bluuebunny/crossref_metadata_2025 huggingface dataset:
Gasdermin E-mediated keratinocyte pyroptosis participates in the pathogenesis of psoriasis by promoting skin inflammation
Authors: Li Yingfei , He Yi , Yang Fangyuan , Liang Rongmei , Xu Wenchao , Li Yehao , Cheng Jingbo , Liang Baozhu , Tang Ming , Shi Xingliang , Zhuang Jian , Luo Minshuang , Li Liuying , Zhang Ruilin , Liu Huijuan , Jie Hongyu , Li Xing , Han Xinai , Sun Erwei , Zhai Zeqing
Published: April 2024

Background

Psoriasis is a common chronic inflammatory disease with an unclear aetiology. Keratinocytes in psoriasis are susceptible to exogenous triggers that induce inflammatory cell death.

Objectives

To investigate whether gasdermin E (GSDME)-mediated pyroptosis in keratinocytes contributes to the pathogenesis of psoriasis.

Methods

Skin samples from patients with psoriasis and from healthy controls were collected to evaluate the expression of GSDME, cleaved caspase-3 and inflammatory factors. We then analysed the data series GSE41662 to further compare the expression of GSDME between lesional and nonlesional skin samples in those with psoriasis. In vivo, a caspase-3 inhibitor and GSDME-deficient mice (Gsdme–/–) were used to block caspase-3/GSDME activation in an imiquimod-induced psoriasis model. Skin inflammation, disease severity and pyroptosis-related proteins were analysed. In vitro, tumour necrosis factor (TNF)-α-induced caspase-3/GSDME-mediated pyroptosis in the HACAT cell line was explored.

Results

Our analysis of the GSE41662 data series found that GSDME was upregulated in psoriasis lesions vs. normal skin. High levels of inflammatory cytokines such as interleukin (IL)-1β, IL-6 and TNF-α were also found in psoriasis lesions. In mice in the Gsdme–/– and caspase-3 inhibitor groups, the severity of skin inflammation was attenuated and GSDME and cleaved caspase-3 levels decreased after imiquimod treatment. Similarly, IL-1β, IL-6 and TNF-α expression was decreased in the Gsdme–/– and caspase-3 inhibitor groups. In vitro, TNF-α induced HACAT cell pyroptosis through caspase-3/GSDME pathway activation, which was suppressed by blocking caspase-3 or silencing Gsdme.

Conclusions

Our study provides a novel explanation of TNF-α/caspase-3/GSDME-mediated keratinocyte pyroptosis in the initiation and ­acceleration of skin inflammation and the progression of psoriasis.
Laparoscopic liver resection versus radiofrequency ablation for small hepatocellular carcinoma: randomized clinical trial
Authors: Song Juxian , Cao Li , Ma Kuansheng , Li Jianwei , Wang Xiaojun , Chen Jian , Zheng Shuguo
Published: April 2024

Background

The aim of this study was to compare the efficacy of laparoscopic liver resection versus radiofrequency ablation for treatment of small hepatocellular carcinoma.

Methods

This single-centre RCT was conducted at a tertiary referral centre in China. Patients with small hepatocellular carcinoma who had a single nodule no larger than 5 cm, or up to three nodules of 3 cm or smaller, were eligible. Patients were assigned randomly in a 1 : 1 ratio to either laparoscopic liver resection or radiofrequency ablation. Blinding was not attempted. Sample size calculations led to 75 patients per group. The primary outcome was overall survival, and the secondary outcome was recurrence-free survival.

Results

Seventy-five patients were included in each group. Overall survival (HR 1.26, 95% c.i. 0.69 to 2.30; P = 0.451) and recurrence-free survival (HR 1.34, 0.86 to 2.08; P = 0.189) did not differ between the resection and ablation groups. The 1-, 3- and 5-year overall survival rates were 94.7, 80.0, and 74.7% respectively after laparoscopic liver resection versus 93.3, 78.7, and 67.9% after radiofrequency ablation. Corresponding recurrence-free survival rates were 78.7, 61.3, and 51.6%, and 69.3, 53.3, and 41.0%, respectively.

Conclusion

For small hepatocellular carcinoma, percutaneous radiofrequency ablation provides therapeutic effects similar to those of laparoscopic liver resection.

Registration number

NCT02243384 (http://www.clinicaltrials.gov).
IL-22, a vital cytokine in autoimmune diseases
Authors: Li Jiajin , Wu Zhen , Wu Yuxin , Hu XinYu , Yang Jun , Zhu Dacheng , Wu Mingyue , Li Xin , Bentum-Ennin Lutterodt , Wanglai Hu
Published: April 2024

Interleukin-22 (IL-22) is a vital cytokine that is dysregulated in various autoimmune conditions including rheumatoid arthritis (RA), multiple sclerosis (MS), and Alzheimer’s disease (AD). As the starting point for the activation of numerous signaling pathways, IL-22 plays an important role in the initiation and development of autoimmune diseases. Specifically, imbalances in IL-22 signaling can interfere with other signaling pathways, causing cross-regulation of target genes which ultimately leads to the development of immune disorders. This review delineates the various connections between the IL-22 signaling pathway and autoimmune disease, focusing on the latest understanding of the cellular sources of IL-22 and its effects on various cell types. We further explore progress with pharmacological interventions related to targeting IL-22, describing how such therapeutic strategies promise to usher in a new era in the treatment of autoimmune disease.
Genomic testing identifies monogenic causes in patients with very early-onset inflammatory bowel disease: a multicenter survey in an Iranian cohort
Authors: Eslamian Golnaz , Jamee Mahnaz , Momen Tooba , Rohani Pejman , Ebrahimi Sarehossadat , Mesdaghi Mehrnaz , Ghadimi Soodeh , Mansouri Mahboubeh , Mahdaviani Seyed Alireza , Sadeghi-shabestari Mahnaz , Fallahpour Morteza , Shamsian Bibi Shahin , Eslami Narges , Sharafian Samin , Dara Naghi , Nasri Peiman , Amini Niloufar , Enayat Javad , Fallahi Mazdak , Ghasemi Hashtrodi Leila , Shojaei Mohammad , Guevara Becerra Martha , Uhlig Holm H , Chavoshzadeh Zahra
Published: April 2024

Patients with very early-onset inflammatory bowel disease (VEO-IBD) may present because of underlying monogenic inborn errors of immunity (IEI). Strong differences have been observed in the causes of monogenic IBD among ethnic populations. This multicenter study was carried out on 16 Iranian patients with VEO-IBD. We reviewed clinical and basic immunologic evaluation including flow cytometry and immunoglobulin levels. All patients underwent clinical whole exome sequencing (WES). Sixteen patients (8 females and 8 males) with a median age of 43.5 months were enrolled. The median age at the onset of symptoms was 4 months. Most patients (12, 75%) had consanguineous parents. Chronic non-bloody diarrhea (13, 81.3%) and perianal diseases including perianal abscess (6, 37.5%), anal fissure (6, 37.5%), or anal fistula (2, 12.5%) were the most common manifestations. WES identified a spectrum of genetic variants in 13 patients (81.3%): IL10RB (6, 37.5%), MVK (3, 18.8%), and CASP8, SLC35C1, G6PC3, and IKBKB in 1 patient, respectively. In 3 patients (18.7%), no variant was identified. Flow cytometry identified a spectrum of abnormalities that helped to assess the evidence of genetic diagnosis. At the end of the survey, 3 (18.8%) patients were deceased. This high rate of monogenic defects with a broad spectrum of genes reiterates the importance of investigating IEI in patients with infantile-onset IBD.
Consistency of metabolite associations with measured glomerular filtration rate in children and adults
Authors: Li Taibo , Grams Morgan E , Inker Lesley A , Chen Jingsha , Rhee Eugene P , Warady Bradley A , Levey Andrew S , Denburg Michelle R , Furth Susan L , Ramachandran Vasan S , Kimmel Paul L , Coresh Josef
Published: April 2024

Background

There is interest in identifying novel filtration markers that lead to more accurate GFR estimates than current markers (creatinine and cystatin C) and are more consistent across demographic groups. We hypothesize that large-scale metabolomics can identify serum metabolites that are strongly influenced by glomerular filtration rate (GFR) and are more consistent across demographic variables than creatinine, which would be promising filtration markers for future investigation.

Methods

We evaluated the consistency of associations between measured GFR (mGFR) and 887 common, known metabolites quantified by an untargeted chromatography- and spectroscopy-based metabolomics platform (Metabolon) performed on frozen blood samples from 580 participants in Chronic Kidney Disease in Children (CKiD), 674 participants in Modification of Diet in Renal Disease (MDRD) Study and 962 participants in African American Study of Kidney Disease and Hypertension (AASK). We evaluated metabolite–mGFR correlation association with metabolite class, molecular weight, assay platform and measurement coefficient of variation (CV). Among metabolites with strong negative correlations with mGFR (r < −0.5), we assessed additional variation by age (height in children), sex, race and body mass index (BMI).

Results

A total of 561 metabolites (63%) were negatively correlated with mGFR. Correlations with mGFR were highly consistent across study, sex, race and BMI categories (correlation of metabolite–mGFR correlations between 0.88 and 0.95). Amino acids, carbohydrates and nucleotides were more often negatively correlated with mGFR compared with lipids, but there was no association with metabolite molecular weight, liquid chromatography/mass spectrometry platform and measurement CV. Among 114 metabolites with strong negative associations with mGFR (r < −0.5), 27 were consistently not associated with age (height in children), sex or race.

Conclusions

The majority of metabolite–mGFR correlations were negative and consistent across sex, race, BMI and study. Metabolites with consistent strong negative correlations with mGFR and non-association with demographic variables may represent candidate markers to improve estimation of GFR.
Detection and classification of mandibular fractures in panoramic radiography using artificial intelligence
Authors: Yari Amir , Fasih Paniz , Hosseini Hooshiar Mohammad , Goodarzi Ali , Fattahi Seyedeh Farnaz
Published: April 2024

Objectives

This study evaluated the performance of the YOLOv5 deep learning model in detecting different mandibular fracture types in panoramic images.

Methods

The dataset of panoramic radiographs with mandibular fractures was divided into training, validation, and testing sets, with 60%, 20%, and 20% of the images, respectively. An equal number of control images without fractures were also distributed among the datasets. The YOLOv5 algorithm was trained to detect six mandibular fracture types based on the anatomical location including symphysis, body, angle, ramus, condylar neck, and condylar head. Performance metrics of accuracy, precision, sensitivity (recall), specificity, dice coefficient (F1 score), and area under the curve (AUC) were calculated for each class.

Results

A total of 498 panoramic images containing 673 fractures were collected. The accuracy was highest in detecting body (96.21%) and symphysis (95.87%), and was lowest in angle (90.51%) fractures. The highest and lowest precision values were observed in detecting symphysis (95.45%) and condylar head (63.16%) fractures, respectively. The sensitivity was highest in the body (96.67%) fractures and was lowest in the condylar head (80.00%) and condylar neck (81.25%) fractures. The highest specificity was noted in symphysis (98.96%), body (96.08%), and ramus (96.04%) fractures, respectively. The dice coefficient and AUC were highest in detecting body fractures (0.921 and 0.942, respectively), and were lowest in detecting condylar head fractures (0.706 and 0.812, respectively).

Conclusion

The trained algorithm achieved promising results in detecting most fracture types, particularly in body and symphysis regions indicating machine learning potential as a diagnostic aid for clinicians.
Predictors of treatment response in lymphogenic metastasized papillary thyroid cancer: a histopathological study
Authors: van Kinschot Caroline M J , Oudijk Lindsey , van Noord Charlotte , Korevaar Tim I M , van Nederveen Francien H , Peeters Robin P , van Kemenade Folkert J , Visser W Edward
Published: April 2024

Background

Lymph node metastases in papillary thyroid cancer (PTC) increase the risk for persistent and recurrent disease. Data on the predictive value of histopathological features of lymph node metastases, however, are inconsistent. The aim of this study was to evaluate the prognostic significance of known and new histopathological features of lymph node metastases in a well-defined cohort of PTC patients with clinically evident lymph node metastases.

Methods

A total of 1042 lymph node metastases, derived from 129 PTC patients, were reexamined according to a predefined protocol and evaluated for diameter, extranodal extension, cystic changes, necrosis, calcifications, and the proportion of the lymph node taken up by tumor cells. Predictors for a failure to achieve a complete biochemical and structural response to treatment were determined.

Results

The presence of more than 5 lymph node metastases was the only independent predictor for a failure to achieve a complete response to treatment (odds ratio [OR] 3.39 [95% CI, 1.57-7.33], P < .05). Diameter nor any of the other evaluated lymph node features were significantly associated with the response to treatment.

Conclusions

Detailed reexamination of lymph nodes revealed that only the presence of more than 5 lymph node metastases was an independent predictor of failure to achieve a complete response to treatment. No predictive value was found for other histopathological features, including the diameter of the lymph node metastases. These findings have the potential to improve risk stratification in patients with PTC and clinically evident lymph node metastases.
Nausea, vomiting and conflict in pregnancy
Authors: Crespi Bernard J
Published: April 2024

Nausea and vomiting in pregnancy (NVP) is heritable, common and aversive, and its extreme, hyperemesis gravidarum (HG), can be highly deleterious to the mother and fetus. Recent influential studies have demonstrated that HG is caused predominantly by high levels of Growth-Differentiation Factor 15 (GDF15), a hormone produced by the placenta in substantial amounts. This work has led to calls for therapeutic modulation of this hormone to reduce GDF15 levels and ameliorate HG risk. I describe three main lines of evidence relevant to the hypothesis that GDF15 production is typically adaptive for the fetus, in the context of enhanced placental invasion, reduced rates of miscarriage and preterm birth and higher birth weight. These considerations highlight the medical implications of maternal-fetal conflict, in the context of tradeoffs between aversive symptoms during gestation, rare disorders of pregnancy with major adverse effects and moderate fitness-enhancing benefits to fetuses.
Is Reiki effective in reducing heart rhythm, cortisol levels, and anxiety and improving biochemical parameters in individuals with cardiac disease? Randomized placebo-controlled trial
Authors: Bektas Akpinar Nilay , Ozcan Yüce Ulviye , Cansız Gizem , Yurtsever Dilek , Özkanat Cemaynur , Unal Nursemin , Sabanoglu Cengiz , Altınbas Akkas Özlem , Yurtsever Sabire
Published: April 2024

Aims

The aim of this study was to examine the effect of Reiki in patients with cardiac disease.

Methods and results

This study was a single-blind, pre–post-test, randomized, placebo-controlled study. Patients from the cardiology outpatient clinic of a training and research hospital were randomized into three groups: Reiki (n = 22), sham (placebo) (n = 21), and control (no treatment) (n = 22). Data were collected using a personal information form, biochemical parameters, cortisol levels, Beck Anxiety Inventory, and electrocardiography analysis. The Reiki group received Reiki to nine main points for 30 min, while the sham Reiki group received the same points during the same period without starting the energy flow. On Day 2, distance Reiki was performed for 30 min. After 1 week, the researchers administered the Beck Anxiety Inventory, assessed the biochemical parameters and cortisol levels, and analysed the electrocardiography again. Of the patients, 52.3% were male and 47.7% were female, and the mean age (years) was 60.45 ± 9.67 years. The control group had a significantly higher post-test cortisol level than the other groups (P = 0.002). According to the post hoc analysis, there was a significant difference between the Reiki vs. control groups and sham vs. control groups (P = 0.002). The control group had a significantly higher post-test cortisol level than the pre-test cortisol level (P = 0.008). Reiki group had a significantly lower mean post-test Beck Anxiety Inventory score than the other groups (P < 0.001). There was no difference between the electrocardiography results of the groups (P > 0.05).

Conclusion

Reiki reduces blood cortisol levels and anxiety levels in patient with cardiac diseases.

Registration

ClinicalTrials.gov: NCT05483842
Personalized pulmonary vein isolation with very high-power short-duration lesions guided by left atrial wall thickness: the QDOT-by-LAWT randomized trial
Authors: Falasconi Giulio , Penela Diego , Soto-Iglesias David , Francia Pietro , Saglietto Andrea , Turturiello Dario , Viveros Daniel , Bellido Aldo , Alderete Jose , Zaraket Fatima , Franco-Ocaña Paula , Huguet Marina , Cámara Óscar , Vătășescu Radu , Ortiz-Pérez José-Tomás , Martí-Almor Julio , Berruezo Antonio
Published: April 2024

Aims

Pulmonary vein isolation (PVI) for paroxysmal atrial fibrillation (PAF) using very high-power short-duration (vHPSD) radiofrequency (RF) ablation proved to be safe and effective. However, vHPSD applications result in shallower lesions that might not be always transmural. Multidetector computed tomography-derived left atrial wall thickness (LAWT) maps could enable a thickness-guided switching from vHPSD to the standard-power ablation mode. The aim of this randomized trial was to compare the safety, the efficacy, and the efficiency of a LAWT-guided vHPSD PVI approach with those of the CLOSE protocol for PAF ablation (NCT04298177).

Methods and results

Consecutive patients referred for first-time PAF ablation were randomized on a 1:1 basis. In the QDOT-by-LAWT arm, for LAWT ≤2.5 mm, vHPSD ablation was performed; for points with LAWT > 2.5 mm, standard-power RF ablation titrating ablation index (AI) according to the local LAWT was performed. In the CLOSE arm, LAWT information was not available to the operator; ablation was performed according to the CLOSE study settings: AI ≥400 at the posterior wall and ≥550 at the anterior wall. A total of 162 patients were included. In the QDOT-by-LAWT group, a significant reduction in procedure time (40 vs. 70 min; P < 0.001) and RF time (6.6 vs. 25.7 min; P < 0.001) was observed. No difference was observed between the groups regarding complication rate (P = 0.99) and first-pass isolation (P = 0.99). At 12-month follow-up, no significant differences occurred in atrial arrhythmia-free survival between groups (P = 0.88).

Conclusion

LAWT-guided PVI combining vHPSD and standard-power ablation is not inferior to the CLOSE protocol in terms of 1-year atrial arrhythmia-free survival and demonstrated a reduction in procedural and RF times.
Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes
Authors: Le Moan Alan , Stankowski Sean , Rafajlović Marina , Ortega-Martinez Olga , Faria Rui , Butlin Roger K , Johannesson Kerstin
Published: April 2024

Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.
Faecal bacterial communities differ amongst discrete foraging populations of dugongs along the east Australian coast
Authors: Mikkelsen Deirdre , McGowan Alexandra M , Gibson Justine S , Lanyon Janet M , Horsman Sara , Seddon Jennifer M
Published: April 2024

Gut bacterial communities play a vital role in a host's digestion and fermentation of complex carbohydrates, absorption of nutrients, and energy harvest/storage. Dugongs are obligate seagrass grazers with an expanded hindgut and associated microbiome. Here, we characterised and compared the faecal bacterial communities of dugongs from genetically distinct populations along the east coast of Australia, between subtropical Moreton Bay and tropical Cleveland Bay. Amplicon sequencing of fresh dugong faecal samples (n=47) revealed Firmicutes (62%) dominating the faecal bacterial communities across all populations. Several bacterial genera (Bacteroides, Clostridium sensu stricto 1, Blautia and Polaribacter) were detected in samples from all locations, suggesting their importance in seagrass digestion. Principal coordinate analysis showed the three southern-most dugong populations having different faecal bacterial community compositions from northern populations. The relative abundances of the genera Clostridium sensu stricto 13 and dgA-11 gut group were higher, but Bacteroides was lower, in the southern dugong populations, compared to the northern populations, suggesting potential adaptive changes associated with location. This study contributes to our knowledge of the faecal bacterial communities of dugongs inhabiting Australian coastal waters. Future studies of diet selection in relation to seagrass availability throughout the dugong's range will help to advance our understanding of the roles that seagrass species may play in affecting the dugong's faecal bacterial community composition.
Surface loading on a self-gravitating, linear viscoelastic Earth: moving beyond Maxwell
Authors: Lau H C P
Published: April 2024

Constitutive laws are a necessary ingredient in calculations of glacial isostatic adjustment (GIA) or other surface loading problems (e.g. loading by ocean tides). An idealized constitutive law governed by the Maxwell viscoelastic model is widely used but increasing attention is being directed towards more intricate constitutive laws that, in particular, include transient rheology. In this context, transient rheology collectively refers to dissipative mechanisms activated in addition to creep modelled by the Maxwell viscoelastic model. Consideration of such viscoelastic models in GIA is in its infancy and to encourage their wider use, we present constitutive laws for several experimentally derived transient rheologies and outline a flexible method in which to incorporate them into geophysical problems, such as the viscoelastic deformation of the Earth induced by surface loading. To further motivate this need, we demonstrate, via the Love number collocation method, how predictions of crustal displacement depart significantly between Earth models that adopt only Maxwell viscoelasticity and those with transient rheology. Throughout this paper, we highlight the differences in terminology and emphases between the rock mechanics, seismology and GIA communities, which have perhaps contributed towards the relative scarcity in integrating this broader and more realistic class of constitutive laws within GIA. We focus on transient rheology since the associated deformation has been demonstrated to operate on timescales that range from hours to decades. With ice mass loss enhanced at similar timescales as a consequence of anthropogenically caused climate change, the ability to model GIA with more accurate constitutive laws is an important tool to investigate such problems.
Basic Remarks on Lagrangian Submanifolds of Hyperkähler Manifolds
Authors: Mboro René
Published: April 2024

This note presents basic restrictions on the topology of Lagrangian surfaces of hyper-Kähler $4$-folds and a remark on the interaction of a Lagrangian subvariety of a hyper-Kähler variety with a Lagrangian fibration of the latter.
The Macroeconomic Effects of EU Regional Structural Funds
Authors: Canova Fabio , Pappa Evi
Published: April 2024

We examine the macroeconomic effects of two EU regional structural funds. The European regional development fund (ERDF) has positive short term average consequences, but gains typically dissipate within 3 years. The European Social Fund has insignificant average short term effects, but the medium term effect is positive and economically important. There are regional heterogeneities in terms of location, level of development, EU tenure, Euro area membership, and national borders. The reaction of regional government expenditure to shocks in the structural funds accounts for the differences. The implications for the EU Recovery and Resilience Facility are discussed.
Responses of belowground bud bank density of geophytes to environmental perturbations: a meta-analysis
Authors: Fang Tao , Ye Duo , Gao Ju-Juan , Luo Fang-Li , Zhu Yao-Jun , Yu Fei-Hai
Published: April 2024

A belowground bud bank is a collection of asexual propagules produced by the underground storage organs of geophytes. Renewal through belowground bud banks is the main reproductive strategy of geophytes. The belowground bud bank density reflects the potential renewal capacity of geophyte communities. However, the effects of different perturbation regimes and habitats on the belowground bud bank density of geophytes are not comprehensively understood. Moreover, whether different types of belowground bud banks respond differently to perturbations is still unclear. For this meta-analysis, relevant papers on the effects of environmental perturbations on the belowground bud bank density of geophytes were systematically collected. The cumulative effect size of different perturbation regimes and habitats on belowground bud banks among different bud types was analyzed. Overall, the effect of environmental perturbations on belowground bud bank density was small, which may result from opposite or fluctuating responses of bud banks to different perturbations. Drought negatively affected bud bank density. Environmental perturbations decreased rhizome bud density but increased tiller bud density. In wetlands, perturbations decreased belowground bud bank density. However, no significant effect was found for other habitat types. In general, belowground bud banks of geophytes are highly resistant and resilient. Changes in belowground bud bank density depend on the type of perturbations, the habitats in which plants are distributed and the type of bud banks.
Effects of warming conditions on plant nitrogen–phosphorus stoichiometry and resorption of three plant species in alpine meadows on the Tibetan Plateau
Authors: Zheng Lang , Cao Xuan , Yang Zhiyong , Wang Hui , Zang Qiqi , Song Wenchen , Shen Miaogen , Xiao Chunwang
Published: April 2024

Global climate change is expected to have a significant impact on ecosystems worldwide, especially for alpine meadows which are considered as one of the most vulnerable components. However, the effects of global warming on the plant nitrogen–phosphorus stoichiometry and resorption in alpine meadows remain unclear. Therefore, to investigate the plant nitrogen–phosphorus stoichiometry and resorption in alpine meadows on the Qinghai-Tibet Plateau, we conducted an artificial warming study using open-top chambers (OTCs) over the 3 years of warming period. We selected three dominant species, four height types of OTCs (0.4, 0.6, 0.8 and 1 m) and four warming methods (year-round warming, winter warming, summer–autumn–winter warming and spring–summer–autumn warming in the experiment) in this experiment. In our study, soil temperature significantly increased with increasing the height of OCTs under the different warming methods. Kobresia pygmaea presented an increase in nitrogen (N) limitation and Kobresia humilis presented an increase in phosphorus (P) limitation with increasing temperature, while Potentilla saundersiana was insensitive to temperature changes in terms of nitrogen and phosphorus limitations. Both nitrogen resorption efficiency:phosphorus resorption efficiency and N:P trends in response to rising temperatures were in the same direction. The differential responses of the chemical stoichiometry of the three species to warming were observed, reflecting that the responses of nitrogen and phosphorus limitations to warming are multifaceted, and the grassland ecosystems may exhibit a certain degree of self-regulatory capability. Our results show that using chemical dosage indicators of a single dominant species to represent the nitrogen and phosphorus limitations of the entire ecosystem is inaccurate, and using N:P to reflect the nutritional limitations might have been somewhat misjudged in the context of global warming.
Improving transformation and regeneration efficiency in medicinal plants: insights from other recalcitrant species
Authors: Bennur Praveen Lakshman , O’Brien Martin , Fernando Shyama C , Doblin Monika S
Published: April 2024

Medicinal plants are integral to traditional medicine systems worldwide, being pivotal for human health. Harvesting plant material from natural environments, however, has led to species scarcity, prompting action to develop cultivation solutions that also aid conservation efforts. Biotechnological tools, specifically plant tissue culture and genetic transformation, offer solutions for sustainable, large-scale production and enhanced yield of valuable biomolecules. While these techniques are instrumental to the development of the medicinal plant industry, the challenge of inherent regeneration recalcitrance in some species to in vitro cultivation hampers these efforts. This review examines the strategies for overcoming recalcitrance in medicinal plants using a holistic approach, emphasizing the meticulous choice of explants (e.g. embryonic/meristematic tissues), plant growth regulators (e.g. synthetic cytokinins), and use of novel regeneration-enabling methods to deliver morphogenic genes (e.g. GRF/GIF chimeras and nanoparticles), which have been shown to contribute to overcoming recalcitrance barriers in agriculture crops. Furthermore, it highlights the benefit of cost-effective genomic technologies that enable precise genome editing and the value of integrating data-driven models to address genotype-specific challenges in medicinal plant research. These advances mark a progressive step towards a future where medicinal plant cultivation is not only more efficient and predictable but also inherently sustainable, ensuring the continued availability and exploitation of these important plants for current and future generations.
Biodegradation of aliphatic and aromatic hydrocarbons by bacteria isolated from Bahregan area
Authors: Shahidi Rizi Masumeh Sadat , Emtiazi Giti , Akhavan Sepahy Abbas
Published: April 2024

Environmental pollution with aromatic and aliphatic hydrocarbons caused by oil and petrochemical industries has very toxic and carcinogenic effects on living organisms and should be removed from the environment.

In this research, after analyzing the oil sludge of the Bahregan area, it was found that most aliphatic paraffin compounds are related to octadecane, most liquid aliphatic compounds are related to hexadecane, and most aromatic compounds are related to naphthalene, phenanthrene, fluoranthene, and anthracene. Then, we investigated the ability of native bacteria from this area, such as Thalassospira, Chromohalobacter, and a bacterial consortium, to biodegrade the dominant aromatic and aliphatic hydrocarbons found in oil sludge. The results of Gas Chromatography–Mass Spectrometry analysis showed that among the tested hydrocarbon sources, Thalassospira can completely remove octadecane and hexadecane, and Chromohalobacter can reduce hexadecane from 15.9 to 9.9%. The bacterial consortium can completely remove octadecane and reduce hexadecane from 15.9 to 5.1%, toluene from 25.6 to 0.6%, and phenanthrene from 12.93 to 6%.

According to the obtained results, the bacterial consortium effectively plays a role in the biodegradation of aromatic and aliphatic hydrocarbons, making it a viable solution for treating hydrocarbon pollutants in various environments.
Pathovars, occurrence, and characterization of plasmid-mediated quinolone resistance in diarrheal Escherichia coli isolated from farmers and farmed chickens in Tunisia and Nigeria
Authors: AL-GALLAS Nazek , Fadel Mohamed-Elamen , Altammar Khadijah A , Awadi Yasmin , Aissa Ridha Ben
Published: April 2024

The poultry industry is a very important agricultural and industrial sector in Tunisia and Nigeria, with little information about occurrence of diarrheagenic Escherichia coli in the farmers and chickens. This study aimed to detect the prevalence of diarrheal E. coli in humans and poultry and to investigate plasmid-mediated quinolone resistance (PMQR) genes in both countries. Seventy-four isolates of E. coli were studied; nine different virulence genes were screened by PCR. Serotyping was performed only for pathotypes as well as the determining of antibiotic resistance profiles against 21 antibiotics. PMQR genes were investigated by PCR. EAEC was the most abundant pathotype (37/74; 50%) in human and chicken isolates, whereas single EHEC and EPEC (1/74, 1.35%) pathotypes were detected in Tunisia and Nigeria, respectively. About 17 (45.95%) quinolones/fluoroquinolones-resistant isolates were detected, from which the following PMQR genes were detected: aac(6′)-Ib-cr (8/17, 47.05%), qepA (6/17, 35.29%), qnrA + qnrB (2/17, 11.76%), and qnrS gene (1/17, 5.88%). Our findings highlight high occurrence of EAEC pathotype in Tunisia and Nigeria, more frequent than EPEC and EHEC. Additionally, all E. coli pathotypes isolated from different sources (humans, poultry) showed resistance to several antibiotics, which are in use as therapeutic choices in Tunisia and Nigeria.
Taxonomy of Candida parapsilosis complex isolated from neonates and the role of Hsp90 inhibitors to enhanced the antifungal activity of micafungin
Authors: da Silva Carolina Maria , de Lima Neto Reginaldo Gonçalves , de Carvalho Ana Maria Rabelo , Macêdo Danielle Patrícia Cerqueira , de Azevedo Melo Analy Salles , Neves Rejane Pereira
Published: April 2024

Species from Candida parapsilosis complex are frequently found in neonatal candidemia. The antifungal agents to treat this infection are limited and the occurrence of low in vitro susceptibility to echinocandins such as micafungin has been observed. In this context, the chaperone Hsp90 could be a target to reduce resistance. Thus, the objective of this research was to identify isolates from the C. parapsilosis complex and verify the action of Hsp90 inhibitors associated with micafungin. The fungal identification was based on genetic sequencing and mass spectrometry. Minimal inhibitory concentrations were determined by broth microdilution method according to Clinical Laboratory and Standards Institute. The evaluation of the interaction between micafungin with Hsp90 inhibitors was realized using the checkerboard methodology. According to the polyphasic taxonomy, C. parapsilosis sensu stricto was the most frequently identified, followed by C. orthopsilosis and C. metapsilosis, and one isolate of Lodderomyces elongisporus was identified by genetic sequencing. The Hsp90 inhibitor geladanamycin associated with micafungin showed a synergic effect in 31.25% of the isolates, a better result was observed with radicicol, which shows synergic effect in 56.25% tested yeasts. The results obtained demonstrate that blocking Hsp90 could be effective to reduce antifungal resistance to echinocandins.
The S-PLUS Fornax Project (S+FP): SExtractor detection and measurement of nearby galaxies in large photometric surveys
Authors: Haack R F , Smith Castelli A V , Mendes de Oliveira C , Almeida-Fernandes F , Faifer F R , Lopes A R , Jaffe Y , Demarco R , Lima-Dias C , Lomelí-Nuñez L , Montaguth G P , Schoenell W , Ribeiro T , Kanaan A
Published: April 2024

All-sky multiband photometric surveys represent a unique opportunity of exploring rich nearby galaxy clusters up to several virial radii, reaching the filament regions where pre-processing is expected to occur. These projects aim to tackle a large number of astrophysical topics, encompassing both the Galactic and extragalactic fields. In that sense, generating large catalogues with homogeneous photometry for both resolved and unresolved sources that might be interesting to achieve specific goals, imposes a compromise when choosing the set of parameters to automatically detect and measure such a plethora of objects. In this work, we present the acquired experience on studying the galaxy content of the Fornax cluster using large catalogues obtained by the Southern Photometric Local Universe Survey (S-PLUS). We realized that some Fornax bright galaxies are missed in the S-PLUS iDR4 catalogues. In addition, Fornax star-forming galaxies are included as multiple detections due to overdeblending. To solve those issues, we performed specific SExtractor runs to identify the proper set of parameters to recover as many Fornax galaxies as possible with confident photometry and avoiding duplications. From that process, we obtained new catalogues containing 12-band improved photometry for ∼ 3 × 106 resolved and unresolved sources in an area of ∼ 208 deg2 in the direction of the Fornax cluster. Together with identifying the main difficulties to carry out the study of nearby groups and clusters of galaxies using S-PLUS catalogues, we also share possible solutions to face issues that seem to be common to other ongoing photometric surveys.
H α reverberation mapping from broad-band photometry of dwarf type 1 Seyfert galaxy NGC 4395
Authors: Gu Huapeng , Wu Xue-Bing , Wen Yuhan , Ma Qinchun , Guo Hengxiao
Published: April 2024

NGC 4395 is a dwarf type 1 Seyfert galaxy with a possible intermediate-mass black hole of several $\rm {10^4}$ solar masses in its centre. As a well-studied object, its broad-line region size has been measured via H $\rm {\alpha }$ time lag in numerous spectroscopic reverberation mapping (SRM) and narrow-band photometric reverberation mapping (PRM) campaigns. Here, we present its H $\rm {\alpha }$ time lag measurement using broad-band photometric data, with the application of our newly developed ICCF-Cut (Interpolation and Cross-Correlation Function - Cut) method as well as the javelin (Just Another Vehicle for Estimating Lags In Nuclei) and χ2 methods. Utilizing the minute-cadence multiband light curves obtained from the $\rm {2}$-m Faulkes Telescope North and $\rm {10.4}$-m Gran Telescopio Canarias telescopes in recent works, we measured its H $\rm {\alpha }$ lag as approximately 40–90 min from broad-band PRM. With the H $\rm {\alpha }$ emission line velocity dispersion, we calculated its central black hole mass as $M_{\rm BH} = (8\pm 4) \times 10^3\ \mathrm{ M}_{\rm \odot }$. These results are comparable with previous results obtained by narrow-band PRM and SRM, providing further support to an intermediate-mass black hole in NGC 4395. In addition, our study also validates the ICCF-Cut as an effective method for broad-band PRM, which holds the potential for widespread application in the era of large multi-epoch, high-cadence photometric surveys.
Characterizing tidal features around galaxies in cosmological simulations
Authors: Khalid A , Brough S , Martin G , Kimmig L C , Lagos C D P , Remus R -S , Martinez-Lombilla C
Published: April 2024

Tidal features provide signatures of recent mergers and offer a unique insight into the assembly history of galaxies. The Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST) will enable an unprecedentedly large survey of tidal features around millions of galaxies. To decipher the contributions of mergers to galaxy evolution it will be necessary to compare the observed tidal features with theoretical predictions. Therefore, we use cosmological hydrodynamical simulations NewHorizon, eagle, IllustrisTNG, and Magneticum to produce LSST-like mock images of z ∼ 0 galaxies (z ∼ 0.2 for NewHorizon) with $M_{\scriptstyle \star ,\text{ 30 pkpc}}\ge 10^{9.5}$ M$_{\scriptstyle \odot }$. We perform a visual classification to identify tidal features and classify their morphology. We find broadly good agreement between the simulations regarding their overall tidal feature fractions: $f_{{\small NewHorizon}}=0.40\pm 0.06$, $f_{{\small EAGLE}}=0.37\pm 0.01$, $f_{{\small TNG}}=0.32\pm 0.01$, and $f_{{\small Magneticum}}=0.32\pm 0.01$, and their specific tidal feature fractions. Furthermore, we find excellent agreement regarding the trends of tidal feature fraction with stellar and halo mass. All simulations agree in predicting that the majority of central galaxies of groups and clusters exhibit at least one tidal feature, while the satellite members rarely show such features. This agreement suggests that gravity is the primary driver of the occurrence of visually identifiable tidal features in cosmological simulations, rather than subgrid physics or hydrodynamics. All predictions can be verified directly with LSST observations.
Parametric description of intermittent probability distribution functions in solar wind and magnetohydrodynamic turbulence
Authors: Palacios Juan C , Perez Jean C , Bourouaine Sofiane
Published: April 2024

In this work, we find empirical evidence that the scale-dependent statistical properties of solar wind and magnetohydrodynamic (MHD) turbulence can be described in terms of a family of parametric probability distribution functions (PDFs) known as Normal Inverse Gaussian (NIG). Understanding these PDFs is one of the most important goals in turbulence theory, as they are inherently connected to the intermittent properties of solar wind turbulence. We investigate the properties of PDFs of Elsasser increments based on a large statistical sample from solar wind observations and high-resolution numerical simulations of MHD turbulence. In order to measure the PDFs and their corresponding properties, three experiments are presented: fast and slow solar wind for experimental data and a simulation of reduced MHD (RMHD) turbulence. Conditional statistics on a 23-yr-long sample of WIND data near 1 au and high-resolution pseudo-spectral simulation of steadily driven RMHD turbulence on a $2048^3$ mesh are used to construct scale-dependent PDFs. The empirical PDFs are fitted to NIG distributions, which depend on four free parameters. Our analysis shows that NIG distributions accurately capture the evolution of the PDFs, with scale-dependent parameters, from large scales characterized by a Gaussian distribution, turning to exponential tails within the inertial range and stretched exponentials at dissipative scales. We also show that empirically-measured NIG parameters exhibit well-defined scaling properties that are similar across the three empirical data sets, which may be indicative of universal behaviour.
Dynamical instabilities in post-disc evolution: hot Jupiters left isolated
Authors: He Ying , Wu Dong-Hong , Jin Sheng
Published: April 2024

The predominant formation channel of hot Jupiters remains a puzzle in exoplanet science. One potential way to distinguish the different mechanisms is to study the characteristics of close-in companions to hot Jupiters. In this study, our main focus is to investigate the post-disc evolution of planetary systems initially composed of one Jupiter and several super-Earths through numerical N-body simulations spanning a period of 107 yr. By tracing the evolution of each planetary system, we find that only 5.6 per cent of the systems remain stable. Dynamical instabilities are more prevalent in systems with less massive super-Earths and those containing hot Jupiters. Our findings uncover a positive correlation between the presence of close-in companions and the orbital periods of the giant planets. Specifically, we find that approximately 10.9 ± 1.9 per cent of hot Jupiters and 36.4 ± 1.8 per cent of warm Jupiters have close-in companions after 107 yr. Moreover, extending the integration time to 108 yr reveals that only 1.4 ± 1.0 per cent of hot Jupiters and 20.3 ± 2.2 per cent of warm Jupiters host close-in companions. We also investigate the effects of general relativistic, tidal dissipation, and initial spacing between Jupiters and their neighbouring planets on the frequency of close-in companions for these short-period Jupiters. Our simulations suggest that the general relativity effect plays a crucial role in contributing to the isolation of hot Jupiters. Furthermore, we observe that the more compact the planetary systems are initially, the less likely it is for Jupiters to host close-in companions.
Elucidating the impact of massive neutrinos on halo assembly bias
Authors: Song Yunjia , Zu Ying
Published: April 2024

Massive neutrinos have non-negligible impact on the formation of large-scale structures. We investigate the impact of massive neutrinos on the halo assembly bias effect, measured by the relative halo bias $\hat{b}$ as a function of the curvature of the initial density peak $\hat{s}$, neutrino excess ϵν, or halo concentration $\hat{c}$, using a large suite of ΣMν = 0.0 and 0.4 eV simulations with the same initial conditions. By tracing dark matter haloes back to their initial density peaks, we construct a catalogue of halo ‘twins’ that collapsed from the same peaks but evolved separately with and without massive neutrinos, thereby isolating any effect of neutrinos on halo formation. We detect a 2 per cent weakening of the halo assembly bias as measured by $\hat{b}(\epsilon _\nu)$ in the presence of massive neutrinos. As there exists a significant correlation between $\hat{s}$ and ϵν (rcc = 0.319), the impact of neutrinos persists at a reduced level (0.1 per cent) in the halo assembly bias measured by $\hat{b}(\hat{s})$. However, we do not detect any neutrino-induced impact on $\hat{b}(\hat{c})$, consistent with earlier studies and the lack of correlation between $\hat{c}$ and ϵν (rcc = 0.087). We also discover an analogous assembly bias effect for the ‘neutrino haloes’, whose concentrations are anticorrelated with the large-scale clustering of neutrinos.