bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-stage hydrocarbon accumulations in the Middle Permian in the Central Sichuan Basin
Authors: Zhang Jianyong , Liao Yun , Lu Pengda , Li Wenzheng , Zhu Kedan , Li Zeqi , Tian Tengzhen , Wu Juan , Sun Wei , Liu Shugen , Deng Bin
Published: April 2024

The Middle Permain Maokou Formation (P2m) is a new region of natural gas exploration in the Sichuan Basin, is characterized by bioclastic limestone with localized dolomitization, and karst fractured-vuggy reservoirs. Currently, on the gas source, hydrocarbon accumulation process and control factors in the Sichuan Basin during the Permian are lacking. To bridge this gap, herein, we identified the filling sequence minerals inside the pores/vugs, along with the oil charge of the Maokou Formation using drill cores, thin sections, oil inclusion analysis, and U-Pb dating of calcite cements. The results showed that the reservoir space of the Maokou Formation was predominated by the residual dissolved pores/vugs, fractures, and dissolved fractures. The pores/vugs underwent four stages of mineral filling by very fine-fine (-crystalline, CC1) calcite → fine-medium calcite (CC2: from 256.4 ± 1.7 to 244.1 ± 6.3 Ma) → fibrous calcite (FC; ∼183.9 ± 8.2 Ma) → coarse-macro calcite (CC3; ∼171.5 ± 5.3 Ma). Combined with the homogenization temperature and salty of fluid inclusion, we considered that three stages of oil charge were present in the Maokou Formation reservoirs. The first stage involved the formation of paleo-oil reservoirs during the Late Permian to Early Triassic, corresponding to the high-maturity aqueous inclusions in CC2, with a homogenization temperature of 106.7°C–137.8°C. At that time, the oil generation from the Lower Cambrian Qiongzhusi Formation rocks peaked, and the generated hydrocarbons migrated upward into the Maokou Formation through the strike-slip faults in the basin center. The second stage involved the formation of paleo-oil reservoirs during the Early Jurassic. The Permian source rocks reached the oil generation window with hydrocarbon expulsion, which was consistent with the oil inclusions in FC. The third stage involved the formation of paleo-gas reservoirs during the Middle Jurassic to Early Cretaceous, corresponding to the high-density methane inclusions and bitumen inclusions occurring in CC3, with the homogenization temperature peaking at 151.9°C–178°C. The natural gas in the Middle Permian of the Central Sichuan Basin is predominantly sourced from the Lower Cambrian Qiongzhusi Formation mudstone and partially from the source rocks of the Middle Permian, indicating a significant source-reservoir conduit of the strike-slip faults in the basin center. The findings provide considerable baseline data to advance further research in the Sichuan Basin.
Applying machine-learning models to differentiate benign and malignant thyroid nodules classified as C-TIRADS 4 based on 2D-ultrasound combined with five contrast-enhanced ultrasound key frames
Authors: Chen Jia-hui , Zhang Yu-Qing , Zhu Tian-tong , Zhang Qian , Zhao Ao-xue , Huang Ying
Published: April 2024

Objectives

To apply machine learning to extract radiomics features from thyroid two-dimensional ultrasound (2D-US) combined with contrast-enhanced ultrasound (CEUS) images to classify and predict benign and malignant thyroid nodules, classified according to the Chinese version of the thyroid imaging reporting and data system (C-TIRADS) as category 4.

Materials and methods

This retrospective study included 313 pathologically diagnosed thyroid nodules (203 malignant and 110 benign). Two 2D-US images and five CEUS key frames (“2nd second after the arrival time” frame, “time to peak” frame, “2nd second after peak” frame, “first-flash” frame, and “second-flash” frame) were selected to manually label the region of interest using the “Labelme” tool. A total of 7 images of each nodule and their annotates were imported into the Darwin Research Platform for radiomics analysis. The datasets were randomly split into training and test cohorts in a 9:1 ratio. Six classifiers, namely, support vector machine, logistic regression, decision tree, random forest (RF), gradient boosting decision tree and extreme gradient boosting, were used to construct and test the models. Performance was evaluated using a receiver operating characteristic curve analysis. The area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy (ACC), and F1-score were calculated. One junior radiologist and one senior radiologist reviewed the 2D-US image and CEUS videos of each nodule and made a diagnosis. We then compared their AUC and ACC with those of our best model.

Results

The AUC of the diagnosis of US, CEUS and US combined CEUS by junior radiologist and senior radiologist were 0.755, 0.750, 0.784, 0.800, 0.873, 0.890, respectively. The RF classifier performed better than the other five, with an AUC of 1 for the training cohort and 0.94 (95% confidence interval 0.88–1) for the test cohort. The sensitivity, specificity, accuracy, PPV, NPV, and F1-score of the RF model in the test cohort were 0.82, 0.93, 0.90, 0.85, 0.92, and 0.84, respectively. The RF model with 2D-US combined with CEUS key frames achieved equivalent performance as the senior radiologist (AUC: 0.94 vs. 0.92, P = 0.798; ACC: 0.90 vs. 0.92) and outperformed the junior radiologist (AUC: 0.94 vs. 0.80, P = 0.039, ACC: 0.90 vs. 0.81) in the test cohort.

Conclusions

Our model, based on 2D-US and CEUS key frames radiomics features, had good diagnostic efficacy for thyroid nodules, which are classified as C-TIRADS 4. It shows promising potential in assisting less experienced junior radiologists.
Service life estimation of electric vehicle lithium-ion battery pack using arrhenius mathematical model
Authors: Rammohan A. , Wang Yong , Kannappan S Subbu , Kumar P Suresh , Ashok Bragadeshwaran , Kotb Hossam , AboRas Kareem M. , Yousef Amr
Published: April 2024

Durability is a desired characteristic for all battery packs in Electric Vehicles. In this study, the service life of the EV battery pack under real-world operating conditions is projected using an Arrhenius mathematical simulation model. The model comprises a 39.2 kWh EV Lithium-Ion battery pack integrated with a three-phase inverter to convert the battery pack’s Direct Current output to Alternating Current. In addition, the Alternating Current output is coupled to a 100 kW permanent magnet synchronous motor, which is regarded as the load. A field-oriented controller provides pulse width-modulated output signals that are supplied back to the inverter to generate the correct driving current. Variable conditions of charge rate (C-rate: 1.25C − 4C), discharge rate (C-rate: 0.5C − 4C), temperature (25°C–60°C), and depth of discharge (30%–90%) are evaluated to determine the battery pack’s service life. Under a 4C charge rate/0.5C discharge rate and 50% depth of discharge, the modeling results indicate the battery pack has a service life of approximately 6,000 h at low temperatures (25°C) and roughly 3,000 h at high temperatures (60°C). The model has been validated by comparing the results with experimental data from the literature.
StadtWildTiere – added value and impact of transnational urban wildlife community science projects
Authors: Geiger Madeleine , Taucher Anouk Lisa , Gloor Sandra , Lauper Mirco , Kiefer Sarah , Kimmig Sophia E. , Siebert Janette , Walter Theresa , Zink Richard , Bontadina Fabio , Hegglin Daniel
Published: April 2024

We present and exemplify the potential of the long-term community science (= citizen science) project StadtWildTiere (German for ‘urban wildlife’) in a transnational context. StadtWildTiere gathers opportunistic sightings of urban wildlife to raise awareness of, increase knowledge of, and promote biodiversity in urban areas across Central Europe. Transnationally similar methodologies enable direct comparisons concerning occurrence, distribution, and trends of urban wildlife populations and allow for new insights into and potential conservation and management measures of these otherwise unmonitored wildlife populations. We advocate the use and promotion for such community-based science projects, which align with the guiding principles of awareness, knowledge, and action. Such projects should whenever possible connect with similar initiatives in other countries to benefit from comparisons and get a strong impact on a transnational level.
Phenotypic constraints at the top of the world: an Arctic songbird faces the cumulative cost of maintaining a winter-like phenotype during breeding
Authors: Le Pogam Audrey , O’Connor Ryan S. , Love Oliver P. , Young Kevin G. , Drolet Justine , Régimbald Lyette , Roy Gabrielle , Robitaille Francis , Berteaux Dominique , Tam Andrew , Vézina François
Published: April 2024

Among birds, several body composition traits typically decrease in size or mass during breeding likely as a result of competing demands during this critical life history stage. However, a recent outdoor captive study in an Arctic-breeding cold-specialist songbird (snow buntings – Plectrophenax nivalis) demonstrated that these birds maintain winter cold acclimatization during the spring and summer, despite facing summer temperatures much warmer than on their Arctic breeding grounds. This suggests that buntings may face a cumulative physiological cost during breeding: having to support a winter phenotype while also upregulating additional traits for reproduction. The current study aimed to test this hypothesis. Between 2016 and 2019, we examined how body composition and metabolic performance (thermogenic capacity and physiological maintenance costs) changed from pre-breeding to chick provisioning in free-living birds captured at the northern limit of their breeding range in the Canadian Arctic (Alert, NU, 82°). While body mass and fat reserves deceased significantly between pre-breeding and territory defense independent of thermal conditions, cold endurance and associated traits remained stable and elevated up to the nestling provisioning period, as long as ambient temperature remained below a threshold level of 0–2°C. These results indicate that snow buntings must maintain a high thermogenic capacity after arrival on the breeding grounds if temperatures remain below freezing, regardless of whether birds are actively breeding or not. In this context, our research suggests that these birds, and possibly other arctic breeding songbirds, may experience cumulative physiological costs during years with a late onset of spring, when breeding activities (i.e., egg production and incubation) begin while temperatures are still below 0–2°C.
Diverse potential of secretome from natural killer cells and monocyte-derived macrophages in activating stellate cells
Authors: Sauer Julia , Steixner-Kumar Agnes A. , Gabler Svenja , Motyka Maciej , Rippmann Jörg F. , Brosa Stefan , Boettner Dennis , Schönberger Tanja , Lempp Charlotte , Frodermann Vanessa , Simon Eric , Krenkel Oliver , Bahrami Ehsan
Published: April 2024

Chronic liver diseases, such as non-alcoholic steatohepatitis (NASH)-induced cirrhosis, are characterized by an increasing accumulation of stressed, damaged, or dying hepatocytes. Hepatocyte damage triggers the activation of resident immune cells, such as Kupffer cells (KC), as well as the recruitment of immune cells from the circulation toward areas of inflammation. After infiltration, monocytes differentiate into monocyte-derived macrophages (MoMF) which are functionally distinct from resident KC. We herein aim to compare the in vitro signatures of polarized macrophages and activated hepatic stellate cells (HSC) with ex vivo-derived disease signatures from human NASH. Furthermore, to shed more light on HSC activation and liver fibrosis progression, we investigate the effects of the secretome from primary human monocytes, macrophages, and NK cells on HSC activation. Interleukin (IL)-4 and IL-13 treatment induced transforming growth factor beta 1 (TGF-β1) secretion by macrophages. However, the supernatant transfer did not induce HSC activation. Interestingly, PMA-activated macrophages showed strong induction of the fibrosis response genes COL10A1 and CTGF, while the supernatant of IL-4/IL-13-treated monocytes induced the upregulation of COL3A1 in HSC. The supernatant of PMA-activated NK cells had the strongest effect on COL10A1 induction in HSC, while IL-15-stimulated NK cells reduced the expression of COL1A1 and CTGF. These data indicate that other factors, aside from the well-known cytokines and chemokines, might potentially be stronger contributors to the activation of HSCs and induction of a fibrotic response, indicating a more diverse and complex role of monocytes, macrophages, and NK cells in liver fibrosis progression.
CD8+ T cells are necessary for improved sepsis survival induced by CD28 agonism in immunologically experienced mice
Authors: Anyalebechi Jerome C. , Sun Yini , Davis Carolyn , Wagener Maylene E. , Liang Zhe , Burd Eileen M. , Coopersmith Craig M. , Ford Mandy L.
Published: April 2024

Introduction

A hallmark of T cell dysregulation during sepsis is the downregulation of costimulatory molecules. CD28 is one of T cell costimulatory molecules significantly altered on memory T cells during sepsis. We recently showed that treatment with a αCD28 agonist in septic immunologically experienced mice led to improved survival. Therefore, here we aimed to identify the cell subset(s) necessary for the survival benefit observed in the context of CD28 agonism, and to further investigate the mechanism by which CD28 agonism improves sepsis survival in immunologically experienced mice. Methods: Mice received specific pathogen inoculation to generate memory T cell populations similar in frequency to that of adult humans. Once these infections were cleared and the T cell response had transitioned to the memory phase, animals were rendered septic via cecal ligation and puncture in the presence or absence of an agonistic anti-CD28 mAb.

Results

Results demonstrated that CD8+ T cells, and not bulk CD4+ T cells or CD25+ regulatory T cells, were necessary for the survival benefit observed in CD28 agonist-treated septic immunologically experienced mice. Upon examination of these CD8+ T cells, we found that CD28 agonism in septic immunologically experienced mice was associated with an increase in Foxp3+ CD8+ T cells as compared to vehicle-treated controls. When CD8+ T cells were depleted in septic immunologically experienced mice in the setting of CD28 agonism, a significant increase in levels of inflammatory cytokines in the blood was observed.

Discussion

Taken together, these results indicate that CD28 agonism in immunologically experienced mice effectively suppresses inflammation via a CD8+-dependent mechanism to decrease mortality during sepsis.
Coupled scRNA-seq and Bulk-seq reveal the role of HMMR in hepatocellular carcinoma
Authors: Su Zhixiong , He Yufang , You Lijie , Zhang Guifeng , Chen Jingbo , Liu Zhenhua
Published: April 2024

Background

Hyaluronan-mediated motility receptor (HMMR) is overexpressed in multiple carcinomas and influences the development and treatment of several cancers. However, its role in hepatocellular carcinoma (HCC) remains unclear.

Methods

The “limma” and “GSVA” packages in R were used to perform differential expression analysis and to assess the activity of signalling pathways, respectively. InferCNV was used to infer copy number variation (CNV) for each hepatocyte and “CellChat” was used to analyse intercellular communication networks. Recursive partitioning analysis (RPA) was used to re-stage HCC patients. The IC50 values of various drugs were evaluated using the “pRRophetic” package. In addition, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm HMMR expression in an HCC tissue microarray. Flow cytometry (FCM) and cloning, Edu and wound healing assays were used to explore the capacity of HMMR to regulate HCC tumour.

Results

Multiple cohort studies and qRT-PCR demonstrated that HMMR was overexpressed in HCC tissue compared with normal tissue. In addition, HMMR had excellent diagnostic performance. HMMR knockdown inhibited the proliferation and migration of HCC cells in vitro. Moreover, high HMMR expression was associated with “G2M checkpoint” and “E2F targets” in bulk RNA and scRNA-seq, and FCM confirmed that HMMR could regulate the cell cycle. In addition, HMMR was involved in the regulation of the tumour immune microenvironment via immune cell infiltration and intercellular interactions. Furthermore, HMMR was positively associated with genomic heterogeneity with patients with high HMMR expression potentially benefitting more from immunotherapy. Moreover, HMMR was associated with poor prognosis in patients with HCC and the re-staging by recursive partitioning analysis (RPA) gave a good prognosis prediction value and could guide chemotherapy and targeted therapy.

Conclusion

The results of the present study show that HMMR could play a role in the diagnosis, prognosis, and treatments of patients with HCC based on bulk RNA-seq and scRAN-seq analyses and is a promising molecular marker for HCC.
Dry and liquid formulations of IBT-V02, a novel multi-component toxoid vaccine, are effective against Staphylococcus aureus isolates from low-to-middle income countries
Authors: Wang Yu , Mukherjee Ipsita , Venkatasubramaniam Arundhathi , Dikeman Dustin , Orlando Nicholas , Zhang Jing , Ortines Roger , Mednikov Mark , Sherchand Shardulendra P. , Kanipakala Tulasikumari , Le Thao , Shukla Sanjay , Ketner Mark , Adhikari Rajan P. , Karauzum Hatice , Aman M. Javad , Archer Nathan K.
Published: April 2024

Staphylococcus aureus is the leading cause of skin and soft tissue infections (SSTIs) in the U.S. as well as more serious invasive diseases, including bacteremia, sepsis, endocarditis, surgical site infections, osteomyelitis, and pneumonia. These infections are exacerbated by the emergence of antibiotic-resistant clinical isolates such as methicillin-resistant S. aureus (MRSA), highlighting the need for alternatives to antibiotics to treat bacterial infections. We have previously developed a multi-component toxoid vaccine (IBT-V02) in a liquid formulation with efficacy against multiple strains of Staphylococcus aureus prevalent in the industrialized world. However, liquid vaccine formulations are not compatible with the paucity of cold chain storage infrastructure in many low-to-middle income countries (LMICs). Furthermore, whether our IBT-V02 vaccine formulations are protective against S. aureus isolates from LMICs is unknown. To overcome these limitations, we developed lyophilized and spray freeze-dried formulations of IBT-V02 vaccine and demonstrated that both formulations had comparable biophysical attributes as the liquid formulation, including similar levels of toxin neutralizing antibodies and protective efficacy against MRSA infections in murine and rabbit models. To enhance the relevancy of our findings, we then performed a multi-dimensional screen of 83 S. aureus clinical isolates from LMICs (e.g., Democratic Republic of Congo, Palestine, and Cambodia) to rationally down-select strains to test in our in vivo models based on broad expression of IBT-V02 targets (i.e., pore-forming toxins and superantigens). IBT-V02 polyclonal antisera effectively neutralized toxins produced by the S. aureus clinical isolates from LMICs. Notably, the lyophilized IBT-V02 formulation exhibited significant in vivo efficacy in various preclinical infection models against the S. aureus clinical isolates from LMICs, which was comparable to our liquid formulation. Collectively, our findings suggested that lyophilization is an effective alternative to liquid vaccine formulations of our IBT-V02 vaccine against S. aureus infections, which has important implications for protection from S. aureus isolates from LMICs.
Antimalarial drug resistance profiling of Plasmodium falciparum infections in India using Ion Torrent deep sequencing
Authors: Kale Sonal , Uplekar Swapna M. , Bandyopadhyay Nabamita , Rao Pavitra N. , Ali Syed Z. , Sharma Surya Kant , Tandel Nikunj , Patel Ankita , Singh Ranvir , Dank Aaron , Ravishankaran Sangamithra , Priya G. Sri Lakshmi , Asokan Aswin , Eapen Alex , Singh Om. P. , Carlton Jane M. , Mallick Prashant K.
Published: April 2024

Introduction

Tracking the emergence and spread of antimalarial drug resistance is critical for supporting progress towards the control and eventual elimination of malaria in South Asia, especially India. Plasmodium falciparum has evolved resistance to virtually every antimalarial drug, and significant progress has been made to identify the molecular genetic mechanisms involved in the most common types of resistance.

Methods

An amplicon sequencing protocol was used for molecular surveillance of antimalarial drug resistance in a total of 158 patient isolates collected from December 2012 to September 2015 from three sites in south, west and east India: Tamil Nadu, Gujarat, and Odisha respectively. Five full length Plasmodium falciparum genes whose mutant proteins are implicated in antimalarial drug resistance were investigated: Pfcrt for chloroquine, Pfdhfr for pyrimethamine, Pfdhps for sulfadoxine, Pfk13 for artemisinin and Pfmdr1 for resistance to multiple antimalarial drugs.

Results

We observed a high proportion of wild-type Pfcrt and Pfdhfr haplotypes from the P. falciparum-dominant site Rourkela, while mutant Pfcrt and Pfdhfr haplotypes were fixed at the P. vivax dominant sites Chennai and Nadiad. The wild-type Pfdhps haplotype was predominant across all study sites. We identified mutations in the propeller domain of Pfk13, although they are not associated with resistance to artemisinin. Finally, using samples taken from the same patient on day 2, day 7, and day 14 after artemisinin combination treatment, we were able to observe changes in allele frequency of drug resistance genes during the course of an infection.

Discussion

This is the first high-throughput deep sequencing study of five full-length P. falciparum genes in clinical isolates from three different study sites in India with varying transmission ecologies. Amplicon sequencing based on ion-torrent has the potential to track changes in the frequency of drug resistant alleles as a patient is undergoing drug therapy, and to identify new resistance mutations as they increase in frequency in the patient. This study showed possibility of whole gene sequencing, leads to in-depth molecular surveillance of multiple antimalarial resistant candidates and furthermore suggests investigations on reversal of resistant genotypes due to usage of artemisinin combination therapy in P. falciparum prevalent areas of the country.
A meta-analysis on first-trimester blood count parameters—is the neutrophil-to-lymphocyte ratio a potentially novel method for first-trimester preeclampsia screening?
Authors: Mészáros Balázs , Veres Dániel S. , Nagyistók Luca , Kovács Bence G. , Kukor Zoltán , Valent Sándor
Published: April 2024

Objective

Meta-analysis focusing on the role of first-trimester neutrophil-to-lymphocyte ratio (NLR) in the prediction of preeclampsia.

Data sources

PubMed, Scopus, Web of Science, Cochrane Library, and Embase databases were queried from inception up to December 31, 2022.

Study eligibility criteria

The study included all types of original research that was conducted in humans and values of NLR were measured during the first trimester, among patients who later developed preeclampsia, compared to the values of control groups.

Study appraisal and synthesis methods

Two reviewers independently performed data abstraction and quality appraisal, and disagreements were resolved by consensus and, if necessary, by the opinion of a third reviewer. During the analysis, PRISMA and MOOSE guidelines were followed. All statistical analyses were made with R.

Results

For the research on the predictive role of NLR values in the first trimester for preeclampsia, a total of 6 studies were selected for analysis, covering 2,469 patients. The meta-analysis revealed a 95% confidence interval (CI) for the effect size of 0.641 to 1.523, with a prediction interval of 0.027 to 2.137.

Conclusion

Based on the analysis, NLR is a promising biochemical marker for future pieces of research that try to find new screening methods for first-trimester preeclampsia. We encourage other researchers to examine NLR’s predictive value combined with other markers in preeclampsia screening, this way being able to find new and affordable protocols for first-trimester preeclampsia screening.

Systematic review registration

identifier CRD42023392663.
Assessing multidisciplinary follow-up pattern efficiency and cost in follow-up care for patients in cervical spondylosis surgery: a non-randomized controlled study
Authors: Fu Zhongmin , Xie Yan , Li Peifang , Gao Menghui , Chen Jiali , Ning Ning
Published: April 2024

Background

The use of multidisciplinary treatment programs in out-of-hospital healthcare is a new area of research. Little is known about the benefits of this method in the management of discharged patients undergoing cervical spondylosis surgery.

Objective

This study aimed to explore the effect of a contracted-based, multidisciplinary follow-up plan in patients after cervical spondylosis surgery.

Methods

This non-blinded non-randomized controlled study was conducted with 88 patients (44 in the intervention group, 44 in the control group). The clinical outcomes, including Neck Disability Index (NDI), pain score (VAS), Self-Efficacy for Managing Chronic Disease 6-item Scale (SECD-6), and 12-Item Short-Form Health Survey (SF-12) score were assessed at the time of discharge, 24–72 h, 1 month, and 3 months post-discharge. The complications, patient satisfaction, and economic indicators were assessed at the final follow-up (3 months).

Results

Patients who received contracted follow-up showed greater improvement in neck dysfunction at 24–72 h, 1 month, and 3 months after discharge compared to those who received routine follow-up (p < 0.001). At 1 month after discharge, the intervention group exhibited better self-efficacy (p = 0.001) and quality of life (p < 0.001) than the control group, and these improvements lasted for 3 months. The intervention group reported lower pain scores at 24–72 h and 1 month (p = 0.008; p = 0.026) compared to the control group. The incidence of complications was significantly lower in the intervention group (11.4%) compared to the control group (40.9%). The total satisfaction score was significant difference between the two groups (p < 0.001). Additionally, the intervention group had lower direct medical costs (p < 0.001), direct non-medical costs (p = 0.035), and total costs (p = 0.04) compared to the control group. However, there was no statistically significant difference in indirect costs between the two groups (p = 0.59).

Conclusion

A multidisciplinary contract follow-up plan has significant advantages regarding neck disability, self-efficacy, quality of life, postoperative complications, patient satisfaction, and direct costs compared with routine follow-up.
Transcriptomic analysis of the response of Avena sativa to Bacillus amyloliquefaciens DGL1
Authors: Yang Xue , Xie Yongli , Wang Tian , Qiao Youming , Li Junxi , Wu Lingling , Gao Ying
Published: April 2024

Introduction

Bacillus amyloliquefaciens DGL1, isolated from the arid sandy areas in Dagler, Qinghai Province, China, promotes the growth of Avena sativa variety “Qing Yan 1”.

Methods

To elucidate the transcriptomic changes in the oat root system following interaction with DGL1 and to reveal the molecular mechanism by which DGL1 promotes oat growth, treatment and control groups of oat roots at 2, 4, 8, and 12 h after inoculation with a suspension of strain DGL1 were analyzed using Illumina high-throughput transcriptome sequencing technology. The differentially expressed genes were determined through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and the metabolic pathways and key genes were analyzed.

Results

The results showed that 7874, 13,392, 13,169, and 19,026 differentially expressed genes were significantly enriched in the glycolysis/gluconeogenesis pathway, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction, and other related metabolic pathways in the oat roots at 2, 4, 8, and 12 h after inoculation with a DGL1 suspension. The GO and KEGG enrichment analyses revealed that the genes encoding plasma membrane ATPase, phosphoglycerate kinase gene PGK, ammonium transporter protein gene AMT, cellulose synthase gene CSLF6, and growth hormone response family gene IAA18 were significantly upregulated.

Discussion

It is hypothesized that the pro-growth mechanism of strain DGL1 in oats is the result of the coordination of multiple pathways through the promotion of oat energy metabolism, phytohormone signaling, secondary metabolite synthesis, and amino acid metabolism.
Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ‘Igneacidithiobacillus’
Authors: Arisan Dilanaz , Moya-Beltrán Ana , Rojas-Villalobos Camila , Issotta Francisco , Castro Matías , Ulloa Ricardo , Chiacchiarini Patricia A. , Díez Beatriz , Martín Alberto J. M. , Ñancucheo Iván , Giaveno Alejandra , Johnson D. Barrie , Quatrini Raquel
Published: April 2024

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is ‘Igneacidithiobacillus’, a novel genus-level taxon, represented by ‘Igneacidithiobacillus copahuensis’ VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including ‘Ca. Igneacidithiobacillus chanchocoensis’ (mCHCt20-1TS), ‘Igneacidithiobacillus siniensis’ (S30A2T), ‘Ca. Igneacidithiobacillus taupoensis’ (TVZ-G3 TS), and ‘Ca. Igneacidithiobacillus waiarikiensis’ (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus ‘Igneacidithiobacillus’.
Evaluating disinfectant efficacy on mixed biofilms comprising Shiga toxigenic Escherichia coli, lactic acid bacteria, and spoilage microorganisms
Authors: Koti Kavitha , Rodas-Gonzalez Argenis , Nadon Celine , McAllister Tim , Yang Xianqin , Narváez-Bravo Claudia
Published: April 2024

This study aimed to investigate the impact of temperature and the presence of other microorganisms on the susceptibility of STEC to biocides. Mature biofilms were formed at both 10°C and 25°C. An inoculum of planktonic bacteria comprising 106 CFU/mL of spoilage bacteria and 103 CFU/mL of a single E. coli strain (O157, O111, O103, and O12) was used to form mixed biofilms. The following bacterial combinations were tested: T1: Carnobacterium piscicola + Lactobacillus bulgaricus + STEC, T2: Comamonas koreensis + Raoultella terrigena + STEC, and T3: Pseudomonas aeruginosa + C. koreensis + STEC. Tested biocides included quaternary ammonium compounds (Quats), sodium hypochlorite (Shypo), sodium hydroxide (SHyd), hydrogen peroxide (HyP), and BioDestroy®-organic peroxyacetic acid (PAA). Biocides were applied to 6-day-old biofilms. Minimum Bactericidal Concentrations (MBC) and Biofilm Eradication Concentrations (BEC) were determined. Planktonic cells and single-species biofilms exhibited greater susceptibility to sanitizers (p < 0.0001). Lactobacillus and Carnobacterium were more susceptible than the rest of the tested bacteria (p < 0.0001). Single species biofilms formed by E. coli O111, O121, O157, and O45 showed resistance (100%) to Shypo sanitizer (200 ppm) at 25°C. From the most effective to the least effective, sanitizer performance on single-species biofilms was PAA > Quats > HyP > SHyd > Shypo. In multi-species biofilms, spoilage bacteria within T1, T2, and T3 biofilms showed elevated resistance to SHyd (30%), followed by quats (23.25%), HyP (15.41%), SHypo (9.70%), and BioDestroy® (3.42%; p < 0.0001). Within T1, T2, and T3, the combined STEC strains exhibited superior survival to Quats (23.91%), followed by HyP (19.57%), SHypo (18.12%), SHyd (16.67%), and BioDestroy® (4.35%; p < 0.0001). O157:H7-R508 strains were less tolerant to Quats and Shypo when combined with T2 and T3 (p < 0.0001). O157:H7 and O103:H2 strains in mixed biofilms T1, T2, and T3 exhibited higher biocide resistance than the weak biofilm former, O145:H2 (p < 0.0001). The study shows that STEC within multi-species biofilms’ are more tolerant to disinfectants.
Graph-based EEG approach for depression prediction: integrating time-frequency complexity and spatial topology
Authors: Liu Wei , Jia Kebin , Wang Zhuozheng
Published: April 2024

Depression has become the prevailing global mental health concern. The accuracy of traditional depression diagnosis methods faces challenges due to diverse factors, making primary identification a complex task. Thus, the imperative lies in developing a method that fulfills objectivity and effectiveness criteria for depression identification. Current research underscores notable disparities in brain activity between individuals with depression and those without. The Electroencephalogram (EEG), as a biologically reflective and easily accessible signal, is widely used to diagnose depression. This article introduces an innovative depression prediction strategy that merges time-frequency complexity and electrode spatial topology to aid in depression diagnosis. Initially, time-frequency complexity and temporal features of the EEG signal are extracted to generate node features for a graph convolutional network. Subsequently, leveraging channel correlation, the brain network adjacency matrix is employed and calculated. The final depression classification is achieved by training and validating a graph convolutional network with graph node features and a brain network adjacency matrix based on channel correlation. The proposed strategy has been validated using two publicly available EEG datasets, MODMA and PRED+CT, achieving notable accuracy rates of 98.30 and 96.51%, respectively. These outcomes affirm the reliability and utility of our proposed strategy in predicting depression using EEG signals. Additionally, the findings substantiate the effectiveness of EEG time-frequency complexity characteristics as valuable biomarkers for depression prediction.
Decreased incidence of Kawasaki disease in South Korea during the SARS-CoV-2 pandemic
Authors: Oh Kyung Jin , Lee Sang-Yun
Published: April 2024

Purpose

Analyzing Kawasaki disease epidemiology during the SARS-CoV-2 pandemic in South Korea using 2012–2020 National Health Insurance Service data.

Methods

The incidence of Kawasaki disease for 2012–2020 was investigated to identify changes in incidence after the start of the pandemic. National Health Insurance Service data from the Republic of Korea were used. Kawasaki disease was defined based on the International Statistical Classification of Diseases and Related Health Problems, the Tenth Revision diagnostic code (M30.3), and the intravenous immunoglobulin prescription code. Prescription history was collected for the following medications: intravenous immunoglobulin, aspirin, corticosteroids, tumor necrosis factor-α antagonist, clopidogrel, and anticoagulation drugs.

Results

The Kawasaki disease incidence per 100,000 individuals younger than 5 years was 238.9, 230.0, and 141.2 in 2018, 2019, and 2020, respectively. Regarding the incidence from 2012 to 2020, it was the highest in 2018 and decreased to 141.2 (p < 0.001) in 2020, after the start of the pandemic. In 2020, 28.3% of all patients with KD were infants, a percentage significantly higher than that of the previous year (p < 0.001). There was biphasic seasonality in the monthly Kawasaki disease incidence. The Kawasaki disease incidence was the highest in winter followed by that in early summer.

Conclusion

After the start of the pandemic, the Kawasaki disease incidence decreased, and the percentage of patients with Kawasaki disease aged <1 year increased. These findings provide support for the hypothesis suggesting an infectious trigger in Kawasaki disease.
Network pharmacology and molecular docking reveal the mechanisms of curcumin activity against esophageal squamous cell carcinoma
Authors: Wang Jian , Zhang Zhilong , Li Qian , Hu Zilong , Chen Yuan , Chen Hao , Cai Wei , Du Qiancheng , Zhang Peng , Xiong Dian , Ye Shugao
Published: April 2024

Background: Curcumin (CUR), an effective traditional Chinese medicinal extract, displays good anti-cancer activity against various cancers. Nevertheless, the impacts and fundamental mechanisms of CUR to treat esophageal squamous cell carcinoma (ESCC) yet to be comprehensively clarified. This study examined the suppressive impacts of CUR on ESCC.

Methods: For a comprehensive understanding of the effect of CUR in ESCC. The CUR targets and ESCC-related genes were identified respectively, and the intersection targets between CUR and ESCC were acquired. Then, we examined the intersection targets and discovered genes that were expressed differently in ESCC. Using DAVID, enrichment analyses were conducted on the targets of CUR-ESCC. The STRING database and Cytoscape v.3.9.1 were utilized to build networks for protein-protein interaction (PPI) and drug-target-pathway. Furthermore, the interactions between CUR and its core targets were confirmed by molecular docking studies. To confirm the effects of CUR on ESCC cells, in vitro experiments were finally conducted.

Results: Overall, 47 potential CUR targets for ESCC treatment were identified. The KEGG pathway enrichment analysis identified 61 signaling pathways, primarily associated with the FoxO signaling, the cell cycle, cellular senescence, the IL-17 signaling pathway which play important roles in ESCC progression. In the PPI network and the docking results identified CHEK1 and CDK6 as the core targets that positively associated with ESCC survival. CUR arrested ESCC cells at the G2/M and S phases, as shown by flow cytometry. Colony formation and CCK8 assays showed that CUR can inhibit the proliferative ability of ESCC cells. The Transwell invasion results validated that CUR can significantly inhibit the invasion rates of ESCC cells.

Conclusion: Collectively, these findings indicate that CUR exhibits pharmacological effects on multiple targets and pathways in ESCC.
12-mJ 1-kHz cryogenically cooled rod Yb:YAG regenerative amplifier
Authors: Zhang Guangyin , Li Ruixuan , Li Kui , Li Jie , Bai Zhenao , Fan Zhongwei
Published: April 2024

We report on a continuous-wave (CW) pumped cryogenically cooled rod Yb:YAG regenerative amplifier delivering uncompressed 12-mJ, 90-ps, 1030-nm pulses at a 1-kHz repetition rate. The amplifier demonstrates an efficiency of 31.7%. A symmetric cavity design was utilized to compensate for the substantial thermal lensing effect, yielding a final measured beam quality of 1.1 in both horizontal and vertical directions. After significant gain narrowing, the measured spectra exhibit a bandwidth of 0.3 nm corresponding to an approximately 5 ps transform-limited pulse.
Phenological response of European beech (Fagus sylvatica L.) to climate change in the Western Carpathian climatic-geographical zones
Authors: Skvareninova Jana , Sitko Roman , Vido Jaroslav , Snopková Zora , Skvarenina Jaroslav
Published: April 2024

Introduction

The paper analyzes the results of 26 years (1996–2021) of phenological observations of the vegetative organs of European beech (Fagus sylvatica L.) in the Western Carpathians. It evaluates the influence of the heterogeneity of this territory, including relief and elevation, based on climatic-geographical types.

Methods

Phenological stages, including leaf unfolding, full leaves, leaf coloring, and leaf fall, were monitored at 40 phenological stations across eight elevation zones. The study assesses trends in the occurrence of phenological stages, the length of the growing season, and phenological elevation gradients.

Results

The results indicate a statistically significant earlier onset of spring phenological phases and delay in autumn phases, resulting in an average extension of the beech growing season by 12 days. Our findings confirm that the lengthening of the growing season due to warming, as an expression of climate change, is predominantly attributed to the warming in the spring months. The detected delayed onset of autumn phenophases was not due to warming in the autumn months, but other environmental factors influence it. The trend of elongation of the growing season (p<0.01) is observed in all elevation zones, with a less significant trend observed only in zones around 400 and 600 m a.s.l, signaling changes in environmental conditions across most of the elevation spectrum. Moreover, the heterogeneity of climatic-geographical types within each elevation zone increases the variability in the duration of the growing season for sites with similar elevations. By extending the growing season, it is assumed that the beech area will be changed to locations with optimal environmental conditions, especially in terms of adverse climatic events (late spring frosts, drought) during the growing season. The phenological elevation gradients reveal an earlier onset of 2.2 days per 100 m for spring phenophases and a delay of 1.1–2.9 days per 100 m for autumn phenophases.

Discussion

These findings highlight the specific environmental conditions of European beech in the Western Carpathians and their potential for anticipating changes in its original area. Additionally, these observations can aid in forecasting the further development of phenological manifestations related to climate change.
Deposition of silica in sorghum root endodermis modifies the chemistry of associated lignin
Authors: Zexer Nerya , Diehn Sabrina , Elbaum Rivka
Published: April 2024

Silica aggregates at the endodermis of sorghum roots. Aggregation follows a spotted pattern of locally deposited lignin at the inner tangential cell walls. Autofluorescence microscopy suggests that non-silicified (-Si) lignin spots are composed of two distinct concentric regions of varied composition. To highlight variations in lignin chemistry, we used Raman microspectroscopy to map the endodermal cell wall and silica aggregation sites in sorghum roots grown hydroponically with or without Si amendment. In +Si samples, the aggregate center was characterized by typical lignin monomer bands surrounded by lignin with a low level of polymerization. Farther from the spot, polysaccharide concentration increased and soluble silicic acid was detected in addition to silica bands. In -Si samples, the main band at the spot center was assigned to lignin radicals and highly polymerized lignin. Both +Si and -Si loci were enriched by aromatic carbonyls. We propose that at silica aggregation sites, carbonyl rich lignin monomers are locally exported to the apoplast. These monomers are radicalized and polymerized into short lignin polymers. In the presence of silicic acid, bonds typically involved in lignin extension, bind to silanols and nucleate silica aggregates near the monomer extrusion loci. This process inhibits further polymerization of lignin. In -Si samples, the monomers diffuse farther in the wall and crosslink with cell wall polymers, forming a ring of dense lignified cell wall around their export sites.
The impact of job stress on perceived professional benefits among Chinese nurses caring for patients with gynecological cancer: mediating effects of perceived social support and self-efficacy
Authors: Zhang Yuxin , Meng Xinhai , Zhou Lihua
Published: April 2024

Introduction

Nurses caring for patients with gynecological cancer experience significant job stress, which adversely impacts their mental health. Previous studies have indicated that perceived professional benefits serves as a protective factor for nurses’ mental health, and factors such as job stress, perceived social support and self-efficacy influence their perceived professional benefits. However, the relationships between these factors and the associated mechanisms have remained incompletely understood. This study explored the role of perceived social support and self-efficacy in job stress and perceived professional benefits among nurses caring for patients with gynecological cancer.

Methods

During June and July 2023, an investigation was conducted in Anhui Province. The Nurse Job Stressors Scale, Perceived Social Support Scale, Nurses’ Perceived Professional Benefits Questionnaire and General Self-Efficacy Scale were administered to 311 nurses caring for patients with gynecological cancer. A chained-mediated effect model was constructed and validated.

Results

Job stress negatively affected nurses’ perceived professional benefits. Perceived social support was a mediator in job stress and nurses’ perceived professional benefits, with a mediating effect value of −0.093. Additionally, perceived social support and self-efficacy functioned as sequential mediators in this relationship, with a mediating effect value of −0.032.

Conclusion

This study unveils the influencing mechanisms of job stress on perceived professional benefits of nurses caring for patients with gynecological cancer. It is essential for nursing managers to alleviate nurses’ job stress, provide sufficient and effective social support and improve their self-efficacy, ultimately enhancing their perceived professional benefits.