bluuebunny/crossref_metadata_2025_split huggingface dataset:
CanVaxKB: a web-based cancer vaccine knowledgebase
Authors: Asfaw Eliyas , Lin Asiyah Yu , Huffman Anthony , Li Siqi , George Madison , Darancou Chloe , Kalter Madison , Wehbi Nader , Bartels Davis , Fleck Elyse , Tran Nancy , Faghihnia Daniel , Berke Kimberly , Sutariya Ronak , Reyal Farah , Tammam Youssef , Zhao Bin , Ong Edison , Xiang Zuoshuang , He Virginia , Song Justin , Seleznev Andrey I , Guo Jinjing , Pan Yuanyi , Zheng Jie , He Yongqun 
Published: January 2024

Abstract
Cancer vaccines have been increasingly studied and developed to prevent or treat various types of cancers. To systematically survey and analyze different reported cancer vaccines, we developed CanVaxKB (https://violinet.org/canvaxkb), the first web-based cancer vaccine knowledgebase that compiles over 670 therapeutic or preventive cancer vaccines that have been experimentally verified to be effective at various stages. Vaccine construction and host response data are also included. These cancer vaccines are developed against various cancer types such as melanoma, hematological cancer, and prostate cancer. CanVaxKB has stored 263 genes or proteins that serve as cancer vaccine antigen genes, which we have collectively termed ‘canvaxgens’. Top three mostly used canvaxgens are PMEL, MLANA and CTAG1B, often targeting multiple cancer types. A total of 193 canvaxgens are also reported in cancer-related ONGene, Network of Cancer Genes and/or Sanger Cancer Gene Consensus databases. Enriched functional annotations and clusters of canvaxgens were identified and analyzed. User-friendly web interfaces are searchable for querying and comparing cancer vaccines. CanVaxKB cancer vaccines are also semantically represented by the community-based Vaccine Ontology to support data exchange. Overall, CanVaxKB is a timely and vital cancer vaccine source that facilitates efficient collection and analysis, further helping researchers and physicians to better understand cancer mechanisms.
Pythagoreanism in the Middle Ages
Authors: Moyer Ann E. 
Published: January 2024

Pythagorean thought in the postclassical Latin world developed in distinct ways from that of antiquity. Not only were most writers and readers Christian, but the activities of reading and writing took place mainly in the settings of religious institutions and professions, especially in the earlier Middle Ages. Thus the Pythagorean teachings and patterns of life that had often been central to ancient followers, many of which might straddle categories of religion and philosophy, underwent accommodation to Christian settings. Furthermore, ancient writings in Pythagorean traditions had been in Greek, a language largely lost among Latin Christians in late antiquity. A number of patristic writers referred in their works to Pythagorean ideas, some with approval, others not. Augustine of Hippo, who had favored Pythagorean philosophy for some years, provided many such references; so too did Tertullian and Lactantius. A few authors usually considered Neoplatonist and Neopythagorean composed or translated more substantial works. Calcidius translated the first part of Plato’s Timaeus and wrote an extensive commentary in the early 4th century; this work too focuses especially on the cosmos and world soul. Macrobius (b. 370–d. 430) composed a commentary on the section of Cicero’s Republic known as the “Dream of Scipio” (Somnium Scipionis) that describes the order and nature of the cosmos. His near-contemporary Martianus Capella composed De Nuptiis Philologiae et Mercurii (“On the Marriage of Philology and Mercury”), a work that presented the seven liberal arts that came to figure prominently in medieval education. Of greatest importance was Boethius (c 480–524). Among his many works were textbooks for the quadrivium, the four mathematical subjects of the liberal arts: arithmetic, music, geometry, and astronomy. Only the first two have survived; they were loose translations of the writings of the Neopythagorean Nicomachus of Gerasa (c 60–120). These works became foundations of medieval Latin education. Thanks to this cluster of texts, medieval Pythagorean thought centered most often on these quadrivial disciplines. Nonetheless, some theologians, especially during the twelfth century, used Pythagorean ideas in their writings. The writings of Plotinus, more accurately a Neoplatonist, began to become available in the late thirteenth century, and also attracted interest in the fourteenth century. The recovery of ancient sources by humanists in the mid-fifteenth century and beyond marks a transition to Renaissance Pythagorean traditions; Nicholas of Cusa marks that point of transition. Medieval Pythagorean thought is thus characterized by its traditions of textual reception, of invocations of Pythagoras as exemplary figure, and creative reimagining.
Effectiveness of mRNA Booster Vaccine Against Coronavirus Disease 2019 Infection and Severe Outcomes Among Persons With and Without Immune Dysfunction: A Retrospective Cohort Study of National Electronic Medical Record Data in the United States
Authors: Sun Jing , Zheng Qulu , Anzalone Alfred J , Abraham Alison G , Olex Amy L , Zhang Yifan , Mathew Jomol , Safdar Nasia , Haendel Melissa A , Segev Dorry , Islam Jessica Y , Singh Jasvinder A , Mannon Roslyn B , Chute Christopher G , Patel Rena C , Kirk Gregory D 
Published: January 2024

Abstract

Background
Real-world evidence of coronavirus disease 2019 (COVID-19) messenger RNA (mRNA) booster effectiveness among patients with immune dysfunction are limited.

Methods
We included data from patients in the United States National COVID Cohort Collaborative (N3C) who completed ≥2 doses of mRNA vaccination between 10 December 2020 and 27 May 2022. Immune dysfunction conditions included human immunodeficiency virus infection, solid organ or bone marrow transplant, autoimmune diseases, and cancer. We defined incident COVID-19 BTI as positive results from laboratory tests or diagnostic codes 14 days after at least 2 doses of mRNA vaccination; and severe COVID-19 BTI as hospitalization, invasive cardiopulmonary support, and/or death. We used propensity scores to match boosted versus nonboosted patients and evaluated hazards of incident and severe COVID-19 BTI using Cox regression after matching.

Results
Among patients without immune dysfunction, the relative effectiveness of booster (3 doses) after 6 months from the primary (2 doses) vaccination against BTI ranged from 69% to 81% during the Delta-predominant period and from 33% to 39% during the Omicron-predominant period. Relative effectiveness against BTI was lower among patients with immune dysfunction but remained statistically significant in both periods. Boosted patients had lower risk of COVID-19–related hospitalization (hazard ratios [HR] ranged from 0.5 [95% confidence interval {CI}, .48–.53] to 0.63 [95% CI, .56–.70]), invasive cardiopulmonary support, or death (HRs ranged from 0.46 [95% CI, .41–.52] to 0.63 [95% CI, .50–.79]) during both periods.

Conclusions
Booster vaccines remain effective against severe COVID-19 BTI throughout the Delta- and Omicron-predominant periods, regardless of patients’ immune status.
How do patient-reported outcome measures affect treatment intensification and patient satisfaction in the management of psoriatic arthritis? A cross sectional study of 503 patients
Authors: Coyle Conor , Watson Lily , Whately-Smith Caroline , Brooke Mel , Kiltz Uta , Lubrano Ennio , Queiro Ruben , Trigos David , Brandt-Juergens Jan , Choy Ernest , D’Angelo Salvatore , Delle Sedie Andrea , Dernis Emmanuelle , Wirth Théo , Guis Sandrine , Helliwell Philip , Ho Pauline , Hueber Axel , Joven Beatriz , Koehm Michaela , Morales Carlos Montilla , Packham Jon , Pinto Tasende Jose Antonio , Ramírez Julio , Ruyssen-Witrand Adeline , Scrivo Rossana , Twigg Sarah , Welcker Martin , Soubrier Martin , Gossec Laure , Coates Laura C 
Published: January 2024

Abstract

Objectives
The AsseSSing Impact in pSoriatic Treatment (ASSIST) study investigated prescribing in routine PsA care and whether the patient-reported outcome—PsA Impact of Disease questionnaire (PsAID-12)—impacted treatment. This study also assessed a range of patient and clinician factors and their relationship to PsAID-12 scoring and treatment modification.

Methods
Patients with PsA were selected across the UK and Europe between July 2021 and March 2022. Patients completed the PsAID questionnaire and the results were shared with their physician. Patient characteristics, disease activity, current treatment methods, treatment strategies, medication changes and patient satisfaction scores were recorded.

Results
A total of 503 patients were recruited. Some 36.2% had changes made to treatment, and 88.8% of these had treatment escalation. Overall, the mean PsAID-12 score was higher for patients with treatment escalation; increase in PSAID-12 score is associated with increased odds of treatment escalation (odds ratio 1.58; P &lt; 0.0001). However, most clinicians reported that PsAID-12 did not impact their decision to escalate treatment, instead supporting treatment reduction decisions. Physician’s assessment of disease activity had the most statistically significant effect on likelihood of treatment escalation (odds ratio 2.68, per 1-point score increase). Escalation was more likely in patients not treated with biologic therapies. Additional factors associated with treatment escalation included: patient characteristics, physician characteristics, disease activity and disease impact.

Conclusion
This study highlights multiple factors impacting treatment decision-making for individuals with PsA. PsAID-12 scoring correlates with multiple measures of disease severity and odds of treatment escalation. However, most clinicians reported that the PsAID-12 did not influence treatment escalation decisions. Psoriatic Arthritis Impact of Disease (PsAID) scoring could be used to increase confidence in treatment de-escalation.
The emerging role of hypoxia and environmental factors in inflammatory bowel disease
Authors: Villareal Luke B , Xue Xiang 
Published: January 2024

Abstract
Inflammatory bowel disease (IBD) is a chronic and debilitating disorder characterized by inflammation of the gastrointestinal tract. Despite extensive research, the exact cause of IBD remains unknown, hampering the development of effective therapies. However, emerging evidence suggests that hypoxia, a condition resulting from inadequate oxygen supply, plays a crucial role in intestinal inflammation and tissue damage in IBD. Hypoxia-inducible factors (HIFs), transcription factors that regulate the cellular response to low oxygen levels, have gained attention for their involvement in modulating inflammatory processes and maintaining tissue homeostasis. The two most studied HIFs, HIF-1α and HIF-2α, have been implicated in the development and progression of IBD. Toxicological factors encompass a wide range of environmental and endogenous agents, including dietary components, microbial metabolites, and pollutants. These factors can profoundly influence the hypoxic microenvironment within the gut, thereby exacerbating the course of IBD and fostering the progression of colitis-associated colorectal cancer. This review explores the regulation of hypoxia signaling at the molecular, microenvironmental, and environmental levels, investigating the intricate interplay between toxicological factors and hypoxic signaling in the context of IBD, focusing on its most concerning outcomes: intestinal fibrosis and colorectal cancer.
Brain microvascular endothelial cell‐derived exosomes transmitting circ_0000495 promote microglial M1‐polarization and endothelial cell injury under hypoxia condition
Authors: Min Xiao‐li , Jia Wen‐ji , Guo Li , Jing Rui , Zhao Xiao‐hong , Hu Jia‐yi , Li Xu‐hui , Liu Wei , Wang Tao , Dou Xing‐kui 
Published: January 2024

AbstractHuman brain microvascular endothelial cells (HBMVECs) and microglia play critical roles in regulating cerebral homeostasis during ischemic stroke. However, the role of HBMVECs‐derived exosomes in microglia polarization after stroke remains unknown. We isolated exosomes (Exos) from oxygen glucose deprivation (OGD)‐exposed HBMVECs, before added them into microglia. Microglia polarization markers were tested using RT‐qPCR or flow cytometry. Inflammatory cytokines were measured with ELISA. Endothelial cell damage was assessed by cell viability, apoptosis, apoptosis‐related proteins, oxidative stress, and angiogenic activity using CCK‐8, flow cytometry, western blot, ELISA, and endothelial tube formation assay, respectively. We also established middle cerebral artery occlusion (MCAO) mice model to examine the function of circ_0000495 on stroke in vivo. Our study found that HBMVECs‐Exos reduced M2 markers (IL‐10, CD163, and CD206), increased M1 markers (TNF‐α, IL‐1β, and IL‐12), CD86‐positive cells, and inflammatory cytokines (TNF‐α and IL‐1β), indicating the promotion of microglial M1‐polarization. Microglial M1‐polarization induced by HBMVECs‐Exos reduced viability and promoted apoptosis and oxidative stress, revealing the aggravation of endothelial cell damage. However, circ_0000495 silencing inhibited HBMVECs‐Exos‐induced alterations. Mechanistically, circ_0000495 adsorbed miR‐579‐3p to upregulate toll‐like receptor 4 (TLR4) in microglia; miR‐579‐3p suppressed HBMVECs‐Exos‐induced alterations via declining TLR4; furthermore, Yin Yang 1 (YY1) transcriptionally activated circ_0000495 in HBMVECs. Importantly, circ_0000495 aggravated ischemic brain injury in vivo via activating TLR4/nuclear factor‐κB (NF‐κB) pathway. Collectively, OGD‐treated HBMVECs‐Exos transmitted circ_0000495 to regulate miR‐579‐3p/TLR4/NF‐κB axis in microglia, thereby facilitating microglial M1‐polarization and endothelial cell damage.
Unveiling the role of cellular dormancy in cancer progression and recurrence
Authors: Collignon Evelyne 
Published: January 2024

Purpose of review
Cellular dormancy is a major contributor to cancer progression and recurrence. This review explores recent findings on the molecular mechanisms implicated in cancer dormancy and investigates potential strategies to improve therapeutic interventions.

Recent findings
Research on cancer dormancy reveals a complex and multifaceted phenomenon. Providing a latent reservoir of tumor cells with reduced proliferation and enhanced drug-tolerance, dormant cancer cells emerge from a clonally diverse population after therapy or at metastatic sites. These cells exhibit distinct transcriptional and epigenetic profiles, involving the downregulation of Myc and mechanistic target of rapamycin (mTOR) pathways, and the induction of autophagy. Senescence traits, under the control of factors such as p53, also contribute significantly. The tumor microenvironment can either promote or prevent dormancy establishment, notably through the involvement of T and NK cells within the dormant tumor niche. Strategies to combat dormancy-related relapse include direct elimination of dormant tumor cells, sustaining dormancy to prolong survival, or awakening dormant cells to re-sensitize them to antiproliferative drugs.

Summary
Improving our understanding of cancer dormancy at primary and secondary sites provides valuable insights into patient care and relapse prevention.
Sensitive development windows of prenatal air pollution and cognitive functioning in preschool age Mexican children
Authors: Hsu Hsiao-Hsien Leon , Lane Jamil M. , Schnaas Lourdes , Coull Brent A. , Osorio-Valencia Erika , Chiu Yueh-Hsiu Mathilda , Wilson Ander , Just Allan C. , Kloog Itai , Bellinger David , Téllez-Rojo Martha M. , Wright Robert O. 
Published: January 2024

Introduction:
Neurotoxicity resulting from air pollution is of increasing concern. Considering exposure timing effects on neurodevelopmental impairments may be as important as the exposure dose. We used distributed lag regression to determine the sensitive windows of prenatal exposure to fine particulate matter (PM2.5) on children’s cognition in a birth cohort in Mexico.

Methods:
Analysis included 553 full-term (≥37 weeks gestation) children. Prenatal daily PM2.5 exposure was estimated using a validated satellite-based spatiotemporal model. McCarthy Scales of Children’s Abilities (MSCA) were used to assess children’s cognitive function at 4–5 years old (lower scores indicate poorer performance). To identify susceptibility windows, we used Bayesian distributed lag interaction models to examine associations between prenatal PM2.5 levels and MSCA. This allowed us to estimate vulnerable windows while testing for effect modification.

Results:
After adjusting for maternal age, socioeconomic status, child age, and sex, Bayesian distributed lag interaction models showed significant associations between increased PM2.5 levels and decreased general cognitive index scores at 31–35 gestation weeks, decreased quantitative scale scores at 30–36 weeks, decreased motor scale scores at 30–36 weeks, and decreased verbal scale scores at 37–38 weeks. Estimated cumulative effects (CE) of PM2.5 across pregnancy showed significant associations with general cognitive index (

= −0.35, 95% confidence interval [CI] = −0.68, −0.01), quantitative scale (

= −0.27, 95% CI = −0.74, −0.02), motor scale (

= −0.25, 95% CI = −0.44, −0.05), and verbal scale (

= −0.2, 95% CI = −0.43, −0.02). No significant sex interactions were observed.

Conclusions:
Prenatal exposure to PM2.5, particularly late pregnancy, was inversely associated with subscales of MSCA. Using data-driven methods to identify sensitive window may provide insight into the mechanisms of neurodevelopmental impairment due to pollution.
The effect of internal limiting membrane peeling on the inner retinal layers in patients without macular pathology
Authors: Belkin Avner , Harel Gal , Shtayer Chen , Bercovich Or , Rubowitz Alexander 
Published: January 2024

Background:
To examine the effect of internal limiting membrane (ILM) peeling on the inner retinal layers in patients without macular pathology.

Methods:
A prospective nonrandomized trial of patients undergoing pars plana vitrectomy with ILM peeling for pathology outside of the macula was performed. Optical coherence tomography (OCT) including macular ganglion cell layer (GCL), inner plexiform layer (IPL) and peripapillary retinal nerve fiber layer imaging was performed prior to surgery, 1,3 and 6 months post-operatively and at the end of follow up (ranges between 4-17 months). Patients with any macular pathology on OCT prior to surgery were excluded. The main outcome measure was change in thickness of the GCL and IPL.

Results:
Ten patients who underwent pars plana vitrectomy with ILM peeling for macula-on retinal detachment were included in the analysis. The mean age was 55 years and the mean follow up was 10.8 months. All patients completed at least 2 post-operative follow up visits that included an OCT as per the protocol (range 2-6 months). There was an immediate reduction in the global (G), infero-temporal (IT), supero-temporal (ST) and superior (S) GCL thickness at the first follow up as compared to the pre-operative state (P=0.028, P=0.027, P=0.026 and P=0.027 respectively). From the first follow up visit onward until the final follow up the thinning persisted, though there was no further statistically significant thinning.

Conclusion:
Peeling of the ILM causes significant GCL thinning in maculae without pathology prior to surgery. At up to 17 months of follow up, this effect seems to be immediate and non-progressive.
Does Bevacizumab Improve Outcomes After Ahmed Glaucoma Valve Implantation for Refractory Glaucoma?: A Meta-Analysis
Authors: Tran Luke , Vo Joanne , Bell Katharina , Perera Shamira , Crowston Jonathan 
Published: January 2024

Précis:
Mean intraocular pressure (IOP), complete and overall success, mean IOP-lowering medications, incidence of hypertensive phase, and complications were found to be comparable between patients undergoing Ahmed glaucoma valve implantation (AGVI) with adjunctive bevacizumab versus AGVI alone.

Objective:
This meta-analysis aims to assess how adjunctive bevacizumab impacts the surgical outcomes of AGVI compared with AGVI alone in all subtypes of refractory glaucoma.

Methods:
A systematic search of databases for relevant randomized controlled trials (RCTs) was performed in March 2023. Primary outcomes included mean IOP and success rates. Secondary outcomes were mean IOP-lowering medications, incidence of hypertensive phase, and complications. Qualitative assessment, meta-analysis, subgroup analyses, and sensitivity analysis were performed.

Results:
Five RCTs comprising 203 eyes were included in the quantitative analysis. Initial meta-analysis showed a strong yet nonsignificant trend (all P > 0.05) favoring adjunctive bevacizumab in all outcomes of interest. Significant heterogeneity was observed for mean IOP and success outcomes at all time points (all I
2 > 50%). Subgroup analysis of the administration route revealed a reduced incidence of hyphaema in the intravitreal bevacizumab subgroup (odds ratio: 0.10; 95% CI: 0.02 to 0.59; P = 0.01) with significant heterogeneity persisting in the intravitreal bevacizumab subgroup for all measures (all I
2 > 50%). Post hoc sensitivity analysis of studies without concurrent pan-retinal photocoagulation for mean IOP and success outcomes demonstrated more conservative effect sizes with a corresponding decrease in heterogeneity for all measures (all I
2 < 30%).

Conclusion:
Published studies investigating the role of adjunctive bevacizumab show a strong trend to improve outcomes but contain a relatively small number of participants. This analysis underpins the need for an adequately powered RCT to explore the role of anti-vascular endothelial growth factor agents in AGVI surgery.
Pilot Study of a Software Application to Identify Trauma Registry Inconsistencies
Authors: Roden-Foreman Jacob W. , Garlow Laura , Riordan Kathleen M. , Edlund Susie , Suarez Valerie 
Published: January 2024

BACKGROUND:
Trauma registries are essential to the functioning of modern trauma centers, and high-quality data are necessary to identify patient care issues, develop evidence-based practice, and more. However, institutional experience suggested existing methods to evaluate data quality were insufficient.

OBJECTIVE:
This study aims to compare a new software application developed at our trauma center to our existing trauma registry platform on the ability to identify registry inconsistencies (i.e., potential data quality issues).

METHODS:
We conducted a pilot retrospective cohort study of patients from September 2019 to August 2020 who underwent chart review during a Level I verification visit and had been audited several times for accuracy. Registry records were processed by both validation systems, and registry inconsistencies were recorded.

RESULTS:
In registry data for 63 patients, the new software found 225 registry inconsistencies, and the registry systems found 153 inconsistencies. The most frequent inconsistencies identified by the new software were missing or unknown procedure start times, with 18/63 (28.6%) patients affected and prehospital supplemental oxygen being blank, with 29/53 (54.7%) patients with prehospital care affected. None of the 10 most common inconsistencies detected with the registry systems were true issues.

CONCLUSIONS:
This study found the new software application identified 47% more inconsistencies than the standard registry systems, and none of the most frequent inconsistencies detected with the registry systems were true issues pertinent to institutional practice. Centers should consider additional methods to identify registry inconsistencies as existing processes appear insufficient.