bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inequality in uptake of bowel cancer screening by deprivation, ethnicity and smoking status: cross-sectional study in 86 850 citizens
Authors: Creavin Alexandra , Creavin Sam , Kenward Charlie , Sterne Jonathan , Williams Jo 
Published: September 2023

Abstract

Background
Survival from colorectal cancer depends on stage at detection. In England, bowel cancer mortality has historically been highest in deprived areas. During the initial stages of the COVID-19 pandemic, it was necessary to temporarily halt many screening programmes, which may have led to inequalities in uptake since screening restarted.

Methods
Cross-sectional data from the Bristol, North Somerset and South Gloucestershire Systemwide Dataset were analyzed. Associations of baseline characteristics with uptake of bowel screening were examined using logistic regression.

Results
Amongst 86 850 eligible adults aged 60–74 years, 5261 had no screening record. There was little evidence of association between no screening and sex (adjusted odds ratio 0.95 (95% confidence interval 0.90, 1.02)). Absence of screening record was associated with deprivation (1.26 (1.14, 1.40) for the most compared with the least deprived groups), smoking (1.11 (1.04, 1.18)) compared with no smoking record and black (1.36 (1.09, 1.70)) and mixed (1.08 (1.01, 1.15)) ethnicity compared with white ethnicity.

Conclusions
In a data set covering a whole NHS Integrated Care Board, there was evidence of lower uptake of bowel cancer screening in adults living in more deprived areas, of minority ethnic groups and who smoked. These findings may help focus community engagement work and inform research aimed at reducing inequalities.
Further evaluation of inflammatory and non-inflammatory aspects of pain in rheumatoid arthritis patients
Authors: Jansen Niels , ten Klooster Peter M , Vonkeman Harald E , van den Berg Boudewijn , Buitenweg Jan R 
Published: September 2023

Abstract

Objective
A high discrepancy between the number of tender and swollen joints (e.g. ΔTSJ ≥ 7) has previously been used as an indication for the presence of changes in central mechanisms in patients with moderate-to-high disease activity. In this study, we explored whether the ΔTSJ can also be used to obtain insights into the underlying pain mechanisms in patients with on average well-controlled disease activity.

Methods
A 2 year retrospective analysis of routinely obtained 28-joint DAS (DAS28) components was performed on 45 patients with low inflammatory activity at the group level. All patients underwent pressure pain threshold (PPT) and electrical pain threshold (EPT) measurements and completed four self-report questionnaires [short-form 36 (SF-36v2); central sensitization inventory (CSI); generalized pain questionnaire (GPQ); and the pain catastrophizing scale (PCS)].

Results
Patients with a ΔTSJ ≥ 3 at least once in the past 2 years showed significantly lower EPT and PPT values and higher levels of pain and disability on the SF-36v2 compared with the ΔTSJ &lt; 3 group. Furthermore, GPQ scores were significantly higher in those with ΔTSJ ≥ 3, while CSI and PCS scores were similar.

Conclusion
These findings suggest that in patients in the ΔTSJ ≥ 3 group, mechanisms other than inflammation (only) underlie the pain. Moreover, our findings suggest that among the multiple potential underlying psychological mechanisms, pain catastrophizing (as measured by the PCS) and psychological hypervigilance (as measured by the CSI) do not play an important role. These findings could be useful in the clinical management of the patient. Depending on the dominant mechanism underlying the (persistent) pain, patients might respond differently to treatment.
Plating versus Intramedullary Nailing of OTA/AO 43C1 and C2 Intra-articular Distal Tibia Fractures: A Propensity Score and Multivariate Analysis
Authors: Jang Yohan , Wilson Nathaniel , Jones Jenna , Alcaide Doriann , Szatkowski Jan , Sorkin Anthony , Slaven James E , Natoli Roman 
Published: September 2023

Abstract

Objective:
To compare rates of loss of reduction, nonunion, and infection in intra-articular distal tibia fractures (IADTF) treated with limited open reduction internal fixation and intramedullary nailing (IMN) as compared to open reduction internal fixation with plate and screws (PF).

Design:
Retrospective Review

Setting:
Level-I academic trauma center

Patients:
110 patients, age ≥ 18 with operatively treated OTA/AO 43C1 and C2 IADTF between 2013-2021

Primary outcome measurement:
Loss of reduction, surgical site infection (SSI), nonunion, and patient-reported outcomes (PROs)

Results:
110 patients met the inclusion criteria (IMN 33, PF 77). There was no loss of reduction reported. 17 nonunions (15% overall; IMN 4/33, PF 13/77) and 13 SSIs (12% overall; IMN 2/33, PF11/77) were identified. Despite several risk factors being identified for nonunion and SSI in bivariate analysis, only open fracture remained significant as a risk factor for both nonunion (OR 0.09 for closed fracture, 95% CI 0.02-0.56, p=0.009) and SSI (OR 0.07 for closed fracture, 95% CI 0.06-0.26, p=0.012) in the multivariate model. Propensity scoring based on presurgical variables was significantly different between patients that received IMN vs PF (p=0.03); however, logistic regression incorporating the propensity score revealed no significant association with nonunion and SSI. Adjusting for the propensity score, there remained no association comparing IMN versus PF with nonunion and SSI (p=0.54 and p=0.17, respectively). There was also no difference in PROs between IMN and PF (Physical function: p=0.25, Pain interference: p=0.21).

Conclusion:
Overall nonunion and SSI prevalence in our cohort was 15% and 12%, respectively, in operatively treated OTA/AO 43C1 and C2 IADTF. An open fracture is a significant risk factor for nonunion and SSI. Metaphyseal fixation via IMN or PF in IADTF did not affect the loss of reduction, nonunion, SSI, and PROs.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Diagnostic value of 18F-fluoro-2-deoxyglucose positron emission tomography/computed tomography imaging in acral melanoma–predominant Asian patients
Authors: Chen Kuan-Cheng , Chu Po-Yu , Li Cheng-Yuan , Wang Tien-Hsiang , Chiu Yu-Jen 
Published: September 2023

Background:
Tumor staging is crucial for melanoma, of which acral melanoma is the predominant subtype in Asians. 18F-fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) and 18F-FDG-PET/computed tomography (18F-FDG-PET/CT) serve as noninvasive imaging tools for tumor staging. However, the literature is scarce on the diagnostic value of PET for acral melanoma.

Methods:
From January 1, 2006 to November 30, 2022, a total of 352 patients were diagnosed with melanoma at our hospital. Of them, 90 were diagnosed with cutaneous melanoma and underwent preoperative PET/CT for staging and sentinel lymph node biopsy or complete lymph node dissection. Staging of PET/CT was confirmed by histopathology or following imaging. The lymph node biopsy, distant metastasis status, and PET/CT imaging results were analyzed.

Results:
Of all the 90 patients with cutaneous melanoma, 72 of them were diagnosed as acral melanoma (80.0%). Compared with the histopathologic results, the lymph nodes were true-positive, true-negative, false-positive, and false-negative in 12, 54, 7, and 17 cases, respectively. The sensitivity of PET/CT for local lymph nodes was 41.4% (95% CI, 23.5%-61.1%), whereas its specificity was 88.5% (95% CI, 77.8%-95.3%). As for the detection of distal metastasis, the PET results were true-positive, true-negative, false-positive, and false-negative in 6, 65, 15, and 4 cases, respectively. The sensitivity of PET for distal metastasis detection was 60.0% (95% CI, 26.2%-87.8%), whereas its specificity was 81.3% (95% CI, 71.0%-89.1%).

Conclusion:
Although noninvasive, PET/CT has relatively low sensitivity in regional lymph node evaluations, and fair sensitivity in distal metastasis detection in Asian patients with acral melanoma. Thus, PET/CT may be more useful in patients with clinically palpable nodes or more advanced disease stages.
Novosphingobium cyanobacteriorum sp. nov., isolated from a eutrophic reservoir during the Microcystis bloom period
Authors: Kang Mingyeong , Van Le Ve , Ko So-Ra , Lee Sang-Ah , Choi Dong-Yun , Oh Hee-Mock , Ahn Chi-Yong 
Published: September 2023

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, HBC54T, was isolated from periphyton during a

Microcystis

bloom. Based on the results of the 16S rRNA gene sequence analysis, strain HBC54T was closely related to

Novosphingobium aerophilum

4Y4T (98.36 %),

Novosphingobium aromaticivorans

DSM 12444T (98.08 %),

Novosphingobium huizhouense

c7T (97.94 %),

Novosphingobium percolationis

c1T (97.65 %),

Novosphingobium subterraneum

DSM 12447T (97.58 %),

Novosphingobium olei

TW-4T (97.58 %) and

Novosphingobium flavum

UCT-28T (97.37 %). The average nucleotide identity and digital DNA–DNA hybridization values between HBC54T and its related type stains were below 78.97 and 23.7 %, which are lower than the threshold values for species delineation. The major fatty acids (>10.0 %) were identified as C14 : 0 2-OH, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and the respiratory quinone was ubiquinone Q-10. The main polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and three unidentified phospholipids. The genomic DNA G+C content was 64.8 mol%. Strain HBC54T is considered to represent a novel species within the genus

Novosphingobium

, for which the name Novosphingobium cyanobacteriorum sp. nov. is proposed. The type strain is HBC54T (=KCTC 92033T=LMG 32427T).
Low-input and single-cell methods for Infinium DNA methylation BeadChips
Authors: Lee Sol Moe , Loo Christian E. , Prasasya Rexxi D. , Bartolomei Marisa S. , Kohli Rahul M. , Zhou Wanding 
Published: September 2023

ABSTRACTThe Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal’s influence on the DNA methylation level readings. The modified detectionp-values calculation achieved higher sensitivities for low-input datasets and was validated in over 100,000 public datasets with diverse methylation profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
Intronic miR342 is a master regulator of cellular glycolysis in Foxp3+regulatory CD4 T cells
Authors: Yu Rongzhen , Li Silei , Kim Sohee , Kim Giha , Lu Li-Fan , Kim Dongkyun , Min Booki 
Published: September 2023

AbstractFoxp3+regulatory T (Treg) cells are a subset of CD4 T cells that play a potent and indispensable role in regulating immunity and tolerance. The precise mechanisms by which Treg cells mediate such functions have extensively been explored, and there are many cellular and molecular factors that are instrumental for adequate Treg cell functions. miRNAs, small non-coding RNA molecules, are one of the factors capable of controlling Treg cell functions. In this study, we report that miR-342 is essential for Treg cells to mitigate autoimmune inflammation in the central nervous system. Utilizing novel mouse models with Treg cell-specific miR-342 deficiency or overexpression, we demonstrate that miR-342 expression in Treg cells, while dispensable for immune homeostasis at steady-state conditions, is necessary for Treg cells to control inflammatory responses. Mechanistically, we found that Treg cells deficient in miR-342 display dysregulated metabolic profiles, elevated glycolysis and decreased oxidative phosphorylation, a metabolic phenotype associated with functionally defective Treg cells. Interestingly, miR-342-dependent metabolic dysregulation was observed in Treg but not in Th1 type cells. In support, miR-342-mediated Rictor targeting was found in Treg but not in Th1 type cells. Collectively, our findings uncover that miR-342 may serve a master regulator specific for metabolism and functions in Treg cells.
Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in theBreviolum minutumgenome
Authors: Marinov Georgi K. , Chen Xinyi , Swaffer Matthew P. , Xiang Tingting , Grossman Arthur R. , Greenleaf William J. 
Published: September 2023

AbstractIn dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties were originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellateBreviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
An in-silico investigation of the effect of changing cycling crank power and cadence on muscle energetics and active muscle volume
Authors: Riveros-Matthey Cristian D. , Carroll Timothy J. , Connick Mark J. , Lichtwark Glen A. 
Published: September 2023

AbstractThis study used musculoskeletal modelling to explore the relationship between cycling conditions (power output and cadence) and muscle activation and metabolic power. We hypothesized that the cadence that minimized the simulated average active muscle volume would be higher than that which minimized the simulated metabolic power. We validated the simulation by comparing predicted muscle activation and fascicle velocities from select muscles with experimental records of electromyography and ultrasound images. We found strong correlations for averaged muscle activations and moderate to good correlations for fascicle dynamics. These correlations tended to weaken when analyzed at the individual participant level. Our study revealed a curvilinear relationship between average active muscle volume and cadence, with the minimum active volume being aligned to the self-selected cadence. The simulated metabolic power was consistent with previous results and was minimized at lower cadences than that which minimized active muscle volume across power outputs. Whilst there are some limitations to the musculoskeletal modelling approach, the findings suggest that minimizing active muscle volume may be a more important factor than minimizing metabolic power for self-selected cycling cadence preferences. Further research is warranted to explore the potential of an active muscle volume based objective function for control schemes across a wider range of cycling conditions.
Embryogenesis in myrmicine ants combines features of short and long germ-band modes of development
Authors: Fang Chi-Chun , Rajakumar Arjuna , Kenny Andrew , Mueller Ulrich G. , Abouheif Ehab , Stein David 
Published: September 2023

ABSTRACTAnts exhibit complex social organization, morphologically distinct castes with division of labor, and the exploitation of diverse ecological niches. The extent to which these features have influenced embryonic development relative to other insects remains unclear. Insect embryogenesis has been classified into one of three modes: long, short, and intermediate germ-band. In long germ-band development, exemplified by the fruit flyDrosophila melanogaster, segments along the entire anterior-posterior axis of the embryonic primordium are established almost simultaneously, prior to gastrulation, with the initial embryonic primordium surrounding almost the entire volume of the egg. In short and intermediate germ-band modes, the embryonic primordium occupies a smaller proportion of the egg surface, with anterior segments initially specified, and remaining segments being added sequentially from a posterior growth zone. Here, we show a novel pattern of development in three myrmicine ants, the fungus-gardening antsAtta texanaandMycocepurus smithii, and the red imported fire antSolenopsis invicta. Early in embryogenesis, they exhibit features of short germ-band development, while later in development they exhibit a newly-characterized progressive pattern of segmentation that has been associated with some long germ-band-developing insects. Moreover, despite similarities in the size of ant andDrosophilaeggs, the duration of embryogenesis in the three ant species is 10 to 20-fold longer than inDrosophilaand is also significantly longer than in the honeybeeApis melliferaand the jewel waspNasonia vitripennis. In addition, the embryos produced byA. texanafoundress queens develop to first instar larvae 25% faster than embryos produced by mature queens. We discuss these results in the context of the eusocial lifestyle of ants.
Exploring the mechanisms and potential therapeutic targets of Ferroptosis Related Genes in ankylosing spondylitis
Authors: Liu Zhen-Gang , Yang Fan , Chen Bing , Li Peng-Fu , Zhang Bo-Yin 
Published: September 2023

AbstractBackgroundFerroptosis is a novel type of regulated cell death, and there is growing evidence that it is directly associated with the disease. Therefore, this study aimed to investigate the relevance of iron Ferroptosis-related genes to ankylosing spondylitis (AS) to propose a novel targeted therapy for AS patients.MethodsAS samples were downloaded from the Gene Expression Omnibus (GEO) database (GSE41038). Ferroptosis-related genes were obtained from the FerrDb database, and differential expression analysis was performed using the GEO2R tool. Additionally, we constructed a protein-protein interaction (PPI) network and identified the central genes using Cytoscape. A neural network model was developed utilizing the data mining software Clementine. cMap technology was used to screen potential pharmacological compounds that target the central gene,and a predictive model was built by machine learning methods.ResultsWe discovered 786 differentially expressed genes in AS samples compared to normal tissue, including 359 up-regulated and 427 down-regulated genes. The intersection of ferroptosis-related genes and differential genes yielded 20 overlapping genes. We constructed a hub gene co-expression network with 20 nodes and 14 edges and obtained the ten most recommended drugs for AS.ConclusionBioinformatics analysis identified 20 potential genes associated with Ferroptosis in AS. Genes such as CAV1, NOX4, and NQO1 were revealed to influence the development of AS by regulating Ferroptosis. Our study provides new insights into the function of iron Ferroptosis-related genes in AS, suggesting that targeting Ferroptosis may be a potential therapeutic option for AS.
Detecting Differential Alternative Splicing in Mass Spectrometry-based Proteomics Data
Authors: Ammar Constantin , Csaba Gergely , Hadziahmetovic Armin , Vasilopoulou Catherine G. , Gruber Markus , Mann Matthias , Zimmer Ralf 
Published: September 2023

SummaryAlternative splicing can substantially diversify biological cell states and influence cellular function. The functional impact of splicing has to be estimated at protein level, typically by mass spectrometry (MS) -based proteomics. Although this technology measures increasingly large peptides sets, distinguishing isoform-specific peptides are rare, limiting detection and quantification of splicing. We introduce MS-EmpiReS, a quantification-based computational approach for differential alternative splicing detection in proteomics data. Its core principle is to differentially quantify peptides mapping to different regions of genes. This approach increased the number of testable peptides hundred-fold in a clinical cancer cohort, resulting in a large number of cancer-relevant splicing candidates. Splicing events detected by both MS-EmpiReS and deep RNA sequencing correlated well but also provided complementary information. The proteomics data allowed us to define a per-sample splicing score to separate cancer conditions. Finally, deep brain proteomes from different mice separated strongly by the lower abundance protein splicing isoform.
Cancer immunotherapy response persists after lymph node resection
Authors: Zhou Hengbo , Menzel Lutz , Baish James W. , O’Melia Meghan J. , Darragh Laurel B. , Effiom Derek N. , Specht Emma , Czapla Juliane , Lei Pin-ji , Rajotte Johanna J. , Liu Lingshan , Nikmaneshi Mohammad R. , Razavi Mohammad S. , Vander Heiden Matthew G. , Ubellacker Jessalyn M. , Munn Lance L. , Karam Sana D. , Boland Genevieve M. , Cohen Sonia , Padera Timothy P. 
Published: September 2023

AbstractLymphatic transport facilitates the presentation of cancer antigens in tumor-draining lymph nodes (tdLNs), leading to T cell activation and the generation of systemic antitumor immune surveillance. Surgical removal of LNs to control cancer progression is routine in clinical practice. However, whether removing tdLNs impairs immune checkpoint blockade (ICB) is still controversial. Our analysis demonstrates that melanoma patients remain responsive to PD-1 checkpoint blockade after LN dissection. We were able to recapitulate the persistent response to ICB after complete LN resection in murine melanoma and mammary carcinoma models. Mechanistically, soluble antigen and antigen- carrying migratory dendritic cells are diverted to non-directly tumor draining LNs (non-tdLNs) after tdLN dissection. Consistently, robust ICB responses in patients with head and neck cancer after primary tumor and tdLN resection correlated with the presence of reactive LNs in distant areas. These findings indicate that non-tdLNs sufficiently compensate for the removal of direct tdLNs and sustain the response to ICB.