bluuebunny/crossref_metadata_2025_split huggingface dataset:
On sheaves on semicartesian quantales and their truth values
Authors: Luiza Tenorio Ana , de Andrade Mendes Caio , Luiz Mariano Hugo 
Published: January 2024

Abstract
In this paper, we introduce a new definition of sheaves on semicartesian quantales, providing first examples and categorical properties. We note that our sheaves are similar to the standard definition of a sheaf on a locale; however, we prove that in general it is not an elementary topos—since the lattice of external truth values of $Sh(Q)$, $Sub(1)$, is canonically isomorphic to the quantale $Q$—placing this paper as part of a greater project towards a monoidal (not necessarily cartesian) closed version of elementary topos. To start the study the logical aspects of the category of sheaves we are introducing, we explore the nature of the ‘internal truth value objects’ in such sheaves categories. More precisely, we analyse two candidates for subobject classifier for different subclasses of commutative and semicartesian quantales.
The extremely young planetary nebula M 3-27: an analysis of its evolution, physical conditions, and abundances
Authors: Ruiz-Escobedo Francisco , Peña Miriam , Beltrán-Sánchez Ana Valeria 
Published: January 2024

ABSTRACT
Spectrophotometric data of the young planetary nebula M 3-27, from 2004 to 2021, are presented and discussed. We corroborate that the H i Balmer lines present features indicating they are emitted by the central star, therefore He i lines were used to correct line fluxes by effects of reddening. Important variability on the nebular emission lines between 1964 and 2021, probably related to density changes in the nebula, is reported. Diagnostic diagrams to derive electron temperatures and densities have been constructed. The nebula shows a very large density contrast with an inner density of the order of 107 cm−3 and an outer density of about 103–104 cm−3. With these values of density, electron temperatures of 16 000–18 000 K have been found from collisionally excited lines. Because the central star emits in the H+ lines, ionic abundances relative to He+ were calculated from collisionally excited and recombination lines, and scaled to H+ by considering that He+/H+ = He/H = 0.11. Abundance discrepancy factor (O+2) values were also determined. Total abundance values obtained indicate sub-solar abundances, similar to what is found in other comparable objects like IC 4997.
Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize
Authors: Zhou Yan , Kusmec Aaron , Schnable Patrick S 
Published: January 2024

Abstract
The efficiency of solar radiation interception contributes to the photosynthetic efficiency of crop plants. Light interception is a function of canopy architecture, including plant density; leaf number, length, width, and angle; and azimuthal canopy orientation. We report on the ability of some maize (Zea mays) genotypes to alter the orientations of their leaves during development in coordination with adjacent plants. Although the upper canopies of these genotypes retain the typical alternate-distichous phyllotaxy of maize, their leaves grow parallel to those of adjacent plants. A genome-wide association study (GWAS) on this parallel canopy trait identified candidate genes, many of which are associated with shade avoidance syndrome, including phytochromeC2. GWAS conducted on the fraction of photosynthetically active radiation (PAR) intercepted by canopies also identified multiple candidate genes, including liguleless1 (lg1), previously defined by its role in ligule development. Under high plant densities, mutants of shade avoidance syndrome and liguleless genes (lg1, lg2, and Lg3) exhibit altered canopy patterns, viz, the numbers of interrow leaves are greatly reduced as compared to those of nonmutant controls, resulting in dramatically decreased PAR interception. In at least the case of lg2, this phenotype is not a consequence of abnormal ligule development. Instead, liguleless gene functions are required for normal light responses, including azimuth canopy re-orientation.
Positive affect disrupts neurodegeneration effects on cognitive training plasticity in older adults
Authors: Anthony Mia , Turnbull Adam , Tadin Duje , Lin F Vankee 
Published: January 2024

Abstract
Cognitive training for older adults varies in efficacy, but it is unclear why some older adults benefit more than others. Positive affective experience (PAE), referring to high positive valence and/or stable arousal states across everyday scenarios, and associated functional networks can protect plasticity mechanisms against Alzheimer’s disease neurodegeneration, which may contribute to training outcome variability. The objective of this study is to investigate whether PAE explains variability in cognitive training outcomes by disrupting the adverse effect of neurodegeneration on plasticity. The study’s design is a secondary analysis of a randomized control trial of cognitive training with concurrent real or sham brain stimulation (39 older adults with mild cognitive impairment; mean age, 71). Moderation analyses, with change in episodic memory or executive function as the outcome, PAE or baseline resting-state connectivity as the moderator and baseline neurodegeneration as the predictor are the methods used in the study. The result of the study is that PAE stability and baseline default mode network (DMN) connectivity disrupted the effect of neurodegeneration on plasticity in executive function but not episodic memory. The study concludes that PAE stability and degree of DMN integrity both explained cognitive training outcome variability, by reducing the adverse effect of neurodegeneration on cognitive plasticity. We highlight the need to account for PAE, brain aging factors and their interactions with plasticity in cognitive training.
Direct Reprogramming of Hepatocytes Into JAK/Stat-Dependent LGR5+ Liver Cells Able to Initiate Intrahepatic Cholangiocarcinoma
Authors: Chaker Diana , Desterke Christophe , Moniaux Nicolas , Bani Mohamed-Amine , Oudrhiri Noufissa , Faivre Jamila , Turhan Ali G , Bennaceur-Griscelli Annelise , Griscelli Frank 
Published: January 2024

Abstract
Somatic cells that have been partially reprogrammed by the factors Oct4, Sox2, Klf4, and cMyc (OSKM) have been demonstrated to be potentially tumorigenic in vitro and in vivo due to the acquisition of cancer-associated genomic alterations and the absence of OSKM clearance over time. In the present study, we obtained partially reprogrammed, SSEA1-negative cells by transducing murine hepatocytes with Δ1Δ3-deleted adenoviruses that expressed the 4 OSKM factors. We observed that, under long-term 2D and 3D culture conditions, hepatocytes could be converted into LGR5-positive cells with self-renewal capacity that was dependent on 3 cross-signaling pathways: IL6/Jak/Stat3, LGR5/R-spondin, and Wnt/β-catenin. Following engraftment in syngeneic mice, LGR5-positive cells that expressed the cancer markers CD51, CD166, and CD73 were capable of forming invasive and metastatic tumors reminiscent of intrahepatic cholangiocarcinoma (ICC): they were positive for CK19 and CK7, featured associations of cord-like structures, and contained cuboidal and atypical cells with dissimilar degrees of pleomorphism and mitosis. The LGR5+-derived tumors exhibited a highly vascularized stroma with substantial fibrosis. In addition, we identified pro-angiogenic factors and signaling pathways involved in neo-angiogenesis and vascular development, which represent potential new targets for anti-angiogenic strategies to overcome tumor resistance to current ICC treatments.
Disparities in the Receipt of Systemic Treatment in Metastatic Melanoma
Authors: Kakish Hanna , Pawar Omkar , Bhatty Maira , Doh Susan , Mulligan Kathleen M. , Rothermel Luke D. , Bordeaux Jeremy S. , Mangla Ankit , Hoehn Richard S. 
Published: January 2024

Introduction:
In 2011, immunotherapy and targeted therapy revolutionized melanoma treatment. However, inequities in their use may limit the benefits seen by certain patients.

Methods:
We performed a retrospective review of patients in the National Cancer Database for patients with stage IV melanoma from 2 time periods: 2004–2010 and 2016–2020, distinguishing between those who received systemic therapy and those who did not. We investigated the rates and factors associated with treatment omission. We employed Kaplan-Meier analysis to explore the impact of treatment on overall survival.

Results:
A total of 19,961 patients met the inclusion criteria: 7621 patients were diagnosed in 2004–2010 and 12,340 patients in 2016–2020, of whom 54.9% and 28.3% did not receive systemic treatment, respectively. The rate of “no treatment” has decreased to a plateau of ∼25% in 2020. Median overall survival was improved with treatment in both time periods (2004–2010: 8.8 vs. 5.6 mo [P<0.05]; and 2016–2020: 25.9 vs. 4.3 mo [P<0.05]). Nonmedical factors associated with the omission of treatment in both periods included low socioeconomic status, Medicaid or no health insurance, and treatment at low-volume centers. In the period from 2016 to 2020, patients treated at nonacademic programs were also less likely to receive treatment.

Conclusions:
Systemic therapies significantly improve survival for patients with metastatic melanoma, but significant disparities exist with their receipt. Local efforts are needed to ensure all patients benefit from these revolutionary treatments.
Chinese Population Reference Curves for Ultrasound-Measured Amniotic Fluid Deepest Vertical Pocket in Dichorionic Twin Pregnancies, and Their Associations With Pregnancy Outcomes
Authors: Lyu Zhengxin , Wu Tianchen , Lu Shan , Yuan Pengbo , Zhao Yangyu , Wei Yuan 
Published: January 2024

Abstract

Objective
To establish the Chinese population's amniotic fluid deepest vertical pocket (DVP) reference curves for dichorionic twin pregnancies and to investigate DVP links with adverse perinatal outcomes.

Methods
This retrospective cohort study, conducted at Peking University Third Hospital from August 2011 to December 2020, used data from 375 women aged 20 to 45 years who had dichorionic twin pregnancies that were confirmed through first-trimester ultrasound. After exclusions, reference curves were developed using 318 women with 3,299 DVP scans, and the data analyzed included maternal demographics, pregnancy outcomes, ultrasound measurements, and neonatal information. DVPs were assessed via ultrasound at regular intervals and grouped by gestational age (GA) for analyses. Linear mixed models were used to create amniotic fluid reference curves. Associations between abnormalities and adverse perinatal outcomes were examined using Chi-squared or Fisher's exact tests. Logistic regression provided both crude and adjusted odds ratios, adjusting for pre-pregnancy weight, age, ethnicity, parity, and conception mode. Significance was set at P < 0.05 with 95% confidence intervals (CI), and the analyses were conducted using SPSS ver. 26.0 (IBM Corp., Armonk, NY) and SAS ver. 9.4 (SAS Institute Inc., Cary, NC, USA) software.

Results
DVP increased from the first trimester to a maximum at 26 weeks (95% confidence interval (CI), 2.7–8.3 cm for twin 1 and 2.8–7.9 cm for twin 2) and then decreased gradually toward term. Differences between twins 1 and 2 were significant after 26 weeks (95% CI for twin 1: 5.3, 5.5; 95% CI for twin 2: 4.4, 4.5; P < 0.010). Polyhydramnios of twin 1 increased the risk of large for GA. Oligohydramnios of twin 1 increased the risk of small for GA. Polyhydramnios of twin 2 increased the risk of small for GA, premature birth, and neonatal complications. Oligohydramnios of twin 2 increased the risk of preeclampsia, hypertensive disorder complicating pregnancy, and premature rupture of membranes.

Conclusion
Reference curves for twin amniotic fluid volumes vary by GA and differ between twins, with potential implications for pregnancy outcomes.
Modulation of canonical Wnt signaling regulates peribiliary mesenchymal identity during homeostasis and injury
Authors: Singh Serrena , Budiman Tifanny , Redmond David , Gupta Vikas 
Published: January 2024

Background:
The matrix and associated mesenchyme of the extrahepatic bile ducts are distinct, which could drive diseases with a predilection for these ducts, such as primary sclerosing cholangitis. We aimed to understand the molecular drivers of peribiliary mesenchymal cell (PMC) identity in the extrahepatic bile ducts and dissect how this changed in the context of injury using an entirely in vivo approach with transcriptomic analysis.

Methods and Results:
Single-cell sequencing with a receptor-ligand analysis showed that PMCs had the most interactions with surrounding cells. Wnt4, Wnt5a, and Wnt7b were identified as the major ligands secreted from PMCs and cholangiocytes that interacted in both paracrine and autocrine fashion. Bile duct ligation caused an increase in all 3 Wingless/Integrated ligands and Axin2 with an associated increase in the transcription factors T-box transcription factor (Tbx)2 and Tbx3. Conversely, Indian hedgehog secretion decreased without an associated decrease in hedgehog signaling effectors. Loss of smoothened within PMCs did not impact hedgehog signaling effectors or cellular identity, whereas smoothened gain of function led to myofibroblast transdifferentiation with upregulation of Tbx2 and Tbx3 without injury. Loss of β-catenin caused a decrease in expression of all 3 Gli transcription factors and associated mesenchymal gene expression, which was phenocopied with compound Gli2 and Gli3 loss in uninjured PMCs. With injury, loss of β-catenin resulted in decreased myofibroblast transdifferentiation with reduced Tbx2 and Tbx3 expression.

Conclusions:
Our results show how modulation of canonical Wingless/Integrated signaling in PMCs is important for regulating basal mesenchymal gene expression and initiating a myogenic gene transcriptional program during injury. They also highlight reciprocating interactions between the hedgehog and Wingless/Integrated signaling pathways within PMCs.
Changing Course: Understanding the Legal Landscape of Race-Conscious Admission Practices and Implications to Diversity-Promoting Strategies in Higher Education
Authors: Noller Diana T. , Bañuelas Angela , Diallo Shannon 
Published: January 2024

Abstract
The 2023 US Supreme Court holding in Students for Fair Admissions, Inc. v. President and Fellows of Harvard College and Students for Fair Admissions, Inc. v. University of North Carolina, et al. has changed the landscape in higher education admissions processes by declaring affirmative action unlawful. It is imperative that those working in higher education admissions understand the ruling and implement contemporary best practices. Institutions of higher education who wish to promote student diversity are tasked with developing alternative strategies to affirmative action and must steer clear from using race as a determinant factor in admissions decisions. Aiming to identify diversity in individuals' lived experiences, focusing on recruitment efforts that organically lead to diverse applicants, adopting holistic, mission-driven admissions processes, and enhancing robust retention efforts may be effective means of fostering student diversity.
Variation in proliferative and cell cycle markers in Barrett’s esophagus in relation to circumferential and axial location in the esophagus
Authors: Umar Nosheen , Alleyne Lance , Cheung Danny , Rees James , Trudgill Caitlin , Zanetto Ulises , Muzaffar Suhail , Trudgill Nigel 
Published: January 2024

Background
Adenocarcinoma in Barrett’s esophagus (BE) occurs more frequently between 12 and 3 o’clock at the gastroesophageal junction (GEJ).

Methods
BE patients were prospectively recruited from December 2013 to July 2016. Expression of p53, Ki-67, cyclin-D1, COX-2 and p21 was assessed in quadrantic biopsies from the proximal and distal margins of the BE segments. Cell cycle marker association with current or subsequent dysplasia or adenocarcinoma was examined.

Results
110 patients: median age 64 (IQR, 56–71) years; median BE segment length C4M6; and a median follow-up of 4.7 (IQR, 3.6–5.7) years. In total 13 (11.8%) had evidence of dysplasia or neoplasia (2.7% indefinite for dysplasia, 5.5% low grade, 1.8% high grade and 1.8% adenocarcinoma) at index endoscopy. Six (7%) developed dysplasia or neoplasia (1 low grade, 2 high grade and 3 adenocarcinoma) during follow-up. Ki-67 expression was highest at 3 o’clock, and overall was 49.6% higher in the 12-6 o’clock position compared to 6-12 o’clock [odds ratio (OR), 1.42 (95% confidence interval (CI), 1.00–2.12)]. A similar pattern was found with p21 [1.82 (1.00–3.47)]. There was increased expression of several markers in distal BE biopsies; cyclin-D1 [1.74 (1.29–2.34)]; Cyclo-oxygenase 2 [2.03 (1.48–2.78]) and p21 [2.06 (1.16–3.68)]. Expression of Ki-67 was lower in distal compared to proximal biopsies [0.58 (0.43–0.78)]. P53 expression had high specificity (93.8%) for subsequent low-grade dysplasia, high-grade dysplasia or adenocarcinoma.

Conclusion
Increased cellular proliferation was seen at 12-6 o’clock at the GEJ. Cell-cycle marker expression was increased at the GEJ compared to the proximal BE segment. These findings mirror reflux esophagitis and suggest ongoing reflux contributes to the progression of dysplasia and malignancy in BE.
The prevalence of fibromyalgia in adults at Al-Karak Jordan: a cross-sectional study
Authors: Akel Alaa , Sarhan Mohammed Y. , Dwairy Majed Al , Al-zu’bi Belal , Al-Qudah Ala , Alsmarat Omar A. , Alsaraireh Taif , Abu-Jeyyab Mohammad 
Published: January 2024

Introduction:
Fibromyalgia is a chronic and intricate musculoskeletal disorder characterized by widespread pain, fatigue, and tenderness in specific anatomical regions. Although its prevalence varies among populations, understanding the prevalence in different geographical areas is crucial for healthcare planning. This cross-sectional study aims to determine the prevalence of fibromyalgia in adults residing in Al-Karak, Jordan. The city’s unique demographic and environmental characteristics may influence the occurrence of fibromyalgia among its adult population. The study aims to address gaps in knowledge, provide localized insights, and shed light on fibromyalgia’s burden on the community’s health. Accurate prevalence data aids healthcare planning and resource allocation.

Methods:
This research collected data from 965 social media participants using Google Forms. The American College of Rheumatology survey criteria for diagnosing fibromyalgia were used. To investigate the predictive value of various parameters, univariate and multivariate logistic regression analyses were performed.

Results:
The study found a 26.5% prevalence of fibromyalgia in the studied population. Female gender, mental health illnesses, and comorbidities like irritable bowel syndrome, psychiatric disorders, and rheumatological and neurological diseases were significantly associated with fibromyalgia. Age, BMI, marital status, employment status, and certain comorbidities did not show statistically significant predictive value.

Conclusion:
This study sheds light on fibromyalgia’s prevalence and associated factors in the Al-Karak population. The identified predictors highlight the necessity for comprehensive healthcare strategies and interventions to mitigate the disease burden. These findings aid policymakers and healthcare professionals in planning and implementing effective measures for fibromyalgia management and prevention. Further research is warranted to deepen our understanding of fibromyalgia’s complexity and its implications in this region.
Race and Ethnic Group Enrollment and Outcomes for Wilms Tumor: Analysis of the Current Era Children’s Oncology Group Study, AREN03B2
Authors: Lovvorn Harold N , Renfro Lindsay A , Benedetti Daniel J , Kotagal Meera , Phelps Hannah M , Ehrlich Peter F , Lo Andrea C , Sandberg Jesse K , Treece Amanda L , Gow Kenneth W , Glick Richard D , Davidoff Andrew M , Cost Nicholas G , Dix David B , Fernandez Conrad V , Dome Jeffrey S , Geller James I , Mullen Elizabeth A 
Published: January 2024

BACKGROUND:
To review race and ethnic group enrollment and outcomes for Wilms tumor (WT) across all 4 risk-assigned therapeutic trials from the current era Children’s Oncology Group Renal Tumor Biology and Risk Stratification Protocol, AREN03B2.

STUDY DESIGN:
For patients with WT enrolled in AREN03B2 (2006 to 2019), disease and biologic features, therapeutic study-specific enrollment, and event-free (EFS) and overall (OS) 4-year survival were compared between institutionally reported race and ethnic groups.

RESULTS:
Among 5,146 patients with WT, no statistically significant differences were detected between race and ethnic groups regarding subsequent risk-assigned therapeutic study enrollment, disease stage, histology, biologic factors, or overall EFS or OS, except the following variables: Black children were older and had larger tumors at enrollment, whereas Hispanic children had lower rates of diffuse anaplasia WT and loss of heterozygosity at 1p. The only significant difference in EFS or OS between race and ethnic groups was observed among the few children treated for diffuse anaplasia WT with regimen UH-1 and -2 on high-risk protocol, AREN0321. On this therapeutic arm only, Black children showed worse EFS (hazard ratio = 3.18) and OS (hazard ratio = 3.42). However, this finding was not replicated for patients treated with regimen UH-1 and -2 under AREN03B2 but not on AREN0321.

CONCLUSIONS:
Race and ethnic group enrollment appeared constant across AREN03B2 risk-assigned therapeutic trials. EFS and OS on these therapeutic trials when analyzed together were comparable regarding race and ethnicity. Black children may have experienced worse stage-specific survival when treated with regimen UH-1 and -2 on AREN0321, but this survival gap was not confirmed when analyzing additional high-risk AREN03B2 patients.
PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation
Authors: Sang Christopher Chin , Moore Gaelen , Tereshchenko Maria , Nosella Michael L. , Zhang Hongshan , Alderson T. Reid , Dasovich Morgan , Leung Anthony , Finkelstein Ilya J. , Forman-Kay Julie D. , Lee Hyun O. 
Published: January 2024

ABSTRACTPoly(ADP-ribose) polymerase 1 (PARP1) is one of the first responders to DNA damage and plays crucial roles in recruiting DNA repair proteins through its activity – poly(ADP-ribosyl)ation (PARylation). The enrichment of DNA repair proteins at sites of DNA damage has been described as the formation of a biomolecular condensate. However, it is not understood how PARP1 and PARylation contribute to the formation and organization of DNA repair condensates. Using recombinant human PARP1in vitro, we find that PARP1 readily forms viscous biomolecular condensates in a DNA-dependent manner and that this depends on its three zinc finger (ZnF) domains. PARylation enhances PARP1 condensation in a PAR chain-length dependent manner and increases the internal dynamics of PARP1 condensates. DNA and single-strand break repair proteins XRCC1, LigIII, Polβ, and FUS partition in PARP1 condensates, although in different patterns. While Polβ and FUS are both homogeneously mixed within PARP1 condensates, FUS enrichment is greatly enhanced upon PARylation whereas Polβ partitioning is not. XRCC1 and LigIII display an inhomogeneous organization within PARP1 condensates; their enrichment in these multiphase condensates is enhanced by PARylation. Functionally, PARP1 condensates concentrate short DNA fragments and facilitate compaction of long DNA and bridge DNA ends. Furthermore, the presence of PARP1 condensates significantly promotes DNA ligation upon PARylation. These findings provide insight into how PARP1 condensation and PARylation regulate the assembly and biochemical activities in DNA repair foci, which may inform on how PARPs function in other PAR-driven condensates.