bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fungal co-expression network analyses identify pathogen gene modules associated with host insect invasion
Authors: Huang Shuaishuai , Zhao Xin , Luo Zhibing , Tang Xiaohan , Zhou Yonghong , Keyhani Nemat , Zhang Yongjun 
Published: September 2023

ABSTRACT

The broad host range fungal insect pathogen,
Beauveria bassiana
, has been commercialized as an alternative to chemical insecticides for pest control worldwide.
B. bassiana
represents a unique model system with which to examine host-pathogen interactions, and a wide range of genes and processes have been studied. However, significant aspects of virulence, particularly on the genomic scale, remain poorly studied. Here, we have combined available transcriptomes with three newly generated data sets for a combined total analysis of 76 deep-sequenced samples covering growth, development, stress responses, and infection during the life cycle of
B. bassiana
. Co-expression network analyses resulted in the identification of gene modules enriched during two critical stages of the infection process, namely (i) cuticle penetration and (ii)
in vivo
hyphal body (dimorphic transition) growth capable of avoiding innate and humoral immune defenses. These analyses identify unique signatures of metabolism, signaling, secondary metabolite production, host defense suppression, membrane reorganization, effector production, and secretion for each stage, including genetic regulators and epigenetic patterns. These data provide a comprehensive framework for understanding and probing fungal adaptations to its pathogenic life cycle and expand the candidate repertoire for continued dissection of the host-pathogen interaction.

IMPORTANCE

Insect fungal pathogens have evolved unique strategies for overcoming host structural and immunological defenses that span from the sclerotized cuticle to innate and humoral cellular responses. Two critical stages of the infection process involve (i) cuticle penetration and (ii) immune evasion within the insect hemocoel. A set of 76 global transcriptomic data for
B. bassiana
that include the cuticle penetration and hemocoel growth stages were analyzed for patterns (gene modules) of expression, yielding unique insights into these different life stages. These analyses integrate gene networks involved in fungal development, stress response and pathogenesis to further the systematic understanding of the global processes integral to the unique adaptation employed by fungal pathogens of insects.
Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages
Authors: Wang Xing , He Shan-Wen , He Qing , Ju Zhi-Cheng , Ma Yi-Nan , Wang Zhe , Han Jia-Cheng , Zhang Xiao-Xia 
Published: September 2023

ABSTRACT

The core endophytes of plants are regarded as promising resources in future agroecosystems. How they affect the assembly of rice-related bacterial communities after early inoculation remains unclear. Here, we examined bacterial communities across 148 samples, including bulk and rhizosphere soils, sterilized roots, stems, and seeds at the seedling, tillering, booting, and maturity stages. Tissue cultured rice seedlings were inoculated with
Xathomonas sacchari
JR3-14, a core endophytic bacterium of rice seeds, before transplanting. The results revealed that α-diversity indices were significantly enhanced in the root and stem endosphere at the seedling stage. β-diversity was altered at most plant developmental stages, except for the root and stem at the booting stage. Network complexity consequently increased in the root and stem across rice growth stages, other than the stem endosphere at the booting stage. Four abundant beneficial bacterial taxa,
Bacillus
,
Azospira
,
Azospirillum
, and
Arthrobacter
, were co-enriched during the early growth stage. Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis revealed a higher relative contribution of drift and other eco-evolutionary processes mainly in root compartments across all growth stages, but the opposite pattern was observed in stem compartments.

IMPORTANCE

Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant’s ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium
Xanthomonas sacchari
could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding.
Association between catheter ablation of atrial fibrillation and mortality or stroke
Authors: Akerström Finn , Hutter Julie , Charitakis Emmanouil , Tabrizi Fariborz , Asaad Fahd , Bastani Hamid , Bourke Tara , Braunschweig Frieder , Drca Nikola , Englund Anders , Friberg Leif , Insulander Per , Jönsson Anders Hassel , Kennebäck Göran , Paul-Nordin Astrid , Sadigh Bita , Saluveer Ott , Saygi Serkan , Schwieler Jonas , Svennberg Emma , Tapanainen Jari , Türkmen Yusuf , Jensen-Urstad Mats 
Published: September 2023

ObjectiveCatheter ablation of atrial fibrillation effectively reduces symptomatic burden. However, its long-term effect on mortality and stroke is unclear. We investigated if patients with atrial fibrillation who undergo catheter ablation have lower risk for all-cause mortality or stroke than patients who are managed medically.MethodsWe retrospectively included 5628 consecutive patients who underwent first-time catheter ablation for atrial fibrillation between 2008 and 2018 at three major Swedish electrophysiology units. Control individuals with an atrial fibrillation diagnosis but without previous stroke were selected from the Swedish National Patient Register, resulting in a control group of 48 676 patients. Propensity score matching was performed to produce two cohorts of equal size (n=3955) with similar baseline characteristics. The primary endpoint was a composite of all-cause mortality or stroke.ResultsPatients who underwent catheter ablation were healthier (mean CHA2DS2-VASc score 1.4±1.4 vs 1.6±1.5, p<0.001), had a higher median income (288 vs 212 1000 Swedish krona [KSEK]/year, p<0.001) and had more frequently received university education (45.1% vs 28.9%, p<0.001). Mean follow-up was 4.5±2.8 years. After propensity score matching, catheter ablation was associated with lower risk for the combined primary endpoint (HR 0.58, 95% CI 0.48 to 0.69). The result was mainly driven by a decrease in all-cause mortality (HR 0.51, 95% CI 0.41 to 0.63), with stroke reduction showing a trend in favour of catheter ablation (HR 0.75, 95% CI 0.53 to 1.07).ConclusionsCatheter ablation of atrial fibrillation was associated with a reduction in the primary endpoint of all-cause mortality or stroke. This result was driven by a marked reduction in all-cause mortality.
Patterns in hospital admissions for adults with congenital heart disease for non-cardiac procedures
Authors: Friess Jan Oliver , França Urbano L , Valente Anne Marie , DiNardo James A , McManus Michael L , Nasr Viviane G 
Published: September 2023

ObjectiveAdvances in management of congenital heart disease (CHD) have led to an increasing population of adults with CHD, many of whom require non-cardiac procedures. The objectives of this study were to describe the characteristics of these patients, their distribution among different hospital categories and the characteristics determining this distribution, and mortality rates following noncardiac procedures.MethodsWe retrospectively analysed 27 state inpatient databases. Encounters with CHD and non-cardiac procedures were included. The location of care was classified into two categories: hospitals with and without cardiac surgical programmes. Variables included were demographics, comorbidity index, mortality. Multivariable logistic regression was used to explore predictors for care in different locations.ResultsThe cohort consisted of 12 944 encounters in 1206 hospitals. Most patients were cared for in hospitals with a cardiac surgical programme (78.1%). Patients presenting to hospitals with a cardiac surgical programme presented with higher comorbidity index (6 (IQR: 0–19) vs 2 (IQR: −3–14), p<0.001) than patients presenting to hospitals without a cardiac surgical programme. Mortality was higher in hospitals with cardiac surgical programmes compared with hospitals without cardiac surgical programmes (4.0% vs 2.3%, p<0.001). Factors associated with provision of care at a hospital with a cardiac surgical programme were comorbidity index (>7: OR 2.01 (95% CI 1.83 to 2.21), p<0.001; 2–7: OR 1.59 (95% CI 1.41 to 1.79), p<0.001) and age (18–44 years: OR 1.43 (95% CI 1.26 to 1.62), p<0.001; 45–64 years: OR 1.21 (95% CI 1.08 to 1.34), p<0.001).ConclusionAdults with CHD undergoing non-cardiac procedures are mainly cared for in hospitals with a cardiac surgical programme and have greater comorbidities and higher mortality than those in centres without cardiac surgical programmes. Risk stratification and locoregional accessibility need further assessment to fully understand admission patterns.
Experimental observation of phase transitions of a deformed Dicke model using a reconfigurable, bi-parametric electronic platform
Authors: Quiroz-Juárez Mario A. , Corps Ángel L. , Molina Rafael A. , Relaño Armando , Aragón José L. , León-Montiel Roberto de J. , Hirsch Jorge G. 
Published: September 2023

AbstractWe experimentally study the infinite-size limit of the Dicke model of quantum optics with a parity-breaking deformation strength that couples the system to an external bosonic reservoir. We focus on the dynamical consequences of such symmetry breaking, which makes the classical phase space asymmetric with non-equivalent energy wells. We present an experimental implementation of the classical version of the deformed Dicke model using a state-of-the-art bi-parametric electronic platform. Our platform constitutes a playground for studying representative phenomena of the deformed Dicke model in electrical circuits with the possibility of externally controlling parameters and initial conditions. In particular, we investigate the dynamics of the ground state, various phase transitions and the asymmetry of the energy wells as a function of the coupling strength $$\gamma $$
γ
and the deformation strength $$\alpha $$
α
in the resonant case. Additionally, to characterize the various behavior regimes, we present a two-dimensional phase diagram as a function of the two intrinsic system parameters. The onset of chaos is also analyzed experimentally. Our findings provide a clear connection between theoretical predictions and experimental observations, demonstrating the usefulness of our bi-parametric electronic setup.
Two fluid cosmological models in f(R,T) theory of gravity
Authors: Solanke Y. S. , Mhaske Sandhya , Pawar D. D. , Dagwal V. J. 
Published: August 2023

This work deals with the two fluid Bianchi type-V cosmological models consisting of matter and radiating source in the [Formula: see text] theory of gravity studied by Harko et al. [Phys. Rev. D 84, 024020 (2011)]. In this paper, we developed a new idea about [Formula: see text] gravity with the help of two fluids: one fluid is matter field modeling material content of the Universe and other fluid is radiation field modeling the cosmic microwave background (CMB). We have determined the solution of the two fluid gravitational field equations with the systematic structure in [Formula: see text] gravity. Here, we have deliberated four types of universe such as dust universe, radiation universe, hard universe and Zel’dovich universe and also extended our work to observe the big rip and big bang singularity. We have also tested the cosmological parameters.
Cold Case of Thrombolysis: Cold Recombinant Tissue Plasminogen Activator Confers Enhanced Neuroprotection in Experimental Stroke
Authors: Huang Yuyou , Gu Shanshan , Han Ziping , Yang Zhenghong , Zhong Liyuan , Li Lingzi , Wang Rongliang , Yan Feng , Luo Yumin , Borlongan Cesario , Lu Jie 
Published: September 2023

Background
Thrombolysis and endovascular thrombectomy are the primary treatment for ischemic stroke. However, due to the limited time window and the occurrence of adverse effects, only a small number of patients can genuinely benefit from recanalization. Intraarterial injection of rtPA (recombinant tissue plasminogen activator) based on arterial thrombectomy could improve the prognosis of patients with acute ischemic stroke, but it could not reduce the incidence of recanalization‐related adverse effects. Recently, selective brain hypothermia has been shown to offer neuroprotection against stroke. To enhance the recanalization rate of ischemic stroke and reduce the adverse effects such as tiny thrombosis, brain edema, and hemorrhage, we described for the first time a combined approach of hypothermia and thrombolysis via intraarterial hypothermic rtPA.

Methods and Results
We initially established the optimal regimen of hypothermic rtPA in adult rats subjected to middle cerebral artery occlusion. Subsequently, we explored the mechanism of action mediating hypothermic rtPA by probing reduction of brain tissue temperature, attenuation of blood–brain barrier damage, and sequestration of inflammation coupled with untargeted metabolomics. Hypothermic rtPA improved neurological scores and reduced infarct volume, while limiting hemorrhagic transformation in middle cerebral artery occlusion rats. These therapeutic outcomes of hypothermic rtPA were accompanied by reduced brain temperature, glucose metabolism, and blood–brain barrier damage. A unique metabolomic profile emerged in hypothermic rtPA‐treated middle cerebral artery occlusion rats characterized by downregulated markers for energy metabolism and inflammation.

Conclusions
The innovative use of hypothermic rtPA enhances their combined, as opposed to stand‐alone, neuroprotective effects, while reducing hemorrhagic transformation in ischemic stroke.
Deladenus taedae n. sp. (Nematoda: Neotylenchidae) in Loblolly pine (Pinus taeda) woods from USA intercepted in Ningbo, P.R. China
Authors: Yu Qing , Gu Jianfeng , Ye Weimin 
Published: September 2023

Summary
Deladenus taedae n. sp. was isolated from loblolly pine wood (Pinus taeda) intercepted in Ningbo, P.R. China, in imports from the USA. This new species is morphologically described and illustrated and characterised molecularly. Both mycetophagous and infective forms were recovered and described. The new species, D. taedae n. sp., resembles some other species of Deladenus in which the excretory pore is situated anterior to the hemizonid. The new species is characterised by the lateral fields with six lines, pointed tail ending and small spermatheca in mycetophagous females and short stylet in infective females. In mycetophagous females, the excretory pore is 74-98 μm from the anterior end and 37-54 μm anterior to the hemizonid. The partial rDNA 18S, complete internal transcribed spacer, 5.8S and partial 28S D2/D3 genes were amplified and sequenced. Phylogenetic analyses of the genes distinguished this new species from all other sequenced Deladenus species.
The Ascetics of Mount Aṭṭhāvaya Become Jain Monks
Authors: Dundas Paul , Bisschop Peter C. 
Published: August 2023

Abstract
This study presents a detailed analysis of the narrative of Goyama and the ascetics of Mount Aṭṭhāvaya in the Āvaśyaka Cūrṇi, including text and translation. By identifying a range of themes, intertexts and allusions in the narrative, a variety of Jain perspectives on the nature of asceticism are uncovered. Topics covered include the Āvaśyaka Cūrṇi as “commentary”, the Āvaśyaka Niryukti background to the Āvaśyaka Cūrṇi narrative, some possible Śaiva allusions in the narrative, the significance of Goyama’s physical appearance, Goyama’s explanation of the canonical story of Puṃḍarīa, and Goyama’s power of bestowing limitless food. In addition to the narrative told in the Āvaśyaka Cūrṇi, its earliest metrical version in the Uttarādhyayana Niryukti is discussed and translated as well.
The Impact of Frailty on Adjuvant Therapies Not Offered to or Declined by Breast Cancer Surgery Patients
Authors: Solsky Ian , Cairns Ashley , Martin Tamriage , Perko Allison , Friday Sarah , Levine Edward , Howard-McNatt Marissa 
Published: September 2023

Introduction The impact of frailty on adjuvant therapies not offered to or declined by elderly breast cancer surgery patients has been understudied. Methods This is a retrospective review of a prospectively managed single-center database including all breast cancer patients >65 years undergoing surgery in 2021. Frailty was determined using an electronic frailty index (eFI) derived from electronic health data. Patients were categorized as Fit (eFI ≤ .10), Pre-frail (.10 < eFI ≤.21), or Frail (eFI > .21). Chart review was performed to collect data on adjuvant therapies not offered or declined. Descriptive statistics and logistic regression were performed. Results Of 133 patients, 16.5% were frail, 46.6% were pre-frail, and 36.8% were fit. Demographics were similar among groups except age and comorbidities. Of those with adjuvant therapy indicated (n = 123), 15.4% were not offered at least one indicated therapy. Of those offered therapy, some therapy was declined in 22.7%. Frail patients more often were not offered or declined some therapy (frail: 63.2%, pre-frail 36.2%, fit: 28.2%, P = .03). Frailty was associated with having some therapy not offered or declined on univariate modeling (OR 4.4 95% CI 1.4-13.5, P = .01) but not on multivariate. Being frail was associated with higher odds of readmission at 6 months on multivariate analysis (OR 9.5, 95% CI: 1.7-54.2. P = .01). Conclusion Over half of frail patients are not offered or decline some adjuvant therapy. The impact of this requires further study. Given their higher odds of readmission, frail patients require close postoperative monitoring to prevent the interruption of adjuvant therapies.
Treatment consistent with idiopathic multicentric Castleman disease guidelines is associated with improved outcomes
Authors: Pierson Sheila K. , Lim Megan S. , Srkalovic Gordan , Brandstadter Joshua D. , Sarmiento Bustamante Mateo , Shyamsundar Saishravan , Mango Natalie , Lavery Criswell , Austin Bridget , Alapat Daisy , Lechowicz Mary Jo , Bagg Adam , Li Hongzhe , Casper Corey , van Rhee Frits , Fajgenbaum David C. 
Published: September 2023

Abstract
Idiopathic multicentric Castleman disease (iMCD) is a rare hematologic disorder with an unknown etiology. Clinical presentation is heterogeneous, ranging from mild constitutional symptoms with lymphadenopathy to life-threatening multiorgan dysfunction. International, consensus treatment guidelines developed in 2018 relied upon a limited number of clinical trials and small case series; however, to our knowledge, real-world performance of these recommendations has not been subsequently studied. Siltuximab, a monoclonal antibody against interleukin 6 (IL6), is approved for the treatment of iMCD and recommended first-line, and tocilizumab, a monoclonal antibody directed against the IL6 receptor, is recommended when siltuximab is unavailable. Chemotherapy, rituximab, and immunomodulators are recommended as second- and third-line treatments based on limited evidence. Corticosteroid monotherapy is used by clinicians, although not recommended. Here, we draw upon the ACCELERATE Natural History Registry to inventory regimens and evaluate regimen response for 102 expert–confirmed iMCD cases. Siltuximab with/without (w/wo) corticosteroids was associated with a 52% response, whereas corticosteroid monotherapy was associated with a 3% response. Anti-IL6–directed therapy with siltuximab or tocilizumab demonstrated better response and more durability than was observed with rituximab w/wo corticosteroids. Cytotoxic chemotherapy was associated with a 52% response and was predominantly administered in patients characterized by thrombocytopenia, anasarca, fever, renal failure/reticulin fibrosis, and organomegaly. Our results provide evidence in support of current recommendations to administer anti-IL6 as first-line treatment, to administer cytotoxic chemotherapy in patients with severe refractory disease, and to limit corticosteroid monotherapy. Evidence remains limited for effective agents for patients who are refractory to anti-IL6–directed therapy. This trial was registered at www.clinicaltrials.gov as #NCT02817997.
Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations
Authors: Laso-Jadart Romuald , O’Malley Michael , Sykulski Adam M. , Ambroise Christophe , Madoui Mohammed-Amin 
Published: September 2023

Abstract
Background
Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method.

Results
We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors.

Conclusion
Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.