bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preoperative indicators of the effectiveness of surgical release in de Quervain patients: a prospective cohort study
Authors: Bosman Romy , Hundepool C. A. , van der Oest Mark JW , Duraku Liron S. , Souer J. S. , Selles Ruud W. ,   Hand-Wrist Study Group, Zuidam J Michiel 
Published: November 2023

Background:
A significant proportion of patients still report pain following a surgical release for de Quervain disease (DQ). This study aimed to investigate the effectiveness of a surgical release for DQ and to identify the preoperative factors associated with pain after a surgical release for DQ.

Methods:
This prospective cohort study includes 707 patients who underwent a surgical release and completed the Visual Analog Scale Questionnaire (VAS, range 0-100). We used a paired t-test to analyse the effectiveness of the surgical release on pain at three months post-operatively compared to the pre-operatively measured outcome. A hierarchical multivariable linear regression model was created to investigate the contribution of the patient- and disease characteristics to post-operative pain.

Results:
All VAS domains showed improvement after surgical release. On average, the mean VAS pain decreased by 44 points (95% CI 42; 46). Smoking (B=6.37; p<0.01), younger age (B=-0.35; p<0.01), longer duration of complaints (B=0.13; p<0.01), concomitant surgery (B=14.40; p<0.01) and higher VAS pain scores at intake (B=0.15; p<0.01) were associated with worse VAS pain scores post-operatively. Together, the variables explained 11% of the variance in mean VAS pain score at three months of follow-up.

Conclusion:
This study confirms that surgical treatment for patients with DQ significantly reduces patient-reported pain. Smoking, younger age, concomitant surgery, duration of complaints, and higher VAS pain scores at intake are associated with worse patient-reported pain three months after surgical release. However, the small effects suggest that these factors should not be considered the only important factors.

Level of Evidence:
Therapeutic, II.
Death by the minute: Inequities in trauma care for victims of firearm violence
Authors: Poulson Michael , Jay Jonathan , Kenzik Kelly , Torres Crisanto , Sanchez Sabrina E. , Saillant Noelle , Holena Daniel , Galea Sandro , Scantling Dane 
Published: November 2023

BACKGROUND
Gunshot wounds (GSWs) remain a significant source of mortality in the United States. Timely delivery of trauma care is known to be critical for survival. We sought to understand the relationship of predicted transport time and death after GSW. Given large racial disparities in firearm violence, we also sought to understand disparities in transport times and death by victim race, an unstudied phenomenon.

METHODS
Firearm mortality data were obtained from the Boston Police Department 2005 to 2023. Firearm incidents were mapped using ArcGIS. Predicted transport times for each incident to the closest trauma center were calculated in ArcGIS. Spatial autoregressive models were used to understand the relationship between victim race, transport time to a trauma center, and mortality associated with the shooting incidents.

RESULTS
There were 4,545 shooting victims with 758 deaths. Among those who lived, the median transport time was 9.4 minutes (interquartile range, 5.8–13.8) and 10.5 minutes (interquartile range, 6.4–14.6; p = 0.003) for those who died. In the multivariable logistic regression, increased transport time to the nearest trauma center (odds ratio, 1.024; 95% confidence interval, 1.01–1.04) and age (odds ratio, 1.016; 95% confidence interval, 1.01–1.02) were associated with mortality. There was a modest difference in median transport time to the nearest trauma center by race with non-Hispanic Black at 10.1 minutes, Black Hispanic 9.2 minutes, White Hispanic 8.5 minutes, and non-Hispanic White 8.3 minutes (p < 0.001).

CONCLUSION
Our results highlight the relationship of transport time to a trauma center and death after a GSW. Non-White individuals had significantly longer transport times to a trauma center and predicted mortality would have been lower with White victim transport times. These data underscore the importance of timely trauma care for GSW victims and can be used to direct more equitable trauma systems.

LEVEL OF EVIDENCE
Prognostic/Epidemiological; Level III.
Structural Basis for Mis18 Complex Assembly: Implications for Centromere Maintenance
Authors: Thamkachy Reshma , Medina-Pritchard Bethan , Park Sang Ho , Chiodi Carla G. , Zou Juan , de la Torre-Barranco Maria , Shimanaka Kazuma , Abad Maria Alba , Páramo Cristina Gallego , Feederle Regina , Ruksenaite Emilija , Heun Patrick , Davies Owen R. , Rappsilber Juri , Schneidman-Duhovny Dina , Cho Uhn-Soo , Arockia Jeyaprakash A. 
Published: November 2023

AbstractThe centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18 complex (Mis18α, Mis18ý and Mis18BP1), which recruits the CENP-A specific chaperone HJURP to centromeres for CENP-A deposition. Here, using a multi-pronged approach, we characterise the structure of the Mis18 complex and show that multiple hetero- and homo-oligomeric interfaces facilitate the hetero-octameric Mis18 complex assembly composed of 4 Mis18α, 2 Mis18ý and 2 Mis18BP1. Evaluation of structure-guided/separation-of-function mutants reveals structural determinants essential for Mis18 complex assembly and centromere maintenance. Our results provide new mechanistic insights on centromere maintenance, highlighting that while Mis18α can associate with centromeres and deposit CENP-A independently of Mis18ý, the latter is indispensable for the optimal level of CENP-A loading required for preserving the centromere identity.
MPRAbase: A Massively Parallel Reporter Assay Database
Authors: Zhao Jingjing , Baltoumas Fotis A. , Konnaris Maxwell A. , Mouratidis Ioannis , Liu Zhe , Sims Jasmine , Agarwal Vikram , Pavlopoulos Georgios A. , Georgakopoulos-Soares Ilias , Ahituv Nadav 
Published: November 2023

AbstractMassively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene regulatory activity. There are several different variations of MPRA technology and they are used for numerous applications, including regulatory element discovery, variant effect measurement, saturation mutagenesis, synthetic regulatory element generation or characterization of evolutionary gene regulatory differences. Despite their many designs and uses, there is no comprehensive database that incorporates the results of these experiments. To address this, we developed MPRAbase, a manually curated database that currently harbors 129 experiments, encompassing 17,718,677 elements tested across 35 cell types and 4 organisms. The MPRAbase web interface (http://www.mprabase.com) serves as a centralized user-friendly repository to download existing MPRA data for independent analysis and is designed with the ability to allow researchers to share their published data for rapid dissemination to the community.
Crosstalk between salicylic acid signaling and the circadian clock promotes an effective immune response
Authors: Fraser Olivia , Cargill Samantha J , Spoel Steven H , van Ooijen Gerben 
Published: November 2023

AbstractThe rotation of Earth creates a cycle of day and night, leading to predictable changes in environmental conditions. The circadian clock synchronizes an organism with these environmental changes and alters their physiology in anticipation. Prediction of the probable timing of pathogen infection enables plants to prime their immune system without wasting resources or sacrificing growth. Here, we explore the relationship between the immune hormone salicylic acid (SA), and the circadian clock in Arabidopsis. We found that SA altered circadian rhythmicity through the SA receptor and master transcriptional coactivator, NPR1. Reciprocally, the circadian clock gates SA-induced expression of NPR1-dependent immune genes. Furthermore, the clock gene CCA1 is essential for SA-induced immunity to the major bacterial plant pathogenPseudomonas syringae. These results reveal new interactions between the circadian clock and SA signaling which produce an effective immune response. Understanding how and why the immune response in plants is linked to the circadian clock is crucial in working towards improved crop productivity.
Genetic adaptation to ammonium sustains wheat grain quality and alleviates acclimation to CO2enrichment
Authors: Kasemsap Pornpipat , Bloom Arnold J. 
Published: November 2023

AbstractPlants synthesize protein through assimilating inorganic nitrogen. Yet, the extent to which soil nitrogen sources alter crop responses to atmospheric CO2remains uncertain. We assessed wheat (Triticum aestivumL.) biomass under CO2enrichment in genotypes that demonstrated a preference for ammonium (NH4+) or nitrate (NO3−), and contrasting degrees of NH4+tolerance. Nitrogen-form preference, but not NH4+tolerance, correlated with CO responses. Notably, NH4+-preferring genotypes maintained higher biomass and sustained grain nitrogen concentrations, thus avoiding CO2acclimation, the decline in biomass stimulation after prolonged exposure to CO2enrichment. Furthermore, NH4+nutrition accelerated flowering and increased spike biomass. Breeding for NH4+-adapted genotypes may not only improve climate resilience, but also potentially accelerate development and increase yield without any penalty on grain quality. Because wheat provides 20% of the protein and carbohydrate in the human diet, our study provided strategies to sustain food security under the atmospheric conditions anticipated in the future.HighlightBreeding for NH4+-adapted genotypes may not only improve climate resilience, but also potentially accelerate development and increase yield without any penalty on grain quality under elevated CO2atmospheres.
Profiling functional networks identify activation of corticostriatal connectivity in ET patient after MRgFUS thalamotomy
Authors: Lin Jiaji , Kang Xiaopeng , Zhou Jiayou , Zhang Dekang , Hu Jianxing , Lu Haoxuan , Pan Longsheng , Lou Xin 
Published: November 2023

AbstractObjectiveMR-guided focused ultrasound (MRgFUS) thalamotomy is a novel and effective treatment for medication-refractory tremor in essential tremor (ET), but how the brain responds to this deliberate lesion is not clear. The current study aimed to evaluate the immediate and longitudinal alterations of functional networks after MRgFUS thalamotomy.MethodsWe retrospectively obtained preoperative and postoperative 30-day, 90-day, and 180-day data of 31 ET patients subjected with MRgFUS thalamotomy from 2018 to 2020. Their archived resting-state functional MRI data were used to functional network comparison as well as graph-theory metrics analysis. Both partial least squares (PLS) regression and linear regression were conducted to associate functional features to tremor symptoms.ResultsMRgFUS thalamotomy dramatically abolished tremors, while global functional network only sustained immediate fluctuation within one week postoperatively. Network-based statistics have identified a long-term enhanced corticostriatal subnetwork by comparison between 180-day and preoperative data (P= 0.019). Within this subnetwork, network degree, global efficiency and transitivity were significantly recovered in ET patients right after MRgFUS thalamotomy compared to the pre-operative timepoint (P< 0.05), as well as hemisphere lateralization (P< 0.001). The PLS main component significantly accounted for 33.68% and 34.16% of the total variances of hand tremor score and clinical rating scale for tremor (CRST)-total score (P= 0.037 and 0.027). Network transitivity of this subnetwork could serve as a reliable biomarker for hand tremor score control prediction at 180-day postoperatively (β = 2.94,P= 0.03).ConclusionsMRgFUS thalamotomy promoted corticostriatal connectivity activation correlated with tremor improvement in ET patient after MRgFUS thalamotomy.
VTA projections to M1 are essential for reorganization of layer 2-3 network dynamics underlying motor learning
Authors: Ghanayim Amir , Benisty Hadas , Cohen-Rimon Avigail , Schwartz Sivan , Talmon Ronen , Schiller Jackie 
Published: November 2023

SummaryThe primary motor cortex (M1) is crucial for motor skill learning. Previous studies demonstrated that skill acquisition requires dopaminergic VTA (ventral-tegmental area) signaling in M1, however little is known regarding the effect of these inputs at the neuronal and network levels. Using dexterity task, calcium imaging, chemogenetic silencing, and geometric data analysis, we demonstrate VTA-dependent reorganization of M1 layer 2-3 during motor learning. While average activity and average functional connectivity of layer 2-3 network remain stable during learning, the activity kinetics, the correlational configuration of functional connectivity, and average connectivity strength of layer 2-3 neurons gradually transform towards an expert configuration. In addition, task success-failure outcome signaling gradually emerges. Silencing VTA dopaminergic inputs to M1 during learning, prevents all these changes. Our findings demonstrate dopaminergic VTA-dependent formation of outcome signaling and new connectivity configuration of the layer 2-3 network, supporting reorganization of the M1 network for storing new motor skills.
Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease
Authors: Polonsky Michal , Gerhardt Louisa M. S. , Yun Jina , Koppitch Kari , Colón Katsuya Lex , Amrhein Henry , Zheng Shiwei , Yuan Guo-Cheng , Thomson Matt , Cai Long , McMahon Andrew P. 
Published: November 2023

AbstractKidney injury disrupts the intricate renal architecture and triggers limited regeneration, and injury-invoked inflammation and fibrosis. Deciphering molecular pathways and cellular interactions driving these processes is challenging due to the complex renal architecture. Here, we applied single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics revealed injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predictedClcf1-Crfl1in a molecular interplay between persistently injured proximal tubule cells and neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis revealed cellular microenvironments resembling early tertiary lymphoid structures and identified associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.One-Sentence Summary:Spatial transcriptomics predicted a molecular interplay amongst neighboring cell-types in the injured mammalian kidneyMain Text:
A successional shift enhances stability in ant symbiont communities
Authors: Parmentier Thomas , Bonte Dries , De Laender Frederik 
Published: November 2023

AbstractThroughout succession, communities undergo structural shifts, which can alter the relative abundances of species and how they interact. It is frequently asserted that these alterations beget stability, i.e. that succession selects for communities better able to resist perturbations. Yet, whether and how alterations of network structure affects stability during succession in complex communities is rarely studied in natural ecosystems. Here, we explore how network attributes influence stability of different successional stages of a natural network: symbiotic arthropod communities forming food webs inside red wood ant nests. We conducted extensive field sampling to compare the composition of the symbiont community across 51 host nests of varying age, representing different succession stages. We recorded abundance of 16 functional groups of symbionts spanning different specialization and trophic levels. Joint species distribution modelling indicated nest age as the driver of the compositional shifts: symbiont communities in old nests contained a greater proportion of specialists and more even species abundance distributions. We then reconstructed community matrices and showed that this enhanced evenness lead to an augmented food web stability of the symbiont communities in older nests. Overall, this study demonstrates that succession begets stability in a natural ecological network by making the community more even.
Testing of various protocols for human skin cryopreservation by vitrification method
Authors: Riabinin Andrei , Pankratova Maria , Rogovaya Olga , Vorotelyak Ekaterina , Vasiliev Andrey 
Published: November 2023

AbstractOptimization of skin cryopreservation technology is an important task for translational medicine, pharmacology, and a list of other fields. One of the promising approaches is vitrification. This rapid freezing technique allows one to ensure minimal damage to the sample by equating the formation of ice crystals and dehydration both in the cytoplasm of cells and in the extracellular space. This study is aimed at finding the optimal combination of cryoprotective agents (DMSO, glycerol, sucrose and polyethylene glycol) to achieve the highest viability of skin samples after vitrification.
Development of attenuated coxsackievirus B3 vectored intranasal pre-emptive pan-coronavirus vaccine
Authors: Deng Huixiong , He Xuanting , Li Yanlei , Wang Haoyang , Wang Shenmiao , Gu Liming , Zhang Hengyao , Zhu Jiacheng , Li Rui , Wang Gefei 
Published: November 2023

AbstractSARS-CoV-2 has the ability to evade immunity, resulting in breakthrough infections even after vaccination. Similarly, zoonotic coronaviruses pose a risk of spillover to humans. There is an urgent need to develop a pre-emptive pan-coronavirus vaccine that can induce systemic and mucosal immunity. Here, we employed a combination of immune-informatics approaches to identify shared immunodominant linear B- and T-cell epitopes from SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs), as well as zoonotic coronaviruses. Epitope-guided vaccine were designed and the attenuated coxsackievirus B3 vectored intranasal vaccines rCVB3-EPI and rCVB3-RBD-trimer were constructed. The immunogenicity of these candidate vaccines was evaluated using Balb/c mice. The results demonstrated effective immune responses, including the production of SARS-CoV-2-specific IgG and sIgA antibodies, as well as T cell-mediated responses. However, further verification is required to assess cross-reactivity with various variants. Our intranasal pre-emptive pan-coronavirus vaccine design framework offers an appealing candidate for future vaccine development.
Mechanisms of transcriptional regulation inAnopheles gambiaerevealed by allele specific expression
Authors: Dyer Naomi A. , Lucas Eric R. , Nagi Sanjay C. , McDermott Daniel P. , Brenas Jon H. , Miles Alistair , Clarkson Chris S. , Mawejje Henry D. , Wilding Craig S. , Halfon Marc S. , Asma Hasiba , Heinz Eva , Donnelly Martin J. 
Published: November 2023

AbstractMalaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved by elevated expression of detoxifying enzymes that metabolize the insecticide. In diploid organisms, gene expression is regulated both incis, by regulatory sequences on the same chromosome, and bytransacting factors, affecting both alleles equally. Differing levels of transcription can be caused by mutations incis-regulatory modules (CRM), but few of these have been identified in mosquitoes. We crossed bendiocarb resistant and susceptibleAnopheles gambiaestrains to identifycis-regulated genes that might be responsible for the resistant phenotype using RNAseq, andcis-regulatory module sequences controlling gene expression in insecticide resistance relevant tissues were predicted using machine learning. We found 115 genes showing allele specific expression in hybrids of insecticide susceptible and resistant strains, suggestingcisregulation is an important mechanism of gene expression regulation inAnopheles gambiae. The genes showing allele specific expression included a higher proportion ofAnophelesspecific genes on average younger than genes those with balanced allelic expression.Author SummaryThe evolution of insecticide resistance, including resistance that is due to changes in the expression levels of certain resistance associated genes is threatening progress in malaria control. We investigated how the expression of genes in the malaria vectorAnopheles gambiaeis controlled, by implementing a method for the first time in this species. Each mosquito inherits a set of chromosomes from both parents, so has a maternal and paternal copy of most genes. When a gene is expressed, the DNA encoding that gene is transcribed into messenger RNA. This process is controlled by the cellular environment and by other DNA sequences on the same chromosome as each gene. We crossed mosquitoes from insecticide resistant and susceptible strains to equalize the cellular environment and then measured the levels of messenger RNA from both gene copies. 115 genes showed consistently different messenger RNA levels between gene copies in most crosses, suggesting these genes are regulated by factors on the same chromosome. There were relatively more Anopheles specific genes with imbalanced expression. Using machine learning we identified DNA sequences that may be responsible for controlling gene expression in mosquito tissues; several of these sequences were close to genes with imbalanced expression.
Low-cost 3D printed lenses for brightfield and fluorescence microscopy
Authors: Christopher Jay , Rooney Liam M. , Donnachie Mark , Uttamchandani Deepak , McConnell Gail , Bauer Ralf 
Published: November 2023

AbstractWe present the fabrication and implementation of low-cost optical quality 3D printed lenses, and their application as microscope objectives with different prescriptions. The imaging performance of the 3D printed lenses was benchmarked against commercially available optics including a 20 mm focal length 12.7 mm diameter NBK-7 plano-convex lens used as a low magnification objective, and a separate high magnification objective featuring three 6 mm diameter NBK-7 lenses with different positive and negative focal lengths. We describe the design and manufacturing processes to produce high-quality 3D printed lenses. We tested their surface quality using a stylus profilometer, showing that they conform to that of commercial glass counterpart lenses. The 3D printed lenses were used as microscope objectives in both brightfield and epi-fluorescence imaging of specimens including onion, cyanobacteria, and variegatedHostaleaves, demonstrating a sub-cellular resolution performance obtained with low-cost 3D printed optical elements within brightfield and fluorescence microscopy.