery.
Claims-based algorithm to estimate the Expanded Disability Status Scale for multiple sclerosis in a German health insurance fund: a validation study using patient medical records
Authors: Muros-Le Rouzic Erwan , Ghiani Marco , Zhuleku Evi , Dillenseger Anja , Maywald Ulf , Wilke Thomas , Ziemssen Tjalf , Craveiro Licinio
Published: December 2023

Background

The Expanded Disability Status Scale (EDSS) quantifies disability and measures disease progression in multiple sclerosis (MS), however is not available in administrative claims databases.

Objectives

To develop a claims-based algorithm for deriving EDSS and validate it against a clinical dataset capturing true EDSS values from medical records.

Methods

We built a unique linked dataset combining claims data from the German AOK PLUS sickness fund and medical records from the Multiple Sclerosis Management System 3D (MSDS3D). Data were deterministically linked based on insurance numbers. We used 69 MS-related diagnostic indicators recorded with ICD-10-GM codes within 3 months before and after recorded true EDSS measures to estimate a claims-based EDSS proxy (pEDSS). Predictive performance of the pEDSS was assessed as an eight-fold (EDSS 1.0–7.0, ≥8.0), three-fold (EDSS 1.0–3.0, 4.0–5.0, ≥6.0), and binary classifier (EDSS <6.0, ≥6.0). For each classifier, predictive performance measures were determined, and overall performance was summarized using a macro F1-score. Finally, we implemented the algorithm to determine pEDSS among an overall cohort of patients with MS in AOK PLUS, who were alive and insured 12 months prior to and after index diagnosis.

Results

We recruited 100 people with MS insured by AOK PLUS who had ≥1 EDSS measure in MSDS3D between 01/10/2015 and 30/06/2019 (620 measurements overall). Patients had a mean rescaled EDSS of 3.2 and pEDSS of 3.0. The pEDSS deviated from the true EDSS by 1.2 points, resulting in a mean squared error of prediction of 2.6. For the eight-fold classifier, the macro F1-score of 0.25 indicated low overall predictive performance. Broader severity groupings were better performing, with the three-fold and binary classifiers for severe disability achieving a F1-score of 0.68 and 0.84, respectively. In the overall AOK PLUS cohort (3,756 patients, 71.9% female, mean 51.9 years), older patients, patients with progressive forms of MS and those with higher comorbidity burden showed higher pEDSS.

Conclusion

Generally, EDSS was underestimated by the algorithm as mild-to-moderate symptoms were poorly captured in claims across all functional systems. While the proxy-based approach using claims data may not allow for granular description of MS disability, broader severity groupings show good predictive performance.
Anti-NMDAR antibodies, the blood–brain barrier, and anti-NMDAR encephalitis
Authors: Gong Xiarong , Wang Niya , Zhu Hongyan , Tang Ning , Wu Kunhua , Meng Qiang
Published: December 2023

Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is an antibody-related autoimmune encephalitis. It is characterized by the existence of antibodies against NMDAR, mainly against the GluN1 subunit, in cerebrospinal fluid (CSF). Recent research suggests that anti-NMDAR antibodies may reduce NMDAR levels in this disorder, compromising synaptic activity in the hippocampus. Although anti-NMDAR antibodies are used as diagnostic indicators, the origin of antibodies in the central nervous system (CNS) is unclear. The blood–brain barrier (BBB), which separates the brain from the peripheral circulatory system, is crucial for antibodies and immune cells to enter or exit the CNS. The findings of cytokines in this disorder support the involvement of the BBB. Here, we aim to review the function of NMDARs and the relationship between anti-NMDAR antibodies and anti-NMDAR encephalitis. We summarize the present knowledge of the composition of the BBB, especially by emphasizing the role of BBB components. Finally, we further provide a discussion on the impact of BBB dysfunction in anti-NMDAR encephalitis.
Cohort analysis of novel SPAST variants in SPG4 patients and implementation of in vitro and in vivo studies to identify the pathogenic mechanism caused by splicing mutations
Authors: Ferese Rosangela , Scala Simona , Suppa Antonio , Campopiano Rosa , Asci Francesco , Zampogna Alessandro , Chiaravalloti Maria Antonietta , Griguoli Annamaria , Storto Marianna , Pardo Alba Di , Giardina Emiliano , Zampatti Stefania , Fornai Francesco , Novelli Giuseppe , Fanelli Mirco , Zecca Chiara , Logroscino Giancarlo , Centonze Diego , Gambardella Stefano
Published: December 2023

Introduction

Pure hereditary spastic paraplegia (SPG) type 4 (SPG4) is caused by mutations of SPAST gene. This study aimed to analyze SPAST variants in SPG4 patients to highlight the occurrence of splicing mutations and combine functional studies to assess the relevance of these variants in the molecular mechanisms of the disease.

Methods

We performed an NGS panel in 105 patients, in silico analysis for splicing mutations, and in vitro minigene assay.

Results and discussion

The NGS panel was applied to screen 105 patients carrying a clinical phenotype corresponding to upper motor neuron syndrome (UMNS), selectively affecting motor control of lower limbs. Pathogenic mutations in SPAST were identified in 12 patients (11.42%), 5 missense, 3 frameshift, and 4 splicing variants. Then, we focused on the patients carrying splicing variants using a combined approach of in silico and in vitro analysis through minigene assay and RNA, if available. For two splicing variants (i.e., c.1245+1G>A and c.1414-2A>T), functional assays confirm the types of molecular alterations suggested by the in silico analysis (loss of exon 9 and exon 12). In contrast, the splicing variant c.1005-1delG differed from what was predicted (skipping exon 7), and the functional study indicates the loss of frame and formation of a premature stop codon. The present study evidenced the high splice variants in SPG4 patients and indicated the relevance of functional assays added to in silico analysis to decipher the pathogenic mechanism.
A novel animal model of neuropathic corneal pain–the ciliary nerve constriction model
Authors: Seyed-Razavi Yashar , Kenyon Brendan M. , Qiu Fangfang , Harris Deshea L. , Hamrah Pedram
Published: December 2023

Introduction

Neuropathic pain arises as a result of peripheral nerve injury or altered pain processing within the central nervous system. When this phenomenon affects the cornea, it is referred to as neuropathic corneal pain (NCP), resulting in pain, hyperalgesia, burning, and photoallodynia, severely affecting patients’ quality of life. To date there is no suitable animal model for the study of NCP. Herein, we developed an NCP model by constriction of the long ciliary nerves innervating the eye.

Methods

Mice underwent ciliary nerve constriction (CNC) or sham procedures. Safety was determined by corneal fluorescein staining to assess ocular surface damage, whereas Cochet-Bonnet esthesiometry and confocal microscopy assessed the function and structure of corneal nerves, respectively. Efficacy was assessed by paw wipe responses within 30 seconds of applying hyperosmolar (5M) saline at Days 3, 7, 10, and 14 post-constriction. Additionally, behavior was assessed in an open field test (OFT) at Days 7, 14, and 21.

Results

CNC resulted in significantly increased response to hyperosmolar saline between groups (p < 0.0001), demonstrating hyperalgesia and induction of neuropathic pain. Further, animals that underwent CNC had increased anxiety-like behavior in an open field test compared to controls at the 14- and 21-Day time-points (p < 0.05). In contrast, CNC did not result in increased corneal fluorescein staining or decreased sensation as compared to sham controls (p > 0.05). Additionally, confocal microscopy of corneal whole-mounts revealed that constriction resulted in only a slight reduction in corneal nerve density (p < 0.05), compared to naïve and sham groups.

Discussion

The CNC model induces a pure NCP phenotype and may be a useful model for the study of NCP, recapitulating features of NCP, including hyperalgesia in the absence of ocular surface damage, and anxiety-like behavior.
Prognosis of comatose patients with reduced EEG montage by combining quantitative EEG features in various domains
Authors: Tao Tao , Lu Shiqi , Hu Nan , Xu Dongyang , Xu Chenyang , Li Fajun , Wang Qin , Peng Yuan
Published: December 2023

Objective

As the frontoparietal network underlies recovery from coma, a limited frontoparietal montage was used, and the prognostic values of EEG features for comatose patients were assessed.

Methods

Collected with a limited frontoparietal EEG montage, continuous EEG recordings of 81 comatose patients in ICU were used retrospectively. By the 60-day Glasgow outcome scale (GOS), the patients were dichotomized into favorable and unfavorable outcome groups. Temporal-, frequency-, and spatial-domain features were automatically extracted for comparison. Partial correlation analysis was applied to eliminate redundant factors, and multiple correspondence analysis was used to explore discrimination between groups. Prognostic characteristics were calculated to assess the performance of EEG feature-based predictors established by logistic regression. Analyses were performed on all-patients group, strokes subgroup, and traumatic brain injury (TBI) subgroup.

Results

By analysis of all patients, raised burst suppression ratio (BSR), suppressed root mean square (RMS), raised power ratio of β to α rhythm (β/α), and suppressed phase-lag index between F3 and P4 (PLI [F3, P4]) were associated with unfavorable outcome, and yielded AUC of 0.790, 0.811, 0.722, and 0.844, respectively. For the strokes subgroup, the significant variables were BSR, RMS, θ/total, θ/δ, and PLI (F3, P4), while for the TBI subgroup, only PLI (F3, P4) was significant. BSR combined with PLI (F3, P4) gave the best predictor by cross-validation analysis in the all-patients group (AUC = 0.889, 95% CI: 0.819–0.960).

Conclusion

Features extracted from limited frontoparietal montage EEG served as valuable coma prognostic tools, where PLI (F3, P4) was always significant. Combining PLI (F3, P4) with features in other domains may achieve better performance.

Significance

A limited-montage EEG coupled with an automated algorithm is valuable for coma prognosis.
Synaptic plasticity through a naturalistic lens
Authors: Piette Charlotte , Gervasi Nicolas , Venance Laurent
Published: December 2023

From the myriad of studies on neuronal plasticity, investigating its underlying molecular mechanisms up to its behavioral relevance, a very complex landscape has emerged. Recent efforts have been achieved toward more naturalistic investigations as an attempt to better capture the synaptic plasticity underpinning of learning and memory, which has been fostered by the development of in vivo electrophysiological and imaging tools. In this review, we examine these naturalistic investigations, by devoting a first part to synaptic plasticity rules issued from naturalistic in vivo-like activity patterns. We next give an overview of the novel tools, which enable an increased spatio-temporal specificity for detecting and manipulating plasticity expressed at individual spines up to neuronal circuit level during behavior. Finally, we put particular emphasis on works considering brain-body communication loops and macroscale contributors to synaptic plasticity, such as body internal states and brain energy metabolism.
Evolving trends and burden of iron deficiency among children, 1990–2019: a systematic analysis for the global burden of disease study 2019
Authors: Long Dan , Mao Chenhan , Liu Yaxuan , Zhou Tao , Xu Yin , Zhu Ying
Published: December 2023

Objectives

We aimed to provide a timely, comprehensive, and reliable assessment of the burden of iron deficiency (ID) in children between 1990 and 2019 at the global, regional, and national levels to inform policymakers in developing locally appropriate health policies.

Methods

Data related to ID among children younger than 15 years old were analyzed by sex, age, year, socio-demographic index (SDI), and location according to the Global Burden of Disease Study 2019 (GBD 2019). Age-standardized rates were used to compare the burden between different regions and countries. Furthermore, the Joinpoint regression model was used to assess temporal trends from 1990 to 2019.

Results

In 2019, the number of prevalent cases and disability-adjusted life years (DALYs) for ID in children were 391,491,699 and 13,620,231, respectively. The global age-standardized prevalence and DALY rates for childhood ID in 2019 were 20,146.35 (95% confidence interval: 19,407.85 to 20,888.54) and 698.90 (466.54 to 1015.31) per 100,000, respectively. Over the past 30 years, the global prevalence of ID among children has been highest in low-SDI regions, particularly in Western Sub-Saharan Africa, South Asia, and Eastern Sub-Saharan Africa. Since 1990, the prevalence and DALY of ID in children have been declining in most geographic regions. Nationally, Ecuador, China, and Chile have shown the most significant decreases in prevalence. The greatest decline in age-standardized DALY rate was observed in Ecuador, while Burkina Faso experienced the highest increase. Bhutan had the highest prevalence and DALY rates in 2019. On the age level, the prevalence was relatively higher among the <5 years age group. At the gender dimension, the prevalence of ID in children overall was more pronounced in girls than in boys, as was the case for DALY.

Conclusion

Although the burden of ID in children has been declining, this disease remains a major public health problem, especially in countries with low SDI. Children younger than 5 years of age are an important group for whom targeted measures are needed to reduce the burden of ID.
Efficacy and safety of anti-CD38 monoclonal antibodies in patients with relapsed/refractory multiple myeloma: a systematic review and meta-analysis with trial sequential analysis of randomized controlled trials
Authors: Ye Lu , Zhou Fei , Cheng Dongdong , Xie Ming , Yan Xiaoli , Xue Yuyu , Yang Qian , Jia Rong , Zhong Lili , Yang Li , Zou Liqun , Huang Na
Published: December 2023

Objectives

The current study aims to evaluate the safety and efficacy of anti-CD38 monoclonal antibodies (mAbs) among patients with relapsed/refractory multiple myeloma (RRMM) through meta-analysis.

Methods

As of June 2023, we searched PubMed, Web of Science, Embase and the Cochrane Library. Randomized controlled trials (RCTs) which compared the clinical outcomes of anti-CD38 mAbs plus immunomodulatory drugs (IMiDs) or proteasome inhibitors (PIs) plus dexamethasone and IMiDs (or PIs) and dexamethasone alone for RRMM patients were included. Efficacy outcomes were mainly evaluated with progression-free survival (PFS) and overall survival (OS). The safety was analyzed with hematologic and nonhematologic treatment-emergent adverse events (TEAEs). All results were pooled using hazard ratio (HR), relative risk (RR), and their 95% confidence interval (CI) and prediction interval (PI).

Results

This meta-analysis included 11 RCTs in total. Compared with IMiDs (or PIs) and dexamethasone alone, anti-CD38 mAbs in combination with IMiDs (or PIs) and dexamethasone significantly prolonged PFS (HR: 0.552, 95% CI = 0.461 to 0.659, 95% PI = 0.318 to 0.957) and OS (HR: 0.737, 95% CI = 0.657 to 0.827, 95% PI = 0.626 to 0.868) in patients with RRMM. Additionally, RRMM patients receiving anti-CD38 mAbs in combination with IMiDs (or PIs) and dexamethasone achieved higher rates of overall response (RR: 1.281, 95% CI = 1.144 to 1.434, 95% PI = 0.883 to 1.859), complete response or better (RR: 2.602, 95% CI = 1.977 to 3.424, 95% PI = 1.203 to 5.628), very good partial response (VGPR) or better (RR: 1.886, 95% CI = 1.532 to 2.322, 95% PI = 0.953 to 3.731), and minimum residual disease (MRD)-negative (RR: 4.147, 95% CI = 2.588 to 6.644, 95% PI = 1.056 to 16.283) than those receiving IMiDs (or PIs) and dexamethasone alone. For TEAEs, the rates of hematologic and nonhematologic TEAEs, including thrombocytopenia, neutropenia, upper respiratory tract infection (URTI), pneumonia, bronchitis, dyspnea, diarrhea, pyrexia, back pain, arthralgia, fatigue, insomnia, and hypertension, were higher in the anti-CD38 mAbs in combination with IMiDs (or PIs) and dexamethasone group than in the IMiDs (or PIs) and dexamethasone group.

Conclusion

Our study showed that anti-CD38 mAbs in combination with IMiDs (or PIs) and dexamethasone improved PFS and OS, and achieved higher rates of overall response, complete response or better, VGPR or better, and MRD-negative, as well as higher rates of thrombocytopenia, neutropenia, URTI, pneumonia, bronchitis, dyspnea, diarrhea, pyrexia, back pain, arthralgia, fatigue, insomnia, and hypertension in RRMM patients.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42023431071.
Combined metabolomics and transcriptomics analysis of rats under neuropathic pain and pain-related depression
Authors: Xi Caiyun , He Liqiong , Huang Zhifeng , Zhang Jianxi , Zou Kailu , Guo Qulian , Huang Changsheng
Published: December 2023

Neuropathic pain often leads to negative emotions, which in turn can enhance the sensation of pain. This study aimed to investigate the molecular mechanisms mediating neuropathic pain and negative emotions. Chronic constriction injury (CCI) rats were used as model animals and behavioral tests were conducted to assess pain and negative emotions. Then, the rat anterior cingulate cortex (ACC) was analyzed using UPLC-MS/MS and subsequently integrated with our previously published transcriptome data. Metabolomics analysis revealed that 68 differentially expressed metabolites (DEMs) were identified, mainly in amino acid metabolites and fatty acyls. Combined with our previously published transcriptome data, we predicted two genes that potentially exhibited associations with these metabolites, respectively Apolipoprotein L domain containing 1 (Apold1) and WAP four-disulfide core domain 1 (Wfdc1). Taken together, our results indicated that peripheral nerve injury contributing to neuropathic pain and pain-related depression may be associated with these metabolites and genes. This research provides new insights into the molecular regulatory mechanism, which could serve as a reference for the treatment of neuropathic pain and pain-related depression.
Research on the generation mechanism and characteristics of an Energy Internet backbone network
Authors: Li Xiaopeng , Zhang Zheng , Zhou Yucheng , Li Peng , Ji Liyan
Published: December 2023

The Energy Internet adopts the mechanism of “regional coordination and hierarchical control” to realize the clean power compatibility and reliability in power operation. In the network topology, the traditional tree network is transformed to the hierarchical partition network. First, this paper analyzes the topological features of “hierarchical control, intra-layer partition, interregional interconnection, and regional autonomy” of the Energy Internet. On this basis, the hierarchical ring network autonomy (HRNA) topological generation and evolution mechanism of the Energy Internet is proposed, and the different levels of a Beijing power grid framework are taken as an example to expand and evolve to the Energy Internet. Based on the comparison and analysis of the network characteristics constructed in this paper with relevant literature studies, this mechanism generates a network that is close to the Internet in terms of average degree, network diameter, and aggregation coefficient. However, there is no centrality node with a higher degree of nodes in the Internet topology, which better reflects the equivalence concept of the Energy Internet.
The epigenetic regulatory effect of histone acetylation and deacetylation on skeletal muscle metabolism-a review
Authors: Xu Junjie , Li Chenglong , Kang Xiaolong
Published: December 2023

Skeletal muscles, the largest organ responsible for energy metabolism in most mammals, play a vital role in maintaining the body’s homeostasis. Epigenetic modification, specifically histone acetylation, serves as a crucial regulatory mechanism influencing the physiological processes and metabolic patterns within skeletal muscle metabolism. The intricate process of histone acetylation modification involves coordinated control of histone acetyltransferase and deacetylase levels, dynamically modulating histone acetylation levels, and precisely regulating the expression of genes associated with skeletal muscle metabolism. Consequently, this comprehensive review aims to elucidate the epigenetic regulatory impact of histone acetylation modification on skeletal muscle metabolism, providing invaluable insights into the intricate molecular mechanisms governing epigenetic modifications in skeletal muscle metabolism.
Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis
Authors: Liu Qian , Wu Zinian , Tian Chunyu , Yang Yanting , Liu Lemeng , Feng Yumei , Li Zhiyong
Published: December 2023

Introduction

Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.

Methods

In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.

Results and discussion

The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.
Structural differences of cell walls in earlywood and latewood of Pinus sylvestris and their contribution to biomass recalcitrance
Authors: Liszka Aleksandra , Wightman Raymond , Latowski Dariusz , Bourdon Matthieu , Krogh Kristian B. R. M. , Pietrzykowski Marcin , Lyczakowski Jan J.
Published: December 2023

Scots pine (Pinus sylvestris L.) is an evergreen coniferous tree with wide distribution and good growth performance in a range of habitats. Therefore, wood from P. sylvestris is produced in many managed forests and is frequently used in industry. Despite the importance of pine wood, we still do not fully understand its molecular structure what limits improvements in its processing. One of the basic features leading to variation in wood properties is the presence of earlywood and latewood which form annual growth rings. Here, we characterise biochemical traits that differentiate cell walls of earlywood and latewood in Scots pine. We discover that latewood is less recalcitrant to enzymatic digestion, with galactoglucomannan showing particularly pronounced difference in accessibility. Interestingly, characterisation of lignin reveals a higher proportion of coniferaldehydes in pine latewood and suggests the presence of a different linkage landscape in this wood type. With complementary analysis of wood polysaccharides this enabled us to propose the first detailed molecular model of earlywood and latewood and to conclude that the variation in lignin structure is likely the main determinant of differences in recalcitrance observed between the two wood types in pine. Our discoveries lay the foundation for improvements in industrial processes that use pine wood since we show clear pathways for increasing the efficiency of enzymatic processing of this renewable material. Our work will help guide future breeding of pine trees with desired timber properties and can help link molecular structure of softwood cell walls to function of the different types of xylem in conifers.
Ammonia volatization from conventional and stabilized fertilizers, agronomic aspects and microbiological attributes in a Brazilian coffee crop system
Authors: Sarkis Leonardo Fernandes , Dutra Mateus Portes , Oliveira Damiany Pádua , Fernandes Tales Jesus , de Souza Thaís Regina , Builes Victor Ramirez , Guelfi Douglas
Published: December 2023

We aimed to quantify the N losses through volatilization of the main conventional and stabilized N fertilizers applied in coffee plantations. Additionally, we also assessed microbiological attributes of the soil (microbial biomass carbon (MBC); microbial biomass nitrogen (MBN); microbial basal respiration (MBR); metabolic quotient (qCO2); urease, β-glucosidase, acid phosphatase, and arylsulfatase activities) and agronomic aspects of the crop (N content in the leaves and beans, yield, and N exportation by the beans). Treatments consisted of the combination of three fertilizers (ammonium nitrate - AN, conventional urea - U, and urea with N- (n-butyl) thiophosphoric triamide (NBPT) - UNBPT, and five doses of N (0, 150, 275, 400, and 525 kg ha-1 year-1 of N), with four replicates, totalling 60 experimental plots. In the two crop seasons evaluated, daily and cumulative losses of N-NH3 from the split fertilizer applications were influenced by the N fertilizer technologies. The application of U resulted in losses of 22.0% and 22.8% for the doses of 150 and 400 kg ha-1 year-1 of N. This means that 66 and 182 kg ha-1 of N-NH3 were lost, respectively, at the end of six fertilizations with U. UNBPT reduced urease activity and N-NH3 losses compared to conventional urea, avoiding the volatilization of 15.9 and 24.3 kg ha-1 of N. As for AN, N-NH3 losses did not exceed 1% of the applied dose, regardless of the weather conditions during the fertilization. Urease activity was higher on days of maximum NH3 volatilization. There was an effect of the N sources (NS), soil sampling time (ST), and their interaction (NS × ST) on the MBN and arylsulfatase activity. The N sources also influenced the MBC and the qCO2. A substantial amount of N was removed from the system by the beans and husks of the harvested fruits. Our study showed that N fertilizer technologies are interesting options to reduce N-NH3 losses by volatilization, increase N retention in the soil, and improve microbiological attributes and the sustainability of coffee production systems.