bluuebunny/crossref_metadata_2025 huggingface dataset:
Hypoxia-adenosine axis as therapeutic targets for acute respiratory distress syndrome
Authors: Figarella Katherine , Kim Jieun , Ruan Wei , Mills Tingting , Eltzschig Holger Klaus , Yuan Xiaoyi
Published: January 2024

The human respiratory and circulatory systems collaborate intricately to ensure oxygen delivery to all cells, which is vital for ATP production and maintaining physiological functions and structures. During limited oxygen availability, hypoxia-inducible factors (HIFs) are stabilized and play a fundamental role in maintaining cellular processes for hypoxia adaptation. First discovered during investigations of erythropoietin production regulation, HIFs influence physiological and pathological processes, including development, inflammation, wound healing, and cancer. HIFs promote extracellular adenosine signaling by enhancing adenosine generation and receptor signaling, representing an endogenous feedback mechanism that curbs excessive inflammation, supports injury resolution, and enhances hypoxia tolerance. This is especially important for conditions that involve tissue hypoxia, such as acute respiratory distress syndrome (ARDS), which globally poses significant health challenges without specific treatment options. Consequently, pharmacological strategies to amplify HIF-mediated adenosine production and receptor signaling are of great importance.
Hybrid lineages of CD4+ T cells: a handbook update
Authors: Bensussen Antonio , Torres-Magallanes José Antonio , Álvarez-Buylla Elena R. , de Álvarez-Buylla Elena Roces
Published: January 2024

CD4+ T lymphocytes have been classified into several lineages, according to their gene expression profiles and their effector responses. Interestingly, recent evidence is showing that many lineages could yield hybrid phenotypes with unique properties and functions. It has been reported that such hybrid lineages might underlie pathologies or may function as effector cells with protection capacities against molecular threats. In this work, we reviewed the characteristics of the hybrid lineages reported in the literature, in order to identify the expression profiles that characterize them and the markers that could be used to identify them. We also review the differentiation cues that elicit their hybrid origin and what is known about their physiological roles.
Rejection sampling and agent-based models for data limited fisheries
Authors: Carrella Ernesto , Powers Joseph , Saul Steven , Bailey Richard M. , Payette Nicolas , Vert-pre Katyana A. , Ananthanarayanan Aarthi , Drexler Michael , Dorsett Chris , Madsen Jens Koed
Published: January 2024

Many of the world’s fisheries are “data-limited” where the information does not allow precise determination of fish stock status and limits the development of appropriate management responses. Two approaches are proposed for use in data-limited stock management strategy evaluations to guide the evaluations and to understand the sources of uncertainty: rejection sampling methods and the incorporation of more complex socio-economic dynamics into management evaluations using agent-based models. In rejection sampling (or rejection filtering) a model is simulated many times with a wide range of priors on parameters and outcomes are compared multiple filtering criteria. Those simulations that pass all the filters form an ensemble of feasible models. The ensemble can be used to look for robust management strategies, robust to both model uncertainties. Agent-based models of fishery economics can be implemented within the rejection framework, integrating the biological and economic understanding of the fishery. A simple artificial example of a difference equation bio-economic model is given to demonstrate the approach. Then rejection sampling is applied to an agent-based model for the hairtail (Trichiurus japonicas) fishery, where an operating model is constructed with rejection/agent-based methods and compared to known data and analyses of the fishery. The usefulness of information and rejection filters are illuminated and efficacy examined. The methods can be helpful for strategic guidance where multiple states of nature are possible as a part of management strategy evaluation.
Molecular characterization of the PhiKo endolysin from Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29
Authors: Szadkowska Monika , Kocot Aleksandra Maria , Sowik Daria , Wyrzykowski Dariusz , Jankowska Elzbieta , Kozlowski Lukasz Pawel , Makowska Joanna , Plotka Magdalena
Published: January 2024

Introduction

In the era of increasing bacterial resistance to antibiotics, new bactericidal substances are sought, and lysins derived from extremophilic organisms have the undoubted advantage of being stable under harsh environmental conditions. The PhiKo endolysin is derived from the phiKo bacteriophage infecting Gram-negative extremophilic bacterium Thermus thermophilus HB27. This enzyme shows similarity to two previously investigated thermostable type-2 amidases, the Ts2631 and Ph2119 from Thermus scotoductus bacteriophages, that revealed high lytic activity not only against thermophiles but also against Gram-negative mesophilic bacteria. Therefore, antibacterial potential of the PhiKo endolysin was investigated in the study presented here.

Methods

Enzyme activity was assessed using turbidity reduction assays (TRAs) and antibacterial tests. Differential scanning calorimetry was applied to evaluate protein stability. The Collection of Anti-Microbial Peptides (CAMP) and Antimicrobial Peptide Calculator and Predictor (APD3) were used to predict regions with antimicrobial potential in the PhiKo primary sequence. The minimum inhibitory concentration (MIC) of the RAP-29 synthetic peptide was determined against Gram-positive and Gram-negative selected strains, and mechanism of action was investigated with use of membrane potential sensitive fluorescent dye 3,3′-Dipropylthiacarbocyanine iodide (DiSC3(5)).

Results and discussion

The PhiKo endolysin is highly thermostable with melting temperature of 91.70°C. However, despite its lytic effect against such extremophiles as: T. thermophilus, Thermus flavus, Thermus parvatiensis, Thermus scotoductus, and Deinococcus radiodurans, PhiKo showed moderate antibacterial activity against mesophiles. Consequently, its protein sequence was searched for regions with potential antibacterial activity. A highly positively charged region was identified and synthetized (PhiKo105-133). The novel RAP-29 peptide lysed mesophilic strains of staphylococci and Gram-negative bacteria, reducing the number of cells by 3.7–7.1 log units and reaching the minimum inhibitory concentration values in the range of 2–31 μM. This peptide is unstructured in an aqueous solution but forms an α-helix in the presence of detergents. Moreover, it binds lipoteichoic acid and lipopolysaccharide, and causes depolarization of bacterial membranes. The RAP-29 peptide is a promising candidate for combating bacterial pathogens. The existence of this cryptic peptide testifies to a much wider panel of antimicrobial peptides than thought previously.
Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes
Authors: Mora Jonah Feliza B. , Meclat Vanessa Yvonne B. , Calayag Alyzza Marie B. , Campino Susana , Hafalla Julius C. R. , Hibberd Martin L. , Phelan Jody E. , Clark Taane G. , Rivera Windell L.
Published: January 2024

The integration of next-generation sequencing into the identification and characterization of resistant and virulent strains as well as the routine surveillance of foodborne pathogens such as Salmonella enterica have not yet been accomplished in the Philippines. This study investigated the antimicrobial profiles, virulence, and susceptibility of the 105 S. enterica isolates from swine and chicken samples obtained from slaughterhouses and public wet markets in Metropolitan Manila using whole-genome sequence analysis. Four predominant serovars were identified in genotypic serotyping, namely, Infantis (26.7%), Anatum (19.1%), Rissen (18.1%), and London (13.3%). Phenotypic antimicrobial resistance (AMR) profiling revealed that 65% of the isolates were resistant to at least one antibiotic, 37% were multidrug resistant (MDR), and 57% were extended-spectrum β-lactamase producers. Bioinformatic analysis revealed that isolates had resistance genes and plasmids belonging to the Col and Inc plasmid families that confer resistance against tetracycline (64%), sulfonamide (56%), and streptomycin (56%). Further analyses revealed the presence of 155 virulence genes, 42 of which were serovar-specific. The virulence genes primarily code for host immune system modulators, iron acquisition enzyme complexes, host cell invasion proteins, as well as proteins that allow intracellular and intramacrophage survival. This study showed that virulent MDR S. enterica and several phenotypic and genotypic AMR patterns were present in the food chain. It serves as a foundation to understand the current AMR status in the Philippines food chain and to prompt the creation of preventative measures and efficient treatments against foodborne pathogens.
Effects of water volume of drip irrigation on soil bacterial communities and its association with soil properties in jujube cultivation
Authors: Li Zhaoyang , Yang Yuhui , Liu Jiangfan , Jiang Wenge , Gao Yang
Published: January 2024

Introduction

Jujube is one of an important crop in Xinjiang, China, a area suffered by water scarcity and DI has been proven as a suitable mode for jujube cultivation. Soil bacterial community play a vital role in biogeochemical cycles to support the crop growth, and water content is considered as one of the important factors for them. However, limited research has explored the optimum irrigation strategies, such as water volume of DI, to maximize the benefits of jujube cultivation by regulating the soil bacterial communities.

Methods

Therefore, in this study, we conducted DI experiments on jujube fields in Xinjiang with three different water volume levels, and measured the soil properties and bacterial communities of the flowering and fruit setting (FFS) and end of growth (EG) stages.

Results and discussion

Significant lower jujube yield and soil available nutrients were observed in samples with low water amount. In addition, we discovered significant effects of the water amount of DI and jujube growth stages on soil bacterial communities. Based on the compare of samples among different growth stages and water amounts some growth stage related bacterial genera (Mycobacterium, Bradyrhizobium, and Bacillus) and water amount-related bacterial phyla (Chloroflexi, Nitrospirota, and Myxococcota) were recognized. Moreover, according to the results of null model, soil bacterial communities were governed by stochastic and deterministic processes under middle and low water volumes of DI, respectively. Finally, we deduced that middle water amount (600 mm) could be the optimal condition of DI for jujube cultivation because the higher jujube yield, deterministic assembly, and stronger correlations between soil properties and bacterial community under this condition. Our findings provide guidance for promoting the application of DI in jujube cultivation, and further research is needed to investigate the underlying mechanisms of soil bacterial community to promote the jujube yield.
The effect of a web-based lifestyle intervention on nutritional status and physical activity on prevention of COVID-19: a randomized controlled trial in women's empowerment
Authors: Pourfarzi Farhad , Kamran Aziz , Zare Maryam , Mohammadshahi Jafar
Published: January 2024

Background

Healthy dietary intake and physical activity affect the immune systems. The present study aimed to investigate the effects of a web-based lifestyle intervention on nutritional status, physical activity, and prevention of COVID-19.

Methods

Three hundred-three women (30–60 years old), who did not have COVID-19 in the City of Ardabil, participated in this study. Participants were randomized into an intervention (n = 152) or control group (n = 151). The intervention group received eight online educational sessions focusing on a healthy diet and physical activity via the website. There was no educational session for the control group during the intervention, but they were placed on the waiting list to receive the intervention and given access to the website and educational content after the follow-up. Outcomes were nutritional status, physical activity, immunoglobulin G (IgG), and immunoglobulin M (Ig M) antibody titers against the virus. They were evaluated at the baseline, after 4 and 12 weeks.

Results

Significant improvements in weight (P < 0.001), BMI (P < 0.001), total energy (P = 0.006), carbohydrate (P = 0.001), protein (P = 0.001), and fat (P < 0.001) were found for the intervention group compared to the control group during the study. MET-min/week for moderate physical activity increased during the time for the intervention and control groups (P < 0.001 and P = 0.007, respectively). MET-min/week for walking activity rose in the post-intervention and follow-up compared to that in the baseline in the groups (P < 0.001 for both groups). Total physical activity was increased during the study (P < 0.001) for both groups. The mean of serum IgG and IgM titers against the virus were increased during the study in both groups in time effect (P < 0.001). There was a significant time x group interaction for carbohydrate and fat intakes (P = 0.005 and P = 0.004, respectively).

Conclusion

The web-based lifestyle intervention may improve nutritional status and physical activity, and have the potential to reduce the risk of contracting a COVID-19 infection.
Case report: The first case of concurrent breast myeloid sarcoma and borderline phyllodes tumor with malignant features
Authors: Chun Li , Zeng Zhen , Guo Qianyu , He Yangjun
Published: January 2024

Background

Myeloid sarcoma (MS) is a rare hematological malignancy characterized by the formation of a solid mass of myeloblasts outside the bone marrow, such as in the lymph nodes, skin, or bone. MS may arise de novo or concurrently with acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), or myelodysplastic syndrome (MDS). MS accounts for less than 1% of extramedullary acute myeloid leukemia cases. Phyllodes tumors (PTs) are a rare fibroepithelial breast tumor that can be benign, malignant, or borderline, and account for less than 1% of all breast cancers.

Case presentation

We present a unique case of a 50-year-old woman with both breast MS and borderline PT with malignant features, which presented a diagnostic challenge. The patient initially presented with a mass in her right breast, and the initial fine-needle biopsy revealed the presence of immature myeloperoxidase (MPO)+ myeloid cells consistent with MS. Subsequent pathological analysis of tumor tissues after neoadjuvant radiotherapy and chemotherapy showed a borderline PT with malignant features. Following excision of the tumor, the patient experienced a local recurrence, which was also surgically removed. At 8 months post-surgery, the patient remains free of recurrence under close follow-up.

Conclusion

This case highlights the importance of considering the possibility of concurrent malignancies in the differential diagnosis of complex breast masses and underscores the challenges involved in diagnosing and managing such cases. Additionally, we also emphasize the value of neoadjuvant radiotherapy and chemotherapy in MS.
Primary central nervous system post-transplant lymphoproliferative disorder after allogeneic stem cell transplantation: a case report
Authors: Tugend Margaret , Dattero Jordan , Shore Tsiporah , Korobeynikov Vladislav , Sekula Raymond F.
Published: January 2024

Purpose

Primary central nervous system, diffuse large B-cell lymphoma, post-transplant lymphoproliferative disorder in the cerebellopontine angle after an allogeneic stem cell transplantation has never been reported in the literature. Typically, diffuse large B-cell lymphoma is non-polyploid. We report the first case of a patient with polyploid post-transplant lymphoproliferative disorder in the cerebellopontine angle who presented with back pain.

Case presentation

A 45-year-old man with a history of nodular sclerosing classic Hodgkin lymphoma stage IIB treated with systemic chemotherapy, external radiation and autologous stem cell transplant and double umbilical cord allogeneic transplant presented with several weeks of back pain. He was found to have a small right cerebellopontine angle mass thought to be consistent with a meningioma. Patient presented again two weeks later with acute onset of severe headache, right sided ptosis, right facial numbness, weakness and possible seizure event. Repeat MRI scans showed an interval and significant increase of the right cerebellopontine angle lesion. Biopsy of the cerebellopontine angle lesion was planned with suspicion of lymphoma. Intraoperative pathology consultation findings were not consistent with an acoustic neuroma, meningioma, or epidermoid cyst. Lymphoma could not be definitively identified by intra-operative frozen section. However, it was suspected, and a portion of fresh specimen was submitted for flow cytometry analysis. A near total resection of the tumor and decompression of the brainstem was achieved. Final pathologic analysis was positive for post-transplant lymphoproliferative disorder, monomorphic type, diffuse large B-cell lymphoma, non-germinal center B-cell type, EBV+, post-transplant (allogeneic stem cell) setting (post-transplant lymphoproliferative disorder (PTLD), monomorphic type, diffuse large B-cell lymphoma, non-germinal center B-cell type (non-GCB), EBV-positive under pre-2022 WHO terminology). The patient began a high-dose methotrexate-based regimen (the MATRIX regimen).

Conclusions

Our case illustrates an unusual presentation of post-transplant lymphoproliferative disorder in the cerebellopontine angle in a patient with a remote history of allogeneic stem cell transplantation. It demonstrates the importance of keeping primary central nervous system post-transplant lymphoproliferative disorder on the differential for patients who present with back pain or headache that have a history of allogeneic stem cell transplant.
Non-invasive detection of lymphoma with circulating tumor DNA features and protein tumor markers
Authors: Chang Yu , Li Shiyong , Li Zhiming , Wang Xinhua , Chang Fangyuan , Geng Shuaipeng , Zhu Dandan , Zhong Guolin , Wu Wei , Chang Yinyin , Tu Shichun , Mao Mao
Published: January 2024

Background

According to GLOBOCAN 2020, lymphoma ranked as the 9th most common cancer and the 12th leading cause of cancer-related deaths worldwide. Traditional diagnostic methods rely on the invasive excisional lymph node biopsy, which is an invasive approach with some limitations. Most lymphoma patients are diagnosed at an advanced stage since they are asymptomatic at the beginning, which has significantly impacted treatment efficacy and prognosis of the disease.

Method

This study assessed the performance and utility of a newly developed blood-based assay (SeekInCare) for lymphoma early detection. SeekInCare utilized protein tumor markers and a comprehensive set of cancer-associated genomic features, including copy number aberration (CNA), fragment size (FS), end motif, and lymphoma-related virus, which were profiled by shallow WGS of cfDNA.

Results

Protein marker CA125 could be used for lymphoma detection independent of gender, and the sensitivity was 27.8% at specificity of 98.0%. After integrating these multi-dimensional features, 77.8% sensitivity was achieved at specificity of 98.0%, while its NPV and PPV were both more than 92% for lymphoma detection. The sensitivity of early-stage (I-II) lymphoma was up to 51.3% (47.4% and 55.0% for stage I and II respectively). After 2 cycles of treatment, the molecular response of SeekInCare was correlated with the clinical outcome.

Conclusion

In summary, a blood-based assay can be an alternative to detect lymphoma with adequate performance. This approach becomes particularly valuable in cases where obtaining tissue biopsy is difficult to obtain or inconclusive.
Inflammatory biomarkers and physiomarkers of late-onset sepsis and necrotizing enterocolitis in premature infants
Authors: Kumar Rupin , Kausch Sherry L. , Gummadi Angela K. S. , Fairchild Karen D. , Abhyankar Mayuresh M. , Petri William A. , Sullivan Brynne A.
Published: January 2024

Background

Early diagnosis of late-onset sepsis (LOS) and necrotizing enterocolitis (NEC) in very low birth weight (VLBW, <1,500 g) infants is challenging due to non-specific clinical signs. Inflammatory biomarkers increase in response to infection, but non-infectious conditions also cause inflammation. Cardiorespiratory data contain physiological biomarkers, or physiomarkers, of sepsis that may be useful in combination with inflammatory hematologic biomarkers for sepsis diagnosis.

Objectives

To determine whether inflammatory biomarkers measured at the time of LOS or NEC diagnosis differ from times without infection and whether biomarkers correlate with cardiorespiratory sepsis physiomarkers in VLBW infants.

Methods

Remnant plasma sample collection from VLBW infants occurred with blood draws for routine laboratory testing and suspected sepsis. We analyzed 11 inflammatory biomarkers and a pulse oximetry sepsis warning score (POWS). We compared biomarker levels obtained at the time of gram-negative (GN) bacteremia or NEC, gram-positive (GP) bacteremia, negative blood cultures, and no suspected infection.

Results

We analyzed 188 samples in 54 VLBW infants. Several biomarkers were increased at the time of GN LOS or NEC diagnosis compared with all other samples. POWS was higher in patients with LOS and correlated with five biomarkers. IL-6 had 78% specificity at 100% sensitivity to detect GN LOS or NEC and added information to POWS.

Conclusion(s)

Inflammatory plasma biomarkers discriminate sepsis due to GN bacteremia or NEC and correlate with cardiorespiratory physiomarkers.
Prediction of hyperuricemia in people taking low-dose aspirin using a machine learning algorithm: a cross-sectional study of the National Health and Nutrition Examination Survey
Authors: Zhu Bin , Yang Li , Wu Mingfen , Wu Qiao , Liu Kejia , Li Yansheng , Guo Wei , Zhao Zhigang
Published: January 2024

Background: Hyperuricemia is a serious health problem related to not only gout but also cardiovascular diseases (CVDs). Low-dose aspirin was reported to inhibit uric acid excretion, which leads to hyperuricemia. To decrease hyperuricemia-related CVD, this study aimed to identify the risk of hyperuricemia in people taking aspirin.

Method: The original data of this cross-sectional study were obtained from the National Health and Nutrition Examination Survey between 2011 and 2018. Participants who filled in the “Preventive Aspirin Use” questionnaire with a positive answer were included in the analysis. Six machine learning algorithms were screened, and eXtreme Gradient Boosting (XGBoost) was employed to establish a model to predict the risk of hyperuricemia.

Results: A total of 805 participants were enrolled in the final analysis, of which 190 participants had hyperuricemia. The participants were divided into a training set and testing set at a ratio of 8:2. The area under the curve for the training set was 0.864 and for the testing set was 0.811. The SHapley Additive exPlanations (SHAP) method was used to evaluate the performances of the modeling. Based on the SHAP results, the feature ranking interpretation showed that the estimated glomerular filtration rate, body mass index, and waist circumference were the three most important features for hyperuricemia in individuals taking aspirin. In addition, triglyceride, hypertension, total cholesterol, high-density lipoprotein, low-density lipoprotein, age, race, and smoking were also correlated with the development of hyperuricemia.

Conclusion: A predictive model established by XGBoost algorithms can potentially help clinicians make an early detection of hyperuricemia risk in people taking low-dose aspirin.
Denosumab, teriparatide and bisphosphonates for glucocorticoid-induced osteoporosis: a Bayesian network meta-analysis
Authors: Dong Liang , Jiang Lianghai , Xu Zhengwei , Zhang Xiaobo
Published: January 2024

Background: Several medications have been used for glucocorticoids-induced osteoporosis (GIO). However, the best therapeutic option for GIO is still controversial. A Bayesian network meta-analysis was conducted to compare the efficacy and safety of denosumab, teriparatide and bisphosphonates for patients with GIO.

Methods: Relevant randomized controlled trials published in PubMed, Embase, Cochrane Library and ClinicalTrials.gov up to August 2023 were searched. The following efficiency and safety outcomes were extracted for comparison: bone mineral density (BMD) percentage changes in lumbar spine, femur neck and total hip, and incidences of adverse events (AEs), serious adverse events (SAEs), vertebrae and non-vertebrae fracture. Bayesian random effects models were used for multiple treatment comparisons.

Results: 11 eligible RCTs involving 2,877 patients were identified. All the six medications including alendronate, risedronate, etidronate, zoledronate, teriparatide, and denosumab and were effective in increasing BMD. Teriparatide and denosumab were more effective in improving lumbar spine and femur neck BMD, and reducing vertebrae fracture. Alendronate and denosumab were more effective in improving total hip BMD. Alendronate and teriparatide had the lowest incidences of AEs and SAEs.

Conclusion: Teriparatide denosumab and the bisphosphonates are all effective in improving BMD for GIO patients. Based on this network meta-analysis, teriparatide and denosumab have higher efficiency in improving lumbar spine and femur neck BMD, and reducing vertebrae fracture.

Systematic Review Registration:10.17605/OSF.IO/2G8YA, identifier CRD42023456305.
Deep saliency detection-based pedestrian detection with multispectral multi-scale features fusion network
Authors: Ma Li , Wang Jinjin , Dai Xinguan , Gao Hangbiao
Published: January 2024

In recent years, there has been increased interest in multispectral pedestrian detection using visible and infrared image pairs. This is due to the complementary visual information provided by these modalities, which enhances the robustness and reliability of pedestrian detection systems. However, current research in multispectral pedestrian detection faces the challenge of effectively integrating different modalities to reduce miss rates in the system. This article presents an improved method for multispectral pedestrian detection. The method utilises a saliency detection technique to modify the infrared image and obtain an infrared-enhanced map with clear pedestrian features. Subsequently, a multiscale image features fusion network is designed to efficiently fuse visible and IR-enhanced maps. Finally, the fusion network is supervised by three loss functions for illumination perception, light intensity, and texture information in conjunction with the light perception sub-network. The experimental results demonstrate that the proposed method improves the logarithmic mean miss rate for the three main subgroups (all day, day and night) to 3.12%, 3.06%, and 4.13% respectively, at “reasonable” settings. This is an improvement over the traditional method, which achieved rates of 3.11%, 2.77%, and 2.56% respectively, thus demonstrating the effectiveness of the proposed method.
Evaluation of TIEGCM based on GOCE neutral density
Authors: Li Zheng , Shao Jingjing , Wang Yan , Li Jingyuan , Zhang Hua , Gu Chunli , Xu Xiaojun
Published: January 2024

The Thermosphere Ionosphere Electrodynamic General Circulation Model (TIEGCM), as one of the most advanced physical models of the Earth’s thermosphere and ionosphere, is not only widely used in scientific research, but also has essential reference value in aerospace operations. In this study, we use Gravity field and steady-state Ocean Circulation Explorer (GOCE) neutral density to evaluate the accuracy of the TIEGCM. The assessment is performed on both time and spatial scales. The time scales are conducted annually, monthly, and daily, while the spatial scales are carried out in terms of altitude, latitude, and local time. On the time scales, the performance of the TIEGCM on the monthly time scale is better than that on the annual time scale. Also, the performance on the daily time scale is better than that on the monthly time scale. The relative deviation shows a significant seasonal variation, that is, larger in winter and summer and smaller in spring and autumn. In addition, the relative deviation shows a negative correlation with F10.7 and Ap. On the spatial scale, with the increase in altitude, the average relative deviation of the model becomes larger in general. The relative deviation is usually larger at middle latitudes in the Northern Hemisphere and high latitudes in the Southern Hemisphere. Finally, on the scale of local time, the relative deviation changes more dramatically in local morning than at dusk.
Microscopic theory of current-induced skyrmion transport and its application in disordered spin textures
Authors: Östberg Emil , Viñas Boström Emil , Verdozzi Claudio
Published: January 2024

Introduction: Magnetic skyrmions hold great promise for realizing compact and stable memory devices that can be manipulated at very low energy costs via electronic current densities.

Methods: In this work, we extend a recently introduced method to describe classical skyrmion textures coupled to dynamical itinerant electrons. In this scheme, the electron dynamics is described via nonequilibrium Green’s function (NEGF) within the generalized Kadanoff–Baym ansatz, and the classical spins are treated via the Landau–Lifshitz–Gilbert equation. Here, the framework is extended to open systems by the introduction of a non-interacting approximation to the collision integral of NEGFs. This, in turn, allows us to perform computations of the real-time response of skyrmions to electronic currents in large quantum systems coupled to electronic reservoirs, which exhibit linear scaling in the number of time steps. We use this approach to investigate how electronic spin currents and dilute spin disorder affect skyrmion transport and the skyrmion Hall drift.

Results: Our results show that the skyrmion dynamics is sensitive to a specific form of the spin disorder, such that different disorder configurations lead to qualitatively different skyrmion trajectories for the same applied bias.

Discussion: This sensitivity arises from the local spin dynamics around the magnetic impurities, a feature that is expected not to be well-captured by phenomenological or spin-only descriptions. At the same time, our findings illustrate the potential of engineering microscopic impurity patterns to steer skyrmion trajectories.
Advances in metabolic reprogramming of renal tubular epithelial cells in sepsis-associated acute kidney injury
Authors: Wang Tiantian , Huang Ying , Zhang Xiaobei , Zhang Yi , Zhang Xiangcheng
Published: January 2024

Sepsis-associated acute kidney injury presents as a critical condition characterized by prolonged hospital stays, elevated mortality rates, and an increased likelihood of transition to chronic kidney disease. Sepsis-associated acute kidney injury suppresses fatty acid oxidation and oxidative phosphorylation in the mitochondria of renal tubular epithelial cells, thus favoring a metabolic shift towards glycolysis for energy production. This shift acts as a protective mechanism for the kidneys. However, an extended reliance on glycolysis may contribute to tubular atrophy, fibrosis, and subsequent chronic kidney disease progression. Metabolic reprogramming interventions have emerged as prospective strategies to counteract sepsis-associated acute kidney injury by restoring normal metabolic function, offering potential therapeutic and preventive modalities. This review delves into the metabolic alterations of tubular epithelial cells associated with sepsis-associated acute kidney injury, stressing the importance of metabolic reprogramming for the immune response and the urgency of metabolic normalization. We present various intervention targets that could facilitate the recovery of oxidative phosphorylation-centric metabolism. These novel insights and strategies aim to transform the clinical prevention and treatment landscape of sepsis-associated acute kidney injury, with a focus on metabolic mechanisms. This investigation could provide valuable insights for clinicians aiming to enhance patient outcomes in the context of sepsis-associated acute kidney injury.
Bone resorption by osteoclasts involves fine tuning of RHOA activity by its microtubule-associated exchange factor GEF-H1
Authors: Morel Anne , Douat Christophe , Blangy Anne , Vives Virginie
Published: January 2024

Bone health is controlled by the balance between bone formation by osteoblasts and degradation by osteoclasts. A disequilibrium in favor of bone resorption leads to osteolytic diseases characterized by decreased bone density. Osteoclastic resorption is dependent on the assembly of an adhesion structure: the actin ring, also called podosome belt or sealing zone, which is composed of a unique patterning of podosomes stabilized by microtubules. A better understanding of the molecular mechanisms regulating the crosstalk between actin cytoskeleton and microtubules network is key to find new treatments to inhibit bone resorption. Evidence points to the importance of the fine tuning of the activity of the small GTPase RHOA for the formation and maintenance of the actin ring, but the underlying mechanism is not known. We report here that actin ring disorganization upon microtubule depolymerization is mediated by the activation of the RHOA-ROCK signaling pathway. We next show the involvement of GEF-H1, one of RHOA guanine exchange factor highly expressed in osteoclasts, which has the particularity of being negatively regulated by sequestration on microtubules. Using a CRISPR/Cas9-mediated GEF-H1 knock-down osteoclast model, we demonstrate that RHOA activation upon microtubule depolymerization is mediated by GEF-H1 release. Interestingly, although lower levels of GEF-H1 did not impact sealing zone formation in the presence of an intact microtubule network, sealing zone was smaller leading to impaired resorption. Altogether, these results suggest that a fine tuning of GEF-H1 through its association with microtubules, and consequently of RHOA activity, is essential for osteoclast sealing zone stability and resorption function.
PeHVA22 gene family in passion fruit (Passiflora edulis): initial characterization and expression profiling diversity
Authors: Hou Zhimin , Liang Jianxiang , Cai Xinkai , Lin Jingting , Wang Xiaomei , Liu Ruoyu , Lu Lin , Chai Gaifeng , An Chang , Chen Shengzhen , Qin Yuan , Zheng Ping
Published: January 2024

Passion fruit, an economically valuable fruit crop, is highly vulnerable to adverse climate conditions. The HVA22 genes, recognized as abscisic acid (ABA) and stress-inducible, play vital roles in stress response and growth regulation in diverse eukaryotic organisms. Here, six HVA22 genes were firstly identified in passion fruit genome and all predicted to be localized within the endoplasmic reticulum. Phylogenetic analyses showed that all PeHVA22s were divided into four subgroups. The gene structural features of PeHVA22 genes clustered in the same subgroup were relatively conserved, while the gene structure characteristics of PeHVA22s from different subgroups varied significantly. PeHVA22A and PeHVA22C closely clustered with barley HVA22 in Group II, were also induced by ABA and drought stress treatment, suggesting conserved roles similar to barley HVA22. Meanwhile, most PeHVA22s exhibited induced expression post-drought treatment but were suppressed under salt, low and high-temperature conditions, indicating a unique role in drought response. Additionally, PeHVA22s displayed tissue-specific expression patterns across diverse tissues, except for PeHVA22B which maybe a pseudogene. Notably, PeHVA22C, PeHVA22E, and PeHVA22F predominantly expressed in fruit, indicating their involvement in fruit development. Almost all PeHVA22s showed variable expression at different developmental stages of stamens or ovules, implying their roles in passion fruit’s sexual reproduction. The intricate roles of PeHVA22s may result from diverse regulatory factors including transcription factors and CREs related to plant growth and development, hormone and stress responsiveness. These observations highlighted that PeHVA22s might play conserved roles in ABA response and drought stress tolerance, and also be participated in the regulation of passion fruit growth and floral development.
Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
Authors: Shi Tian-Le , Ma Hai-Yao , Wang Xinrui , Liu Hui , Yan Xue-Mei , Tian Xue-Chan , Li Zhi-Chao , Bao Yu-Tao , Chen Zhao-Yang , Zhao Shi-Wei , Xiang Qiuhong , Jia Kai-Hua , Nie Shuai , Guan Wenbin , Mao Jian-Feng
Published: January 2024

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
Exploring the xylem-sap to unravel biological features of Xylella fastidiosa subspecies pauca ST53 in immune, resistant and susceptible crop species through metabolomics and in vitro studies
Authors: Surano Antony , del Grosso Carmine , Musio Biagia , Todisco Stefano , Giampetruzzi Annalisa , Altamura Giuseppe , Saponari Maria , Gallo Vito , Mastrorilli Piero , Boscia Donato , Saldarelli Pasquale
Published: January 2024

Xylella fastidiosa subsp. pauca ST53 (Xfp) is a pathogenic bacterium causing one of the most severe plant diseases currently threatening the olive-growing areas of the Mediterranean, the Olive Quick Decline Syndrome (OQDS). The majority of the olive cultivars upon infections more or less rapidly develop severe desiccation phenomena, while few are resistant (e.g. Leccino and FS17), being less impacted by the infections. The present study contributes to elucidating the basis of the resistance phenomenon by investigating the influence of the composition of the xylem sap of plant species on the rate of bacterial multiplication. Xylem saps from Xfp host and non-host species were used for growing the bacterium in vitro, monitoring bacterial growth, biofilm formation, and the expression of specific genes. Moreover, species-specific metabolites, such as mannitol, quinic acid, tartaric acid, and choline were identified by non-targeted NMR-based metabolomic analysis in olive, grapevine, and citrus. In general, the xylem saps of immune species, including grapevine and citrus, were richer in amino acids, organic acids, and glucose. The results showed greater bacterial growth in the olive cultivar notoriously susceptible to Xfp (Cellina di Nardò), compared to that recorded in the resistant cultivar Leccino. Conversely, higher biofilm formation occurred in Leccino compared to Cellina di Nardò. Using the xylem saps of two Xfp-immune species (citrus and grapevine), a divergent bacterial behavior was recorded: low planktonic growth and biofilm production were detected in citrus compared to the grapevine. A parallel evaluation of the expression of 15 genes showed that Xfp directs its molecular functions mainly to virulence. Overall, the results gained through this multidisciplinary study contribute to extending the knowledge on the host-pathogen interaction, while confirming that the host response and resistance mechanism have a multifactorial basis, most likely with a cumulative effect on the phenotype.
Straw and phosphorus applications promote maize (Zea mays L.) growth in saline soil through changing soil carbon and phosphorus fractions
Authors: Guo Zhenxin , Ye Wenhua , Wang Hui , He Wei , Tian Yanling , Hu Guoqing , Lou Yanhong , Pan Hong , Yang Quangang , Zhuge Yuping
Published: January 2024

Introduction

Straw return has been widely recognized as an important carbon (C) enhancement measure in agroecosystems, but the C-phosphorus (P) interactions and their effects on plants in saline soils are still unclear.

Methods

In this study, we investigated the effects of straw return and three P application levels, no P fertilizer (Non-P), a conventional application rate of P fertilizer (CP), and a high application rate of P fertilizer (HP), on maize growth and soil C and P fractions through a pot experiment.

Results and discussion

The results revealed that the dry matter weight of maize plant was no difference between the two straw return levels and was 15.36% higher under HP treatments than under Non-P treatments. Plant nutrient accumulations were enhanced by straw addition and increased with increasing P application rate. Straw application reduced the activities of peroxidase (POD), superoxide dismutase (SOD), catalase, and the content of malondialdehyde (MDA) in maize plants by 31.69%, 38.99%, 45.96% and 27.04%, respectively. P application decreased SOD, POD activities and MDA content in the absence of straw. The contents of easily oxidized organic carbon (EOC), particulate organic carbon (POC) and the ratio of POC/SOC in straw-added soils were 10.23%, 17.00% and 7.27% higher, respectively, than those in straw-absent soils. Compared with Non-P treatments, HP treatments led to an increase of 12.05%, 23.04% in EOC, POC contents respectively, while a decrease of 18.12% in the contribution of MAOC to the SOC pool. Straw return improved the P status of the saline soil by increasing soil available P (14.80%), organic P (35.91%) and Ca2-P contents (4.68%). The structural equation model showed that straw and P applications could promote maize growth (indicated by dry matter weight, P accumulation, antioxidant enzyme activity and MDA content) through improving soil C and P availabilities.

Conclusion

This study provides evidence that straw return together with adequate P supply in saline soil can promote crop nutrient accumulation, attenuate the oxidation damage on crop growth, and be beneficial for SOC turnover and soil P activation.
Does stereotype threat influence age-related differences on directed forgetting tasks?
Authors: Chien Jessie Chih-Yuan , Eich Teal S.
Published: January 2024

Objectives

The Directed Forgetting paradigm has proven to be a powerful tool to explore motivated forgetting in the lab. Past work has shown that older adults are less able to intentionally suppress information from memory relative to younger adults, which is often attributed to deficits in inhibitory abilities. Instructions in traditional Directed Forgetting tasks contain terms that may elicit stereotype threat in older adults, which may negatively impact memory. Here, we tested whether the instructions in a Directed Forgetting task affected older adults’ ability to appropriately control the contents of memory.

Methods

In two experiments that differed in the number of words presented (30 vs. 48 items), younger and older adults were randomized into one of four crossed Conditions of a Directed Forgetting task. At encoding, participants were either instructed to remember/ forget items, or to think about/not think about items. At test, they were either asked whether the memory probe was old or new, or whether they had seen it before (yes/no). Each experiment contained data from 100 younger (18– 40 years) and 98 older (60+ years) adults, with ~25 participants per Condition. All participants were recruited from Prolific and tested online.

Results

In neither Experiment 1 nor Experiment 2 did we find evidence of a stereotype threat effect, or age-related effects of directed forgetting. We did find that performance for to-be-forgotten items was worse in conditions with encoding instructions that contained words that might trigger stereotype threat relative to conditions that did not contain such words: when explicitly told to forget items, both older and younger adults forgot more items than did participants who were cued to not think about the words and put them out of mind. However, we found no such difference across the two different remember instructions: regardless of whether participants were told to remember or to think about items, recognition memory for to be retained items was high. The pattern of results across the two experiments was similar, except, not surprisingly, participants performed worse in Experiment 2 than Experiment 1. Interestingly, we found that higher accuracy for to be remembered items was associated with a more positive outlook of one’s own memory relative to others.

Discussion

These results suggest that directed forgetting may not always be impaired in older adults.
Self-perception and perceived parental perception in adolescent girls with anorexia nervosa
Authors: Sokolov Mariana , Levy-Schiff Rachel , Enoch-Levy Adi , Stein Daniel
Published: January 2024

Negative self-perception is associated with poor outcomes in adults with anorexia nervosa (AN). Our study aimed to assess the association between the self-perception of female adolescents with AN and how these adolescents perceive the attitudes of their parents toward them on the severity and short-term outcome of their illness. For this purpose, we assessed 30 adolescent girls hospitalized with AN and 30 female controls. Self-perception and perceived parental attitudes were assessed using the Structural Analysis of Social Behavior (SASB), according to which self-perception is formed via close relations with significant others in early life. Patients with AN responded to the SASB and to questionnaires assessing eating disorder (ED) symptomatology and emotional distress at both admission and discharge. Controls were similarly assessed once. We found that patients with AN showed a more negative self-perception than controls. Negative self-perception was associated with negative perceptions of the mothers’ attitudes toward the girls. There was no between-group difference in the perceived perception of the fathers’ attitude to the girls. Self-perception and perceived parental attitudes were associated with the severity of ED symptoms and emotional distress. Finally, an improvement was found in self-perception and perceived maternal attitudes toward the girl from admission to discharge, alongside a decrease in the severity of ED symptoms and emotional distress. Self-perception at admission was associated with ED pathology and emotional distress at discharge. These findings suggest that self-perception and perceived parental attitudes toward the adolescent with AN may be associated with the severity of the illness and its short-term outcome.