bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application
Authors: Martin Francis M. , van der Heijden Marcel G. A. 
Published: February 2024

SummaryMycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
Intracapsular accommodation mechanism in terms of lens curvature gradient
Authors: Lockett‐Ruiz Veronica , Navarro Rafael , López‐Gil Norberto 
Published: February 2024

AbstractThe intracapsular accommodation mechanism (IAM) may be understood as an increase in the lens equivalent refractive index as the eye accommodates. Our goal was to evaluate the existence of an IAM by analysing observed changes in the inner curvature gradient of the lens. To this end, we fitted a gradient index and curvature lens model to published experimental data on external and nucleus geometry changes during accommodation. For each case analysed, we computed the refractive power and equivalent index for each accommodative state using a ray transfer matrix. All data sets showed an increase in the effective refractive index, indicating a positive IAM, which was stronger for older lenses. These results suggest a strong dependence of the lens equivalent refractive index on the inner curvature gradient.
Scalable Au Metal-Assisted Chemical Etch Nanopatterning Using Enhanced Metal Break Techniques
Authors: Hrdy Mark , Mallavarapu Akhila , Castañeda Mariana , Ajay Paras , Sreenivasan S. V. 
Published: February 2024

Abstract
This paper presents catalyst patterning techniques for promoting wafer-scale uniformity while producing taper-free high aspect ratio Si nanostructures using gold (Au) metal-assisted chemical etch (MacEtch). Typical Au nanopatterning involves the use of liftoff processes which have poor yield in manufacturing settings. We report a technique that takes advantage of adhesive forces during MacEtch to mechanically break the metal catalyst over a patterned resist. Three methods for generating increased uniformity are demonstrated—(i), (ii), (iii). Using these methods, taper-free 100 nm nanopillars are presented with wafer-scale uniformity using techniques that can be readily implemented for scalable nanomanufacturing.
Modelling of the Hypervelocity Impact Performance of a Corrugated Shield with an Integrated Honeycomb Geometry
Authors: Dumitrescu Adrian , Walker Scott J. I. , Bhaskar Atul 
Published: February 2024

Abstract
In the context of spacecraft protection from orbital debris, a wide variety of shield designs revolving around multi shock panels (MSP) has been previously investigated. In parallel with these purpose-built shields there has been work done on understanding the protection capabilities of CFRP-AL honeycomb structures which are also impacted. A widely held view is that a honeycomb core sandwich panel performs poorly under hypervelocity impact (HVI), especially at low impact angles. By contrast, an MSP is very effective in dispersing the impact energy and stopping the projectile across a wide range of impact angles. The objective of this paper is to better understand the relative impact performance between multi shock panels and shields which contain honeycomb geometries in order to more effectively make use of the satellite structure in protecting the components inside a satellite. This research explores a novel shield geometry which combines a multi shock panel with corrugated walls with a honeycomb core in a design that can perform well both structurally and in impact.
Expression activation of over 70% of
Chlamydia trachomatis
genes during the first hour of infection
Authors: Wurihan Wurihan , Wang Yuxuan , Yeung Sydney , Zou Yi , Lai Zhao , Fondell Joseph D. , Li Wei Vivian , Zhong Guangming , Fan Huizhou 
Published: February 2024

ABSTRACT

The obligate intracellular bacterium
Chlamydia
has a unique developmental cycle that alternates between two contrasting cell types. With a hardy envelope and highly condensed genome, the small elementary body (EB) maintains limited metabolic activities yet survives in extracellular environments and is infectious. After entering host cells, EBs differentiate into larger and proliferating reticulate bodies (RBs). Progeny EBs are derived from RBs in late developmental stages and eventually exit host cells. How expression of the chlamydial genome consisting of nearly 1,000 genes governs the chlamydial developmental cycle is unclear. A previous microarray study identified only 29
Chlamydia trachomatis
immediate early genes, defined as genes with increased expression during the first hour postinoculation in cultured cells. In this study, we performed more sensitive RNA sequencing (RNA-Seq) analysis for
C. trachomatis
cultures with high multiplicities of infection. Remarkably, we observed well over 700
C
.
trachomatis
genes that underwent 2- to 900-fold activation within 1 hour postinoculation. Quantitative reverse transcription real-time PCR analysis was further used to validate the activated expression of a large subset of the genes identified by RNA-Seq. Importantly, our results demonstrate that the immediate early transcriptome is over 20 times more extensive than previously realized. Gene ontology analysis indicates that the activated expression spans all functional categories. We conclude that over 70% of
C. trachomatis
genes are activated in EBs almost immediately upon entry into host cells, thus implicating their importance in initiating rapid differentiation into RBs and establishing an intracellular niche conducive with chlamydial development and growth.
Draft genome of
Chloroflexu
s sp. MS-CIW-1, of the
Chloroflexus
sp. MS-G group from Mushroom Spring, Yellowstone National Park
Authors: Shelton Amanda N. , Yu Feiqiao B. , Bunbury Freddy , Yan Jia , Rivas Carlos , Grossman Arthur , Bhaya Devaki 
Published: February 2024

ABSTRACT

Chloroflexus
sp. MS-CIW-1 was isolated from a phototrophic mat in Mushroom Spring, an alkaline hot spring in Yellowstone National Park, WY, USA. We report the draft genome of 4.8 Mb consisting of 6 contigs with 3755 protein-coding genes and a GC content of 54.45%.
Tubercidin inhibits PRRSV replication via RIG-I/NF-κB pathways and interrupting viral nsp2 synthesis
Authors: Xu Yuqian , Zhu Zhenbang , Zhang Meng , Chen Lulu , Tian Kegong , Li Xiangdong 
Published: February 2024

ABSTRACT

Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus with constantly emerging recombinant and mutant strains. Because of the high genetic diversity of PRRSV, current vaccines only provide partial protection against the infection of heterologous strains, which makes it a challenge for PRRSV prevention and control. Tubercidin is a naturally extracted compound with potential antiviral properties. However, whether tubercidin has anti-PRRSV ability is unknown. Our study found that tubercidin showed effective antiviral effects on PRRSV replication. In terms of mechanism, tubercidin suppressed PRRSV at the entry, replication, and release steps of the viral life cycle. Additionally, we demonstrated that tubercidin treatment promoted the activation of retinoic acid-inducible gene I and nuclear factor kappa-light-chain-enhancer of activated B cell signaling pathway, thus increasing the type I interferon and inflammatory cytokine expression. Furthermore, tubercidin restrained the viral non-structural protein 2 expression and viral dsRNA synthesis and ultimately inhibited PRRSV replication. Hence, our data showed that tubercidin is promising and has potential antiviral ability against PRRSV replication
in vitro
.

IMPORTANCE

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important swine diseases, which causes huge economic loss worldwide. However, there is no effective therapeutic method for PRRS prevention and control. Here, we found that tubercidin, a naturally extracted adenosine analog, exhibited strong anti-porcine reproductive and respiratory syndrome virus (PRRSV) activity. Mechanically, tubercidin inhibited viral binding, replication, and release. Tubercidin suppressed PRRSV non-structural protein 2 expression, which is important for the formation of replication and transcription complex, leading to the block of viral RNA synthesis and PRRSV replication. Moreover, tubercidin could activate retinoic acid-inducible gene I/nuclear factor kappa-light-chain-enhancer of activated B cell innate immune signaling pathway and increased the expression of interferons and proinflammatory cytokines, which was the other way to inhibit PRRSV replication. Our work evaluated the potential value of tubercidin as an antiviral agent on PRRSV replication and provided a new way to prevent PRRSV replication
in vitro
.
Machine learning based on blood test biomarkers predicts fast progression in advanced NSCLC patients treated with immunotherapy
Authors: Zhou Jian-Guo , Yang Jie , Wang Haitao , Wong Ada Hang-Heng , Tan Fangya , Chen Xiaofei , He Si-Si , Shen Gang , Wang Yun-Jia , Frey Benjamin , Fietkau Rainer , Hecht Markus , Zhong Wenzhao , Ma Hu , Gaipl Udo 
Published: February 2024

ObjectiveFast progression (FP) represents a desperate situation for advanced non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor therapy. We aimed to develop a predictive framework based on machine learning (ML) methods to identify FP in advanced NSCLC patients using blood test biomarkers.Methods and analysisWe extracted data of 1546 atezolizumab-treated patients from four multicentre clinical trials. In this study, patients from the OAK trial were taken for model training, whereas patients from the other trials were used for independent validations. The FP prediction model was developed using 21 pretreatment blood test variables in seven ML approaches. Prediction performance was evaluated by the receiver operating characteristic (ROC) curve.ResultsThe prevalence of FP was 7.6% (118 of 1546) in all atezolizumab-treated patients. The most important variables for the prediction model were: C reactive protein, neutrophil count, lactate dehydrogenase and alanine transaminase. The Support Vector Machine (SVM) algorithm applied to these four blood test parameters demonstrated good performance: the area under the ROC curve obtained from the training cohort (OAK), validation cohort 1 (BIRCH) and cohort 2 (merged POPLAR and FIR) were 0.908, 0.666 and 0.776, respectively. In addition, the absolute difference in median survival between the SVM-predicted FP and non-FP groups was significant in both progression-free survival and overall survival (p<0.001).ConclusionSVM trained using a 4-biomarker panel has good performance in predicting the occurrence of FP regardless of programmed cell death ligand 1 expression, hence providing evidence for decision-making in single-agent atezolizumab immunotherapy for patients with advanced NSCLC.
Impact of biological therapy in reducing the risk of arthritis development in inflammatory bowel diseases
Authors: Fatica Mauro , Monosi Benedetta , Conigliaro Paola , D’Antonio Arianna , Essofi Sara , Cuccagna Elisa , Bergamini Alberto , Biancone Livia , Monteleone Giovanni , Triggianese Paola , Calabrese Emma , Chimenti Maria Sole 
Published: February 2024

ObjectiveEvaluate spondyloarthritis (SpA) incidence in inflammatory bowel diseases (IBD) between patients treated with biological disease-modifying antirheumatic drugs (bDMARDs) and conventional DMARDs (cDMARDs) and define risk factors associated with SpA development.MethodsRetrospective cohort study was conducted on patients with Crohn’s disease (CD) or ulcerative colitis (UC) and divided into two cohorts: cDMARDs or bDMARDs/targeted synthetic (ts) DMARDs treated patients. Rheumatological assessment was performed in patients presenting musculoskeletal symptoms. Multivariate analysis and Kaplan-Meier curves were used to evaluate the adjusted SpA risk development.Results507 patients were included in the study. 176 patients with CD received bDMARDs, 112 cDMARDs and 106 new SpA diagnosies were formulated. Females (OR 1.7 (95% CI 1.1 to 3), adjusted p=0.04), non-stricturing/non-penetrating phenotype (OR 2 (95% CI 1.1 to 3.4), adjusted p=0.01), psoriasis (OR 2.1 (95% CI 1 to 4.6), adjusted p=0.04) and non-infectious uveitis (OR 6.8 (95% CI 1.4 to 33.4), adjusted p=0.01) were associated with increased SpA risk development, while bDMARDs usage was protective (OR 0.4 (95% CI 0.2 to 0.8), adjusted p=0.01), statistically higher than cDMARDs throughout the entire follow-up (effect size 0.47). 98 patients with UC received b-tsDMARDs, 121 cDMARDs and 56 new SpA diagnoses were formulated. Females (OR 2.1 (95% CI 1 to 4.3), adjusted p=0.02) and psoriasis (OR 2.7 (95% CI 1 to 6.8), adjusted p=0.03) were associated with increased SpA risk development, while bDMARDs were protective for SpA development for up to 12 months of treatment compared with cDMARDs (p=0.03).ConclusionsbDMARDs treatment had an impact in reducing SpA development and clinical associated risk factors to transition from IBD to IBD-SpA emerged.
CHinese Acute Tissue-Based Imaging Selection for Lysis In Stroke Tenecteplase II (CHABLIS-T II): rationale and design
Authors: Cheng Xin , Hong Lan , Lin Longting , Churilov Leonid , Ling Yifeng , Zhang Yiran , Yang Lumeng , Parsons Mark , Dong Qiang 
Published: February 2024

Background and purposeTenecteplase (TNK) has demonstrated non-inferiority to alteplase in patients who had an acute ischaemic stroke presenting within 4.5 hours from symptom onset. The trial is aimed to explore the efficacy and safety of TNK in Chinese patients who had an acute ischaemic stroke with large/medium vessel occlusion in an extended time window.Methods and designChinese Acute Tissue-Based Imaging Selection for Lysis In Stroke Tenecteplase II (CHABLIS-T II) is a multicentre, prospective, block-randomised, open-label, blinded-endpoint, phase IIb study. Eligible patients are 1:1 randomised into two groups: 0.25 mg/kg TNK versus best medical management (excluding TNK). The safety and efficacy of 0.25 mg/kg TNK are assessed through reperfusion status and presence of symptomatic intracranial haemorrhage (sICH).Study outcomesThe primary outcome is major reperfusion without sICH at 24–48 hours after randomisation. Major reperfusion is defined as restoration of blood flow to greater than 50% of the involved ischaemic territory assessed by catheter angiography or repeated perfusion imaging. Secondary outcomes include post-thrombolytic recanalisation, neurological improvements, change in the National Institutes of Health Stroke Scale score, haemorrhagic transformation at 24–48 hours, systematic bleeding at discharge, modified Rankin Scale (mRS) 0–1, mRS 0–2, mRS 5–6, mRS distribution and Barthel index at 90 days.DiscussionCHABLIS-T II will provide important evidence of intravenous thrombolysis with TNK for patients who had an acute stroke in an extended time window.
Repeated short cold-water immersions are sufficient to habituate to the cold, but do not lead to adaptations during exercise in normobaric hypoxia
Authors: Dorsett Geoffrey , Pereira Felipe Gorini , Kuennen Matthew , Waugh Kyren , Barnard Jackson , Bennett Jonluke , Garcia Gabriel , Gillum Trevor 
Published: February 2024

We sought to assess the effects of repeated cold-water immersions (CWI) on respiratory, metabolic, and sympathoadrenal responses to graded exercise in hypoxia. Sixteen (2 female) participants (age: 21.2 ±   1.3 years; body fat: 12.3 ± 7.7%; body surface area 1.87 ± 0.16 m2, VO2peak: 48.7 ± 7.9 mL/kg/min) underwent 6 CWI in 12.0 ± 1.2 °C. Each CWI was 5 min, twice daily, separated by ≥4 h, for three consecutive days, during which metabolic data were collected. The day before and after the repeated CWI intervention, participants ran in normobaric hypoxia (FIO2 = 0.135) for 4 min at 25%, 40%, 60%, and 75% of their sea level peak oxygen consumption (VO2peak). CWI had no effect on VO2 ( p > 0.05), but reduced the VE (CWI #1: 27.1 ± 17.8 versus CWI #6: 19.9 ± 12.1 L/min) ( p < 0.01), VT (CWI #1: 1.3 ± 0.4 vs CWI #6: 1.1 ± 0.4 L) ( p < 0.01), and VE:VO2 (CWI #1: 53.5 ± 24.1 vs CWI #6: 41.6 ± 20.5) ( p < 0.01) during subsequent CWI. Further, post exercise plasma epinephrine was lower after CWI compared to before (103.3 ± 43.1; 73.4 ± 34.6 pg/mL) ( p = 0.03), with no change in pre-exercising values (75.4 ± 30.7; 72.5 ± 25.9 pg/mL). While these changes were noteworthy, it is important to acknowledge there were no changes in pulmonary ( VE, VT, and VE:VO2) or metabolic (VO2, SmO2, and SpO2) variables across multiple hypoxic exercise workloads following repeated CWI. CWI habituated participants to cold water, but this did not lead to adaptations during exercise in normobaric hypoxia.
Axial–Radial–Ulnar Carpal Dislocation with Divergent Intermetacarpal Dislocations, Peritrapezoid and Scaphotrapezial Dislocations: A Case Report
Authors: MATTIA Alexzandra , BUCHANAN Patrick J. , CHOPAN Mustafa , CHIM Harvey 
Published: February 2024

We report a patient with a severe axial–radial–ulnar (ARU) fracture dislocation of the carpus, involving multiple intermetacarpal dislocations as well as divergent carpometacarpal dislocations involving the index, long, ring and small fingers and peritrapezoid and scaphotrapezial dislocations. She also had a degloving injury involving the dorsal hand. Emergent debridement followed by open reduction and internal fixation of all injuries was performed, followed by soft tissue management. At 6-year follow-up, the patient had adequate active range of motion with the ability to make a full fist and was able to use her wrist and hand for most activities of daily living. Disabilities of the arm, shoulder and hand (DASH) score was 47.5. Michigan hand outcomes questionnaire (MHQ) score was 66.8. Mayo wrist score was 65. Patient-rated wrist evaluation (PRWE) score was 42. Severe ARU fracture dislocations of the carpus can result in adequate functional recovery on long-term follow-up. Level of Evidence: Level V (Therapeutic)
Challenges and Solutions in Prosthetic Fitting of Digits after Flap Reconstruction
Authors: LEOW Michael E. L. , DAS DE Soumen , PUHAINDRAN Mark E. , CHONG Alphonsus K. S. 
Published: February 2024

Surgical reconstruction can restore length and function, but cannot adequately resolve the problem of disfigurement. Prosthetic fitting can play a complementary role in enhancing the aesthetic outcomes post reconstruction. However, complex reconstruction involving flaps coupled with the surgical imperative for limb length preservation can lead to outcomes where the reconstructed stumps are challenging to fit with prosthesis. This article describes how prosthetic fitting was tackled in a case of a triple-digit amputation after reconstruction that presented with finger stumps that were bulky, long and stiff in extension contracture, compounded by the presence of substantive scar tissues. We discuss major prosthesis modifications that were unconventional but necessary to enable fitting, the techniques involved, as well as the aesthetic and functional considerations behind the modifications. The results showed that enhanced aesthetic appearance, together with a marginal improvement in hand function, was achieved post-prosthetically, meeting the patient’s and the clinical team’s fitting objective. Level of Evidence: Level V (Therapeutic)
Abstract A012: Molecular profiling of neoductgenesis in early stage breast cancer for the development of novel diagnostic biomarkers
Authors: Lehtinen Laura , Koskinen Leena , Peurla Markus , Huotari Emilia , Kauko Otto , Dean Peter , Hartiala Pauliina , Boström Pia , Peuhu Emilia 
Published: February 2024

Abstract
Ductal carcinoma in situ (DCIS) is the most common precancerous finding in mammography screens. DCIS generally has a good prognosis, and only 20-25% of the cases progress to invasive breast carcinoma (IBC) even if left untreated. Breast pathologists and radiologists have suggested that there are currently more than one kind of DCIS under the same diagnosis. A subset of DCIS cases with reduced survival rate are associated with casting-type calcifications that can be histologically detected within closely packed, contorted, newly formed ducts, a phenomenon called neoductgenesis. Tumors with neoductgenesis are often erroneously diagnosed as DCIS, while in fact, they are associated with higher degree of metastasis and should be considered invasive carcinomas. This tumor category currently lacks specific histopathological markers and the biological processes leading to metastasis via neoductgenesis remain poorly characterised. To reveal new information of this breast tumor type, we are currently conducting comprehensive characterization of FFPE tissue samples of DCIS cases with and without neoductgenesis using imaging mass cytometry analysis and immunohistochemistry of specific tumor areas. Preliminary results on immunofluorescence staining suggest that neoductgenesis is associated with changes in the expression of specific myoepithelial marker proteins compared to areas with pure DCIS. In addition, we are analysing the three-dimensional ductal architecture of these lesions. The information obtained from this study can lead to development of new diagnostic tools for the identification of early breast cancers with a higher risk of spreading. Early detection of these cases is important to ensure the effectiveness and timeliness of treatment, and at the same time to improve the patients' quality of life.
Citation Format: Laura Lehtinen, Leena Koskinen, Markus Peurla, Emilia Huotari, Otto Kauko, Peter Dean, Pauliina Hartiala, Pia Boström, Emilia Peuhu. Molecular profiling of neoductgenesis in early stage breast cancer for the development of novel diagnostic biomarkers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A012.