bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic analysis of early ST32 Acinetobacter baumannii strains recovered in US military treatment facilities reveals distinct lineages and links to the origins of the Tn6168 ampC transposon
Authors: Tobin Liam A , Abu Sabah Eradah , Lebreton Francois , Myers Garry S A , McGann Patrick T , Hamidian Mehrad 
Published: December 2024

Abstract

Objectives
To study the population structure and genomic characteristics, including antimicrobial resistance genes, plasmid types and surface polysaccharide type, of the globally distributed Acinetobacter baumannii belonging to ST32 (Institut Pasteur scheme).

Methods
Antibiotic resistance phenotype for 19 antibiotics was determined using Vitek 2. Whole-genome sequencing was performed using the Illumina MiSeq platform. Genomes were assembled using Newbler. Phylogenetic analysis was done by determining the core-genome alignments using Panaroo v1.3, analysed in IQ-Tree2 v2.2.0.3 to construct Maximum Likelihood trees using the RaxML software. Resistance genes and IS were identified using the Abricate programme, and ISFinder databases.

Results
One hundred and thirty-three (n = 133) ST32 A. baumannii isolates were analysed in this study. These genomes originated mainly from US military treatment facilities (n = 113), but also included additional publicly available genomes in GenBank (n = 20) recovered from a broad geographic distribution extending to Asia and South America. Phylogenetic analysis of all 133 genomes revealed at least four clades, with over 80 genomes forming a tightly clustered branch, suggesting they are likely to represent outbreak strains. Analysis of the ampC region showed that ST32 strains played a significant role in the formation of the widely distributed ampC transposon, Tn6168, and supplying DNA segments containing an ISAba1-ampC from ST32s via homologous recombination.

Conclusions
ST32 strains played a significant role in the evolution of antibiotic resistance in several widely distributed sequence types including ST1 (global clone 1) and ST3.
Impact of Fusobacterium nucleatum in the treatment of cancer, including radiotherapy and its future potential in esophageal cancer
Authors: Ohsawa Manato , Nishi Hiromi , Emi Manabu , Yoshikawa Toru , Hamai Yoichi , Ibuki Yuta , Kurokawa Tomoaki , Hirohata Ryosuke , Kitasaki Nao , Kawada-Matsuo Miki , Komatsuzawa Hitoshi , Kawaguchi Hiroyuki , Okada Morihito 
Published: December 2024

Abstract
Despite advances in multimodality therapy, including surgery, chemotherapy, radiation therapy and chemoradiation, the fatality rate for esophageal cancer remains high. Specifically, Fusobacterium nucleatum, due to its aggregation capacity, has shown a tendency to form biofilms. The biofilm-forming capabilities of microbial communities are of utmost importance in the context of cancer treatment, as they have been shown to drive significant losses in the efficaciousness of various cancer treatments. Therefore, elucidating the dynamics of F. nucleatum will be important for the development of effective treatments for esophageal cancer. Therefore, this review summarizes the current knowledge of F. nucleatum, its involvement in cancer and its impact on chemotherapy and radiation therapy. In conclusion, further research on the role of F. nucleatum is essential for the continued advancement of the treatment of esophageal cancer and patient care.
Time-resolved transcriptomics of single Vitis vinifera fruits: membrane transporters as switches of the double sigmoidal growth
Authors: Savoi Stefania , Shi Mengyao , Sarah Gautier , Weber Audrey , Torregrosa Laurent , Romieu Charles 
Published: December 2024

Abstract
Grape berries lose one H+ per accumulated sucrose at the inception of ripening, but the molecular mechanisms associated with this remain unknown. By investigating single fruits, we elucidated the fundamentals of the malate-sugar nexus, previously obscured by asynchrony in population-based models of ripening. The development of individual fruits was explored to capture simultaneous changes in gene expression and metabolic fluxes from flowering to overripening. Dynamics in water, tartrate, malate, hexoses, and K+ fluxes obtained by combining individual single fruit growth and concentration data, allowed us to define eleven sub-phases in fruit development, with defined groups according to RNA sequencing analysis. Co-expression network analysis revealed a range of transcript level-metabolic rate associations. A set of membrane transporters related to vacuolar over-acidification was found specifically expressed during the first growth phase. Unlike in slightly more acidic citrus, vacuolar H+-pyrophosphatase transcripts were predominantly expressed, followed by vacuolar ATPase, clarifying a thermodynamic limit beyond which their replacement by the tonoplast P3A/P3B ATPase complex is essential. Unexpectedly, expression of aluminium-activated malate transporter was low at this stage, possibly replaced by an uncharacterized anion channel. At the onset of ripening, the role of hexose transporter HT6 as a molecular switch in sugar accumulation was confirmed, electroneutralized by malate vacuolar leakage and H+ pumps activation.
A modular toolbox for the optogenetic deactivation of transcription
Authors: Muench Philipp , Fiumara Matteo , Southern Nicholas , Coda Davide , Aschenbrenner Sabine , Correia Bruno , Gräff Johannes , Niopek Dominik , Mathony Jan 
Published: December 2024

Abstract
Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered induction of gene expression. Here, we inverted this mode of action and created optogenetic systems capable of efficiently terminating transcriptional activation in response to blue light. First, we designed highly compact regulators by photo-controlling the VP16 (pcVP16) transactivation peptide. Then, applying a two-hybrid strategy, we engineered LOOMINA (light off-operated modular inductor of transcriptional activation), a versatile transcriptional control platform for mammalian cells that is compatible with various effector proteins. Leveraging the flexibility of CRISPR systems, we combined LOOMINA with dCas9 to control transcription with blue light from endogenous promoters with exceptionally high dynamic ranges in multiple cell lines. Functionally and mechanistically, the versatile LOOMINA platform and the exceptionally compact pcVP16 transactivator represent valuable additions to the optogenetic repertoire for transcriptional regulation.
Impact of resection location on depressive symptoms following glioma surgery
Authors: Belgers Vera , van Genderen Maisa N G , de Schotten Michel Thiebaut , Cakmak Marcus , Douw Linda , Ferles Alexandros , Barkhof Frederik , Klein Martin , Niers Johanna M , Eijgelaar Roelant S , de Witt Hamer Philip C 
Published: December 2024

Abstract

Background
Glioma surgery aims to maximize tumor removal while preserving functional integrity. Functional outcome usually focuses on neurological and neurocognitive functions, but surgery may also affect mood regulation. We determined the occurrence of depressive symptoms after surgery and investigated associated factors, including preoperative depressive symptoms and the location of the resection.

Methods
We included a single-center retrospective cohort of patients with supratentorial diffuse glioma (WHO grade 2-4) who underwent first-time surgical resection between 2009 and 2021 and who completed the Center for Epidemiologic Studies Depression Scale (CES-D) before and one year after surgery. Resection cavities were segmented on postoperative MRI scans. White matter disconnections were computed, the so-called disconnectome, to examine distant effects. Multivariable regression analysis was used to relate patient, tumor, and treatment characteristics to postoperative depression scores and changes after surgery. Lesion symptom mapping was used to relate resection and disconnectome locations to these scores and changes.

Results
We included 83 patients. Before surgery, 25% of patients had depressive symptoms and one year after surgery 34%, which was not statistically different. Resections of gliomas in the right hemisphere were significantly associated with increased depression scores after surgery. A resection involving the left anterior temporal region was significantly associated with low postoperative depression scores. Disconnectome locations were not associated with either postoperative or change in depression scores.

Conclusions
Resection locations affect depressive symptoms in glioma patients. This information may be useful for patient counseling
News about the economy: a literature survey and methodological guidelines
Authors: Garz Marcel 
Published: December 2024

Abstract
This article surveys the economic literature on the role of mass media and social media for the dissemination of news about gross domestic product (GDP), inflation, unemployment and the economy at large. Focusing on studies that use media content data, two key insights emerge. First, identical macroeconomic facts may receive different levels of attention and can be framed in different ways, depending on political and psychological factors. Second, information spread by mass media and on social media may affect economic outcomes independent of the facts on the ground. These and other findings in the literature have helped to refine various theories in behavioral economics, finance, macroeconomics and other fields. The article also identifies untapped research potential and formulates specific recommendations for future studies, especially in terms of underutilized sources of media content data, the application of computational methods (e.g. large language models, image classification, emotion recognition) and econometric designs supporting causal inference.
Prospects for high-throughput estimates of photosynthetic parameters in tropical trees using the Dynamic Assimilation™ Technique
Authors: Braun Emmelia J , Southwick Charles D , Garcia Maquelle N , Taylor Tyeen C , Acebron Kelvin , Rodrigues João Victor F C , Ferreira Marciel J , de Oliveira Jr Raimundo Cosme , Albert Loren P 
Published: December 2024

Abstract
Amazônia is a species-rich region of immense importance to Earth’s water and carbon cycling. Photosynthesis drives the global carbon cycle, so understanding photosynthetic differences across diverse landscapes is a key task of ecophysiology and ecosystem science. Unfortunately, due to physiological and logistical constraints, ground-based photosynthesis data in Amazônia remains scarce, and the ‘traditional’ steady-state method (SS) of gas exchange is slow and inefficient. The Dynamic Assimilation™ Technique (DAT; Saathoff and Welles 2021) promises a new way to perform A/Ci curves rapidly without requiring steady-state conditions. Thus far, this technique has only been validated in greenhouse or agricultural-field-grown species and has yet to be tested in forest trees of diverse physiology, morphology, and environmental adaptation. To test the utility of the DAT in a complex tropical forest ecosystem, we compared the DAT to the SS method in 13 Amazonian trees in situ. We found strong agreement between Vcmax from DAT curves and SS curves, while Jmax was underestimated in DAT curves. We conclude that the DAT provides a robust and rapid estimation of Vcmax. We also identified diverse and unexpected DAT curve shapes among some trees, including the presence of an ‘overshoot’ in assimilation beyond model-derived RuBP regeneration limitations. The presence of overshoot may elucidate microclimate and species differences in RuBP regeneration rates and emphasizes the considerable importance of DAT curve protocol specifications, such as the effect of ramp rate and direction on Jmax and TPU. Overall, the DAT saved time relative to the SS method and proved to be an effective and rapid method for quantifying Vcmax in tropical trees.
FAPs orchestrate homeostasis of muscle physiology and pathophysiology
Authors: Yin Kai , Zhang Chengmin , Deng Zihan , Wei Xiaoyu , Xiang Tingwen , Yang Chuan , Chen Can , Chen Yueqi , Luo Fei 
Published: December 2024

AbstractAs a common clinical manifestation, muscle weakness is prevalent in people with mobility disorders. Further studies of muscle weakness have found that patients with muscle weakness present with persistent muscle inflammation, loss of muscle fibers, fat infiltration, and interstitial fibrosis. Therefore, we propose the concept of muscle microenvironment homeostasis, which explains the abnormal pathological changes in muscles through the imbalance of muscle microenvironment homeostasis. And we identified an interstitial progenitor cell FAP during the transition from normal muscle microenvironment homeostasis to muscle microenvironment imbalance caused by muscle damage diseases. As a kind of pluripotent stem cell, FAPs do not participate in myogenic differentiation, but can differentiate into fibroblasts, adipocytes, osteoblasts, and chondrocytes. As a kind of mesenchymal progenitor cell, it is involved in the generation of extracellular matrix, regulate muscle regeneration, and maintain neuromuscular junction. However, the muscle microenvironment is disrupted by the causative factors, and the abnormal activities of FAPs eventually contribute to the complex pathological changes in muscles. Targeting the mechanisms of these muscle pathological changes, we have identified appropriate signaling targets for FAPs to improve and even treat muscle damage diseases. In this review, we propose the construction of muscle microenvironmental homeostasis and find the key cells that cause pathological changes in muscle after homeostasis is broken. By studying the mechanism of abnormal differentiation and apoptosis of FAPs, we found a strategy to inhibit the abnormal pathological changes in muscle damage diseases and improve muscle regeneration.
Examining the Interactive Associations of Cannabis and Alcohol Outlets With Self-harm Injuries in California: A Spatiotemporal Analysis
Authors: Charris Rafael , Ahern Jennifer , Apollonio Dorie E. , Jent Victoria , Jacobs Laurie M. , Jung Shelley , Schmidt Laura A. , Gruenewald Paul , Matthay Ellicott C. 
Published: December 2024

Background:
Cannabis use and alcohol use are associated with self-harm injuries, but little research has assessed links between recreational cannabis outlet openings on rates of self-harm within communities or the interactions of cannabis outlets with the density of alcohol outlets. We estimated the associations of recreational cannabis outlets, alcohol outlets, and their interaction on rates of fatal and nonfatal self-harm injuries in California, 2017–2019.

Methods:
Using California statewide data on recreational cannabis outlets, alcohol outlets, and hospital discharges and deaths due to self-harm injuries, we conducted Bayesian spatiotemporal analyses of quarterly ZIP code-level data over 3 years, accounting for confounders and spatial autocorrelation. Using the model posteriors, we estimated parameters corresponding to hypothetical shifts in outlet densities.

Results:
If recreational cannabis outlets had never opened, we estimated that nonfatal self-harm injuries would have been −0.35 per 100,000 lower (95% credible interval [CI]: −1.25, 0.51), while fatal self-harm injuries would have been −0.004 per 100,000 lower (95% CI: −0.26, 0.25). These associations did not depend on alcohol outlet density, but a hypothetical 20% reduction in alcohol outlet densities was associated with fewer self-harm injuries (risk difference per 100,000, nonfatal: −1.59; 95% CI: −2.60, −0.59; fatal: −0.10; 95% CI: −0.37, 0.16). Associations for nonfatal incidents were strongest for people aged 15–34 years, and White and Hispanic people.

Conclusion:
We did not find evidence that the introduction of recreational cannabis outlets was associated with self-harm injuries or that cannabis and alcohol outlet densities interact, but alcohol outlet density had a strong association with nonfatal self-harm injuries.
Integrating network pharmacology and in vivo pharmacological investigation for deciphering the mechanism of Simiao Yong’an decoction in alleviating rheumatoid arthritis
Authors: Jie Shanshan , Gao Yan , Sun Huijuan , Zhao Hongyan , Zhao Yukun , Chen Chen , Zeng Hui , Ma Yaluan 
Published: December 2024

Objective:
To investigate the mechanism of Simiao Yong’an Decoction in alleviating the damage of rheumatoid arthritis (RA), and accordingly provide pharmacological evidence and further experimental support for the application of Simiao Yong’an Decoction, as well as provide a reference direction for the development of new drugs for RA treatments.

Materials and methods:
Arthritis was induced in Balb/c mice. The animals were randomly divided into 4 groups: control, model, methotrexate (MTX), and Simiao Yong’an Decoction group (n = 6). The Simiao Yong’an Decoction group was orally administered 4.5 g·kg−1 of Simiao Yong’an Decoction every day, and the MTX group received a single intraperitoneal injection of 2 mg·kg−1 of MTX. The arthritis symptoms of joints were scored every day after injecting a cocktail antibody. The histopathology injuries and bone destruction of joints were measured by hematoxylin and eosin staining, Safranin-O fast green staining, tartrate-resistant acid phosphatase staining, and micro–computed tomography. The regulation of Simiao Yong’an Decoction on leukocytes was analyzed by flow cytometry. The expression of inflammatory cytokines, chemokines, and matrix metalloproteinases in joints was detected by quantitative real-time polymerase chain reaction. In the network pharmacology analysis, drug targets of Simiao Yong’an Decoction were obtained from Swiss Target Prediction. Disease targets of RA were obtained from the Therapeutic Target Database and Disgenet. The ingredients-targets network, protein-protein interaction network, and gene ontology function enrichment were performed and visualized by Cytoscape software.

Results:
In the collagen antibody-induced arthritis (CAIA) murine model, Simiao Yong’an Decoction effectively improved arthritis symptoms, decreased the expression of inflammatory cytokines, and reduced joint pathologic damage and bone destruction. In the network pharmacology analysis, multiple active ingredients of Simiao Yong’an Decoction were found to regulate genes related to inflammation, chemotaxis, and collagen degradation in RA, and reduce RA damage by regulating biological processes including leukocyte migration, myeloid cell homeostasis, and collagen degradation metabolism. We further verified that Simiao Yong’an Decoction effectively regulated the number of myeloid cells in CAIA mice. Moreover, Simiao Yong’an Decoction suppressed the expression of myeloid cell-associated chemokines and matrix metalloproteinases in inflamed joints of CAIA mice.

Conclusion:
Simiao Yong’an Decoction effectively reduces RA damage by regulating myeloid cells and reducing collagen degradation.
The implementation of infant pain practice change resource to improve infant procedural pain practices: a hybrid type 1 effectiveness-implementation study
Authors: Stevens Bonnie , Bueno Mariana , Barwick Melanie , Campbell-Yeo Marsha , Chambers Christine , Estabrooks Carole , Flynn Rachel , Gibbins Sharyn , Harrison Denise , Isaranuwatchai Wanrudee , LeMay Sylvie , Noel Melanie , Stinson Jennifer , Synnes Anne , Victor Charles , Yamada Janet 
Published: December 2024

Abstract
Implementation of infant pain practice change (ImPaC) is a multifaceted web-based resource to support pain practice change in neonatal intensive care unit (NICU). We evaluated the (1) intervention effectiveness and (2) implementation effectiveness of ImPaC using a hybrid type 1 effectiveness-implementation study (ie, cluster randomized controlled trial and longitudinal descriptive study). Eligible level 2 and 3 Canadian NICUs were randomized to intervention (INT) or waitlisted to usual care (UC) for 6 months. We assessed the number of painful procedures, proportion of procedures accompanied by valid assessment and evidence-based treatment, and pain intensity to determine intervention effectiveness using intention-to-treat (ITT) and wait-list (WL) analyses. Implementation feasibility and fidelity were explored. Twenty-three NICUs participated (12 INT, 11 UC). Thirty infants/NICU were included in the ITT (INT = 354, UC = 325) and the WL (INT = 678, UC = 325) analyses. In the ITT analysis, the average number of painful procedures/infant/day was lower in the INT group [2.62 (±3.47) vs 3.85 (±4.13), P < 0.001] than in the UC group. Pain assessment was greater in the INT group (34.7% vs 25.5%, P < 0.001) and pain intensity scores were lower [1.47 (1.25) vs 1.86 (1.97); P = 0.029]. Similarly, in the WL analysis, there were fewer painful procedures/infant/day [3.11 (±3.98) vs 3.85 (±4.13), P = 0.003] and increased pain assessment (30.4% vs 25.5%, P = 0.0001) and treatment (31.2% vs 24.0%, P < 0.001) in the INT group. Feasibility and implementation fidelity were associated with improved clinical outcomes.
Altered blood and keratinocyte microRNA/transfer RNA fragment profiles related to fibromyalgia syndrome and its severity
Authors: Erbacher Christoph , Vaknine-Treidel Shani , Madrer Nimrod , Weinbender Sofia , Evdokimov Dimitar , Unterecker Stefan , Moshitzky Gilli , Sommer Claudia , Greenberg David S. , Soreq Hermona , Üçeyler Nurcan 
Published: December 2024

Abstract
Fibromyalgia syndrome (FMS) is a debilitating widespread chronic pain condition of unclear pathophysiology. We studied small noncoding RNAs as potential classifiers and mediators of FMS. Blood and keratinocyte microRNAs (miRs) and transfer RNA fragments (tRFs) were profiled by small RNA-sequencing within a comprehensively phenotyped female cohort of 53 patients with FMS vs 34 healthy controls (hCOs) and 15 patients with major depression and chronic physical pain (disease controls). Small RNAs were quantified via RNA-sequencing and candidates validated via qRT-PCR. MicroRNAs and tRFs were tested for association with FMS symptoms and their potential regulatory roles. miR and tRF profiles were altered in FMS compared to hCO in whole blood (n = 69; n = 22) and keratinocytes (n = 41; n = 55). Receiver operating characteristic analysis of blood miR candidates hsa-miR-148a-3p and hsa-miR-182-5p, and tRF candidate tRF-21-WB8647O5D levels separated FMS from hCO. In blood, hsa-miR-182-5p and hsa-miR-576-5p upregulation was validated via qRT-PCR, showing even higher expression in disease control, while TRF-20-40KK5Y93 was selectively increased in FMS. MicroRNAs in blood and keratinocytes were associated with how widespread pain manifested in patients. Keratinocyte tRFs correlated with loss of skin innervation. In blood, altered small RNAs were linked to immune and RNA processes, whereas in keratinocytes, adhesion and epithelial functions were targeted. Modulated tRFs shared sequence motifs in patients with FMS, which may promote concerted pathway regulation. Our findings show miRs/tRFs as key small RNAs dysregulation in FMS pathophysiology and open new perspectives for FMS diagnostics, symptom monitoring, and clinical management.