bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trichoderma-induced restructuring of the cucumber rhizosphere microbiome and the effect of a synthetic, cross-kingdom microbial community on Fusarium wilt disease and growth in cucumber
Authors: Liu Tong , Zhang Manman , Wang Rui , Khan Raja Asad Ali , Zhan Xin , Ren Sen , Jiang Haonan , Wu Yinggu , Yang Fanxing , Yu Xiaoli 
Published: October 2023

Abstract

Trichoderma asperellum FJ035 was introduced into the complex soil microbial community, that included pathogens, present in the soil of a continuous cucumber planting system, to assess the impact of the Trichoderma amendment on the composition of the microbial community and growth and incidence of Fusarium wilt disease caused by Fusarium oxysporum SCCFo1. Results indicated that Trichoderma-induced alterations in the soil microbial community significantly promoted growth and enhanced disease resistance. Additionally, TB11, a cross-kingdom synthetic microbial community consisting of Trichoderma and 30 strains from 11 bacterial genera was constructed. Treatment of SCCFo1-inoculated cucumber plants with TB11 resulted in a 70.0% reduction in Fusarium wilt disease and a 64.59% increase in plant fresh weight compared to control plants. The synthetic community TB11 was then simplified to a TB5 consortium consisting of Trichoderma and 6 strains from 5 bacterial genera. The use of TB5 produced similar benefits in disease control and an even greater growth promotion than was observed withTB11. The bacterial taxa in TB5 directly inhibit the growth of SCCFo1, can solubilize soil nutrients making them more available to cucumber plants and FJ035, and increase the expressionof antioxidant, defense-related enzyme, and growth hormone-related genes in cucumber plants. These findings highlight the potential of utilizing beneficial synthetic microbial assemblies to support sustainable agriculture management systems, and decrease dependence on the use of synthetic chemicals, while boosting crop health and yield.
Comparative Analysis of Software Quality Assurance Approaches in Development Models
Authors: Silva D. I. , Siriwardana L. K. B. 
Published: October 2023

Abstract
This study presents a comprehensive comparison of software quality assurance techniques across several software development methodologies. It addresses critical knowledge gaps by examining the application of quality assurance processes, associated challenges, and outcomes in diverse software development contexts. The study covers a wide spectrum of development approaches, including classical Waterfall procedures and Agile alternatives such as Scrum, Kanban, Iterative, and Extreme Programming. The research delves into the responsibilities, experiences, and domains of experts involved in these approaches, providing valuable insights into the realm of software development approaches. Key findings of the study underscore the pervasive use of core testing approaches such as regression testing, unit testing, integration testing, performance testing, and security testing. The study also emphasizes the importance of guaranteeing requirement traceability, as well as providing insights on the technologies utilized for this purpose. Moreover, the research highlights the critical importance of achieving comprehensive test coverage and provides insights into a range of techniques for accomplishing this goal. The paper discusses the challenges encountered while testing complicated or interconnected software systems and offers practical solutions such as shift-left testing and exploratory testing to mitigate them. Notably, it highlights the substantial financial benefits derived from effective quality assurance processes, including reduced defect-fixing costs, minimized rework, optimized resource utilization, and heightened customer retention. Moreover, the paper delves into cost-effective quality assurance solutions and assesses the impact of quality assurance practices on user experience and customer satisfaction.
An integrin-targeting AAV developed using a novel computational rational design methodology presents improved targeting of the skeletal muscle and reduced liver tropism
Authors: Hong Ai Vu , Suel Laurence , Poupiot Jérôme , Richard Isabelle 
Published: October 2023

Abstract
Current adeno-associated virus (AAV) gene therapy using nature-derived AAVs is limited by non-optimal tissue targeting. In the treatment of muscular diseases (MD), high doses are therefore often required, but can lead to severe adverse effects. To lower treatment doses, we rationally designed an AAV that specifically targets skeletal muscle. We employed a novel computational design that integrated binding motifs of integrin alpha V beta 6 (αVβ6) into a liver-detargeting AAV capsid backbone to target the human αVβ6 complex – a selected AAV receptor for skeletal muscle. After sampling the low-energy capsid mutants, all in silico designed AAVs showed higher productivity compared to their parent. We confirmed in vitro that the enhanced transduction is due to the binding to the αVβ6 complex. Thanks to inclusion of αVβ6-binding motifs, the designed AAVs exhibited enhanced transduction efficacy in human differentiated myotubes as well as in murine skeletal muscles in vivo. One notable variant, LICA1, showed similar muscle transduction to other published myotropic AAVs, while being significantly more strongly liver-detargeted. We further examined the efficacy of LICA1, in comparison to AAV9, in delivering therapeutic transgenes in two mouse MD models at a low dose of 5E12 vg/kg. At this dose, AAV9 was suboptimal, while LICA1 transduced effectively and significantly better than AAV9 in all tested muscles. Consequently, LICA1 corrected the myopathology, restored global transcriptomic dysregulation, and improved muscle functionality. These results underline the potential of our design method for AAV engineering and demonstrate the relevance of the novel AAV variant for gene therapy treatment of MD.
Gut microbiota dysbiosis in hyperuricemia promotes renal injury through the activation of NLRP3 inflammasome
Authors: Zhou Xinghong , Ji Shuai , Chen Liqian , Liu Xiaoyu , Deng Yijian , You Yanting , Wang Ming , He Qiuxing , Peng Baizhao , Yang Ying , Chen Xiaohu , Kwan Hiu Yee , Zhou Lin , Chen Jieyu , Zhao Xiaoshan 
Published: October 2023

Abstract
Background
The prevalence of hyperuricemia (HUA), a metabolic disorder characterized by elevated levels of uric acid, is on the rise, and it is frequently associated with renal injury. Gut microbiota and gut-derived uremic toxins as the critical mediators in the gut-kidney axis that cause damage to kidney function. Gut dysbiosis has been implicated in various kidney diseases. However, the role of microbiota in HUA-induced renal injury and the underlying mechanism reminds unknown.
Results
Uricase-knockout(UOX−/−) rats is a model of HUA exhibited renal function impairment, renal tubular injury, fibrosis, activation of NLRP3 inflammasome and compromised intestinal barrier functions. The 16S rRNA sequencing and function prediction revealed an abnormal gut microbiota profile and activation of pathways associated with uremic toxin production. Metabolomic analysis further confirmed the increase of renal uremic toxins. To provide additional evidence, fecal microbiota transplantation (FMT) was conducted, where mice recolonized with HUA microbiota exhibited severe renal injury and compromised intestinal barrier functions following renal ischemia/reperfusion (I/R) surgery. Notably, in NLRP3-knockout (NLRP3-/-) I/R mice, the deleterious effects of HUA microbiota on renal injury and intestinal barrier were eliminated.
Conclusion
Our results demonstrate that HUA-induced gut dysbiosis promotes the development of renal injury, possibly by promoting the production of gut-derived uremic toxins and subsequently activating NLRP3 inflammasome. Our data suggest a potential therapeutic strategy for the treatment of renal disease by targeting the microbiota and NLRP3 inflammasome.
Acute Sodium Bicarbonate Administration Improves Ventilatory Efficiency in Experimental Respiratory Acidosis: Clinical Implications
Authors: Adrogué Horacio J. , Madias Nicolaos E. 
Published: October 2023

Abstract

Administering sodium bicarbonate (NaHCO3) to patients with respiratory acidosis breathing spontaneously is contraindicated because it increases carbon dioxide load and depresses pulmonary ventilation. Nonetheless, several studies have reported salutary effects of NaHCO3 in patients with respiratory acidosis but the underlying mechanism remains uncertain. Considering that such reports have been ignored, we examined the ventilatory response of unanesthetized dogs with respiratory acidosis to hypertonic NaHCO3 infusion (1 N, 5 mmol/kg) and compared it with that of animals with normal acid-base status or one of the remaining acid-base disorders. Ventilatory response to NaHCO3 infusion was evaluated by examining the ensuing change in PaCO2 and the linear regression of the PaCO2 vs. pH relationship. Strikingly, PaCO2 failed to increase and the ΔPaCO2 vs. ΔpH slope was negative in respiratory acidosis, whereas PaCO2 increased consistently and the ΔPaCO2 vs. ΔpH slope was positive in the remaining study groups. These results cannot be explained by differences in buffering-induced decomposition of infused bicarbonate or baseline levels of blood pH, PaCO2, and pulmonary ventilation. We propose that NaHCO3 infusion improved the ventilatory efficiency of animals with respiratory acidosis, i.e., it decreased their ratio of total pulmonary ventilation to carbon dioxide excretion (VE/VCO2). Such exclusive effect of NaHCO3 infusion in animals with respiratory acidosis might emanate from baseline increased VD/VT (dead space/tidal volume) caused by bronchoconstriction and likely reduced pulmonary blood flow, defects that are reversed by alkali infusion. Our observations might explain the beneficial effects of NaHCO3 reported in patients with acute respiratory acidosis.
Clinical mycology capacity and access to antifungal treatment in Portugal
Authors: Fernandes Raquel , Carvalho Agostinho , Salmanton-García Jon , Cunha Cristina , Sabino Raquel , Cornely Oliver 
Published: October 2023

Abstract
The success of the clinical management of invasive fungal diseases (IFD) is highly dependent on the availability of suitable tools for the timely and accurate diagnosis for effective treatment. Unfortunately, the lack of appropriate diagnostic tools remains still one major hurdle contributing to the high mortality rates associated with these infections. An in-depth analysis of the ability of European institutions to promptly and accurately diagnose IFD was previously conducted to identify limitations and aspects to improve. Here, we evaluated and discuss the specific case of Portugal, for which, to our knowledge, there are no reports describing the national mycological diagnostic capacity and access to antifungal treatments. Data from 16 Portuguese medical institutions were collected via an online electronic case report form covering different parameters, including institution profile, self-perceived IFD incidence, target patients, diagnostic methods and reagents, and available antifungals. The majority of participating institutions (69%) reported a low-very low incidence of IFD, with Candida spp. indicated as the most relevant fungal pathogen, followed by Aspergillus spp., and Cryptococcus spp. All the institutions had access to culture and microscopy, whereas 94% and 88% were able to run antigen-detection assays and molecular tests, respectively. Regarding the antifungal availability in the country, 100% of the institutions capable of providing antifungal therapy, declared to have access to at least one formulation. However, echinocandins were only available at 85% of the sites. Therapeutic drug monitoring (TDM) was reported to remain a very restricted practice in Portugal, being available in 19% of the institutions, with the TDM of itraconazole and posaconazole performed in only 6% of them. Importantly, despite some of these resources being well-represented among Portuguese institutions, most of them are outsourced to external entities. With the exception of TDM, Portugal appears to be well-prepared with regard to the overall capacity to diagnose and treat IFD. Future efforts should focus on promoting the widespread availability of TDM and improved access to multiple classes of antifungals, to further improve patient outcomes.
Identification and analysis of autophagy-related key genes in recurrent pregnancy loss based on integrative bioinformatics analysis
Authors: Zhuo Ai-Ping , Huang Wu-Jia , Tang Li-Chao , Gao Meng , Xie Jia-Xin , Wu Yan-Hong , Yang Ming-xin , Mao Meng-Li , Nie Jia , Fu Xia-Fei 
Published: October 2023

Abstract
Background
Recurrent pregnancy loss (RPL) is a common gynecological and obstetric condition. However, the molecular mechanisms underlying RPL remain unclear. Studies have suggested that autophagy plays an important role in the pathogenesis of RPL. Therefore, this study aimed to identify key genes related to autophagy in RPL using bioinformatics analysis.
Results
A total of 517 differentially expressed genes (DEGs) were identified with significant differences in expression between the RPL and control groups, including IRGQ, NCSTN, IRF2BP1, TSPAN14, PCGF1, ZNF90, PSIP1, SNRPE, LOC148709, and C2orf69. Six autophagy-related DEGs were screened and identified as hub genes, namely FAM115A, RGS11, TRIM59, CENPK, GLRX, and P2RY14, which can identify potential biomarkers for RPL. In addition, immune infiltration analysis revealed significant correlations between FAM115A, RGS11, TRIM59, and monocytes. In patients with RPL, the BILE ACID METABOLISM and KRAS SIGNALING DN signaling pathways were significantly upregulated, whereas FAM115A was associated with several pathways, including HALLMARK_XENOBIOTIC_METABOLISM. The RNA-binding protein (RBP)-mRNA network demonstrated a regulatory relationship between hub mRNA and its RBP, further revealing the correlation between them.
Conclusions
Six key hub DEGs related to autophagy in recurrent miscarriages were identified. These may serve as potential biomarkers with differential abilities in patients with RPL, further providing a theoretical basis for the prediction and diagnosis of the condition.
"Unusual" viral diseases after allogeneic hematopoietic stem cell transplantation: a multicenter, retrospective study
Authors: Lin Zhimin , Wu Yanjun , Zhang Yanming , Cao Junjie , Lin Guoqiang , Wang Tingjing , Xia Jing , Tang Xiaowen , Xue Shengli , Jin Zhengming , Wu Depei , Chen Feng , Zhao Ye 
Published: October 2023

Abstract
Objective
To observe the risk factors, clinical features, diagnosis and treatment, and prognosis of "unusual" viral diseases except "common" viruses such as cytomegalovirus (CMV) and Epstein-Barr virus (EBV) under the background of allogeneic hematopoietic stem cell transplantation dominated by haploidentical transplantation; to explore the optimal detection strategy for rare viruses.
Method
From April 2018 to June 2023, the "uncommon" virus disease cases other than CMV and EBV diagnosed in 3 transplant centers in China: the First Affiliated Hospital of Soochow University, the Second People's Hospital of Huai'an and the Affiliated People's Hospital of Ningbo University were retrospectively observed and analyzed.
Result
There were 10 cases of human adenovirus (HAdV) virus diseases, 7 cases of human herpesvirus 6 (HHV-6) virus diseases and 2 cases of human parvovirus B19 (HPV-B19) virus diseases. Up to the end of follow-up, 1 in 10 HAdV patients had survived and 9 had died, 8 of them died from viral infection and 1 died from recurrence of the primary disease. Of the 7 patients with HHV-6 virus, 6 survived and 1 died from recurrence of the primary disease. Of 2 patients with HPV-B19 virus, 1 survived and 1 died of HPV-B19 pneumonia.
Conclusion
CD3+T cells < 300 /ul, GVHD, ATG, the use of CD25 monoclonal antibody, pre-transplant chimeric antigen receptor T-Cell immunotherapy (CAR-T) or blinatumomab treatment history: may increase the risk of "unusual" viral disease; Pathogenic metagenomic next-generation sequencing(mNGS) of organ-specific samples has the best detection efficiency and can provide information about virus subtypes. The prognosis of HAdV-C infection and HPV-B19 systemic infection is poor, which should be paid more attention to, and high-risk patients should be screened as early as possible.
Intrinsic Piezoelectric Anisotropy of Tetragonal ABO3 Perovskites: A High-Throughput Study
Authors: Jia Fanhao , Xu Shaowen , Hu Shunbo , Chen Jianguo , Wang Yongchen , Li Yuan , Ren Wei , Cheng Jinrong 
Published: October 2023

Abstract

A comprehensive understand of the intrinsic piezoelectric anisotropy stemming from diverse chemical and physical factors is a key step for the rational design of highly anisotropic materials. We performed high-throughput calculations on tetragonal ABO3 perovskites to investigate the piezoelectricity and the interplay between lattice, displacement, polarization and elasticity. Among the 123 types of perovskites, the structural tetragonality is naturally divided into two categories: normal tetragonal (c/a ratio < 1.1) and super-tetragonal (c/a ratio > 1.17), exhibiting distinct ferroelectric, elastic, and piezoelectric properties. Charge analysis revealed the mechanisms underlying polarization saturation and piezoelectricity suppression in the super-tetragonal region, which also produces an inherent contradiction between high d33 and large piezoelectric anisotropy ratio |d33/d31|. The polarization axis and elastic softness direction jointly determine the maximum longitudinal piezoelectric response d33 direction. The validity and deficiencies of the widely utilized |d33/d31| ratio for representing piezoelectric anisotropy were reevaluated.
MIC-GDM Coupled Quantification Model: A New Data-Driven Approach to CBM Reservoir Potential Evaluation
Authors: Luo Jinhui , Chen Yuhua , Zhu Zhen , Wei Chongtao , Sun Luwei , Zhang Huashi , Zhang Huiyuan 
Published: October 2023

Abstract
In coalbed methane (CBM) development, it is imperative to evaluate the reservoir’s potential and identify the favorable areas to achieve higher production. This paper presents a novel quantified model inspired by the reservoir hydrodynamic heterogeneity. Treating the groundwater hydrodynamic zones as the computation units, the Maximal Information Coefficient (MIC) and the Geodetector Model (GDM) are applied to quantify the correlation and the degree of impact of the reservoir parameter on the average daily gas production, respectively. Afterward, an evaluation index system is established and its weight vector is obtained from a Game Theory (GT) model which couples the MIC scores with the GDM q-values. Taking the Gujiao mining area in the northern Qinshui Basin as an example, the reservoir potential classification of the proposed model demonstrates reliability compared to the prior studies and provides a deep insight into the relationship between CBM production and the reservoir heterogeneity. The reservoir spatial heterogeneity, i.e. the differences in hydrodynamics, lead to variations in the ranking of the primary impact factors and result in the uneven production. The model proposed in this study eliminates the subjective influence and can be applied to quantitatively evaluate geoscience issues that are impacted by spatial distribution heterogeneity.
Clinical Outcomes of Pediatric Patients on Topical Ruxolitinib for Acute and Chronic Skin GVHD
Authors: Hudda Zahra , Flannery Amanda , Teusink-Cross Ashley , Davies Stella , Khandelwal Pooja 
Published: October 2023

Abstract
Skin is commonly involved in acute and chronic graft versus host disease (GVHD). Ruxolitinib 1.5% cream is a topical Janus Kinase (JAK)1/2 inhibitor approved for atopic dermatitis and vitiligo but has not been evaluated for treatment of skin GVHD. We conducted a retrospective review of patients with acute or chronic skin GVHD who received topical ruxolitinib. Responses and adverse effects were reviewed. Ten patients, median age 11.5 years (range 0.9-37 years) with acute(n=7) or chronic(n=3) skin GVHD were treated with topical ruxolitinib. Topical ruxolitinib was applied to >20% BSA in all acute GVHD patients and 1 chronic GVHD patient. In 5 evaluable acute skin GVHD patients, 2 had a complete response, 2 had a partial response, and one patient did not respond to topical ruxolitinib. In 2 evaluable chronic GVHD patients, the maculopapular erythematous rash resolved in 1 patient and improved in 1 patient. No infections or allergic reactions to ruxolitinib cream was observed, despite exceeding 20% BSA application. Ruxolitinib topical cream is a promising treatment for acute skin GVHD and non-sclerotic chronic skin GVHD rash.
Test-time Self Supervision for Data Efficient and Cross-domain Robust Particle Tracking in Turbulent Flow
Authors: Zhang Yifei , Gao Huan-ang , Jiang Zhou , Zhao Hao 
Published: October 2023

Abstract
3D particle tracking velocimetry (PTV), which allows the determination of instantaneous velocity, is a key technique for analyzing 3D turbulent flow. While deep learning based methods have fostered advancements in the realm of 3D PTV, they remain heavily dependent on vast volumes of labeled data.This dependency is problematic considering the challenges of collecting particle sets in a large scale, especially when the data collection process is complex or the data itself is rare.Additionally, supervised learning excels primarily with in-domain data, and it may not exhibit the same efficacy with out-of-domain samples.To improve data efficiency and robustness, this paper introduces an innovative test-time self-supervised framework designed for the task of 3D PTV.Notably, we consider an extremely challenging setting of using only 1% data that previous methods use.However, drastically reducing the training samples to this extent can severely hurt performance. To alleviate this, we introduce the zero-divergence loss as an additional regularization mechanism, which draws inspiration from the inherent zero-divergence principle of incompressible fluid's velocity fields.To further enhance cross-domain robustness, we introduce a module named Dynamic Velocimetry Enhancer. During test-time, this module leverages a reconstruction loss to optimize the initial flow predicted by a trained network, enabling the estimated flow to better adjust to unseen samples.Through comprehensive experiments, we reveal that our novel test-time self-supervised framework notably outperforms fully-supervised counterparts with only 1% training samples used by previous methods.Additionally, our cross-domain robustness analysis confirms our framework can naturally generalize to new cases at the merit of test-time optimization. We finally present two evaluations on real-world data in the physical and biological domains, respectively, highlighting the valuable potential for applications in new, noisy real-world scenarios.