bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive analysis of metastatic disease following surgery for clinically localized cutaneous melanoma
Authors: Boutros Christina S , Kakish Hanna , Pawar Omkar S , Loftus Alexander W , Ammori John B , Bordeaux Jeremy , Mangla Ankit , Sheng Iris , Schwartz Gary , Rothermel Luke D , Hoehn Richard S 
Published: September 2024

Abstract

Background
The National Comprehensive Cancer Network considers “baseline staging” (whole body computed tomography or positron emission tomography scans with or without brain magnetic resonance imaging scans) for all patients with asymptomatic melanoma who had a positive sentinel lymph node biopsy result. The true yield of these workups is unknown.

Methods
We created cohorts of adult patients with malignant melanoma using the National Cancer Database (2012-2020) to mimic 3 common scenarios: 1) clinically node-negative disease, with positive sentinel lymph node biopsy results; 2) clinically node-negative disease, with negative sentinel lymph node biopsy results; and 3) clinically node-positive disease, with confirmed lymph node metastases. Multivariable regression, supervised decision trees, and nomograms were constructed to assess the risk of metastases based on key features.

Results
In total, 10 371 patients were in scenario 1, 55 172 were in scenario 2, and 4012 were in scenario 3. The proportion of patients with any metastatic disease (brain metastases) were as follows: 1.4% (0.3%) in scenario 1, 0.3% (&lt;0.1%) in scenario 2, and 11.6% (1.6%) in scenario 3. On multivariable regression, Breslow depth greater than 4, ulceration, and lymphovascular invasion were associated with greater risk of metastatic disease. A supervised decision tree for patients in scenarios 1 and 2 found that the only groups with more than 2% risk of metastases were groups with T4 tumors or T2/T3 tumors with ulceration and lymphovascular invasion. Most groups had a negligible risk (&lt;0.1%) of brain metastases.

Conclusion
This study is the first large analysis to guide the use of imaging for cutaneous melanoma. Among patients with clinically node negative disease, metastatic disease is uncommon, and brain metastases are exceedingly rare. Further investigation could promote a tailored approach to metastatic workups guided by individual risk factors.
kpop: a kernel balancing approach for reducing specification assumptions in survey weighting
Authors: Hartman Erin , Hazlett Chad , Sterbenz Ciara 
Published: September 2024

Abstract
With the precipitous decline in response rates, researchers and pollsters have been left with highly nonrepresentative samples, relying on constructed weights to make these samples representative of the desired target population. Though practitioners employ valuable expert knowledge to choose what variables X must be adjusted for, they rarely defend particular functional forms relating these variables to the response process or the outcome. Unfortunately, commonly used calibration weights—which make the weighted mean of X in the sample equal that of the population—only ensure correct adjustment when the portion of the outcome and the response process left unexplained by linear functions of X are independent. To alleviate this functional form dependency, we describe kernel balancing for population weighting (kpop). This approach replaces the design matrix X with a kernel matrix, K encoding high-order information about X. Weights are then found to make the weighted average row of K among sampled units approximately equal to that of the target population. This produces good calibration on a wide range of smooth functions of X, without relying on the user to decide which X or what functions of them to include. We describe the method and illustrate it by application to polling data from the 2016 US presidential election.
Impacts of innovation school system in Korea: a latent space item response model with Neyman–Scott point process
Authors: Yi Seorim , Kim Minkyu , Park Jaewoo , Jeon Minjeong , Jin Ick Hoon 
Published: September 2024

Abstract
South Korea’s educational system has faced criticism for its lack of focus on critical thinking and creativity, resulting in high levels of stress and anxiety among students. As part of the government’s effort to improve the educational system, the innovation school system was introduced in 2009, which aims to develop students’ creativity as well as their non-cognitive skills. To better understand the differences between innovation and regular school systems in South Korea, we propose a novel method that combines the latent space item response model with the Neyman–Scott point process model. Our method accounts for the heterogeneity of items and students, captures relationships between respondents and items, and identifies item and student clusters that can provide a comprehensive understanding of students’ behaviours/perceptions on non-cognitive outcomes. Our analysis reveals that students in the innovation school system show a higher sense of citizenship, while those in the regular school system tend to associate confidence in appearance with social ability. A comparison with exploratory item factor analysis highlights our method’s advantages in terms of uncertainty quantification of the clustering process and more detailed and nuanced clustering results. Our method is made available to an existing R package, lsirm12pl.
Mode-wise principal subspace pursuit and matrix spiked covariance model
Authors: Tang Runshi , Yuan Ming , Zhang Anru R 
Published: September 2024

Abstract
This paper introduces a novel framework called Mode-wise Principal Subspace Pursuit (MOP-UP) to extract hidden variations in both the row and column dimensions for matrix data. To enhance the understanding of the framework, we introduce a class of matrix-variate spiked covariance models that serve as inspiration for the development of the MOP-UP algorithm. The MOP-UP algorithm consists of two steps: Average Subspace Capture (ASC) and Alternating Projection. These steps are specifically designed to capture the row-wise and column-wise dimension-reduced subspaces which contain the most informative features of the data. ASC utilizes a novel average projection operator as initialization and achieves exact recovery in the noiseless setting. We analyse the convergence and non-asymptotic error bounds of MOP-UP, introducing a blockwise matrix eigenvalue perturbation bound that proves the desired bound, where classic perturbation bounds fail. The effectiveness and practical merits of the proposed framework are demonstrated through experiments on both simulated and real datasets. Lastly, we discuss generalizations of our approach to higher-order data.
It’s not all that bad: associations among pain characteristics and sexual well-being in people living with chronic pain
Authors: Santos-Iglesias Pablo , Estey Justine L , Crump Lyndsay , LaChapelle Diane L , Byers E Sandra 
Published: September 2024

Abstract

Background
Individuals experiencing chronic pain often report adverse effects on their sexual functioning. However, other important aspects of sexual well-being (SWB), such as sexual distress and sexual self-esteem, have received little attention. This is an important omission because a SWB involves more than just good sexual function. Similarly, past research has not examined how chronic pain characteristics affect the different aspects of SWB.

Aim
The goal of this cross-sectional study was to examine the SWB of individuals living with chronic pain and to examine the extent to which SWB is associated with different chronic pain characteristics.

Methods
A total of 310 individuals (28.1% men, 70.6% women, 1.3% transgender men) with ages between 21 and 50 (M = 31.96, SD = 6.13) who were in a romantic relationship and with self-reported chronic pain for three months or longer completed an online survey.

Outcomes
The following indicators of SWB were included in the study: frequency of genital sexual activity, sexual satisfaction, sexual self-esteem, sexual desire, sexual function, genital pain, and sexual distress.

Results
The results show that most individuals with chronic pain maintain an active and satisfying sexual life and feel positive about themselves as a sexual partner. Slightly more than a fourth reported experiencing at least one sexual functioning difficulty and almost three-fourths of them found those difficulties sexually distressing. A first canonical correlation showed that more negative pain characteristics were associated with poorer SWB. The second canonical correlation showed that greater perceived partner support can offset the negative relationship between pain and some aspects of SWB.

Clinical implications
These findings show that individuals living with chronic pain can experience positive SWB. Furthermore, the buffering effect of partner support suggests it is important to involve romantic partners in interventions aimed at improving the SWB of people living with chronic pain.

Strengths and limitations
The study examined a large number of indicators of SWB using a sample of individuals with different types of chronic pain. Limitations include potential self-selection bias and a sample that was predominantly white and highly educated.

Conclusions
The results paint a more positive picture of the SWB of individuals living with pain and show that individuals living with chronic pain can experience positive SWB. These findings can help for researchers, educators, and clinicians about how to conceptualize, understand, and improve the SWB of individuals living with chronic pain.
Differential warming at crown scale impacts walnut primary growth onset and secondary growth rate
Authors: Dusart Nicolas , Moulia Bruno , Saudreau Marc , Serre Christophe , Charrier Guillaume , Hartmann Félix P 
Published: September 2024

Abstract
Trees are exposed to significant spatio-temporal thermal variations, which can induce intra-crown discrepancies in the onset and dynamics of primary and secondary growth. In recent decades, an increase in late winter and early spring temperatures has been observed, potentially accelerating bud break, cambial activation, and their coordination. Intra-crown temperature heterogeneities could lead to asymmetric tree shapes unless there is a compensatory mechanism at the crown level. An original warming experiment was conducted on young Juglans regia trees in a greenhouse. The average temperature difference during the day between warmed and control parts from February to August was 4 °C. The warming treatment advanced the date of budbreak significantly, by up to 14 d. Warming did not alter secondary growth resumption but increased growth rates, leading to higher xylem cell production (by 2-fold) and to an increase in radial increment (+80% compared with control). Meristem resumptions were asynchronous without coordination in response to temperature. Buds on warmed branches began to swell 2 weeks prior to cambial division, which was 1 week earlier than on control branches. A difference in carbon and water remobilization at the end of bud ecodormancy was noted under warming. Overall, our results argue for a lack of compensatory mechanisms at the crown scale, which may lead to significant changes in tree architecture in response to intra-crown temperature heterogeneities.
‘Credulous or the naïve?’ The Irish Department of Health’s response to commercial surrogacy
Authors: O’Connell Claire 
Published: September 2024

Abstract
This article explores the prohibition of commercial surrogacy as currently contained within the Health (Assisted Human Reproduction) Act 2024. The 2024 Act regulates surrogacy for the first time in Irish law and creates a framework for the recognition of intending parentage arising from surrogacy agreements. This article explores the safeguards for surrogates contained within the 2024 Act against the arguments generally cited by the Department of Health against commercial surrogacy—that of commodifying children and exploitation of women. It considers Irish case law on commercial surrogacy and that of the European Court of Human Rights. It also includes passages from the O’Connell Study which was conducted within the author’s PhD thesis. The article concludes that the refusal to recognize the legal parent–child relationship based on the commercial nature of the surrogacy agreement is a violation of the child’s right to respect for private life under Article 8 of the European Convention on Human Rights (the ECHR). It also finds that the Irish Courts have found no public policy reason strong enough to justify the refusal to recognize a foreign adoption order which followed a commercial surrogacy agreement. Primarily it argues that a commercial surrogacy agreement can be ethical; but requires sufficient safeguards for those parties involved.
Molecular characterization of metastatic penile squamous cell carcinoma in developing countries and its impact on clinical outcomes: LACOG 2018 translational study
Authors: Monteiro Fernando Sabino Marques , Alencar Junior Antonio Machado , da Trindade Karine Martins , Rebelatto Taiane Francieli , Maluf Fernando C , Gazzola Antonia A , Barrios Pablo M , Bellmunt Joaquim , de Jesus Rafaela Gomes , Silva Gyl Eanes Barros , Teixeira Junior Antonio Augusto Lima , Spiess Philippe E , Fay Andre P 
Published: September 2024

Abstract

Background
Penile squamous cell carcinoma (PSCC) is a rare malignancy. However, in developing countries the incidence rate is higher. The understanding of molecular alterations is essential for evaluating possible targets for more effective systemic therapies.

Methods
We retrospectively collected clinical data of metastatic PSCC (mPSCC) patients who had received at least one prior systemic treatment from 3 Brazilian hospitals. Tumor samples were evaluated using the next-generation sequencing (NGS) Foundation One DX and immunohistochemistry (IHC). The objective was to identify and describe somatic genomic alterations known to be functional or pathogenic and their association with survival outcomes.

Results
Twenty-three patients were identified, 22 and 18 patients had tumor samples analyzed by IHC and NGS, respectively. PD-L1 expression (CPS ≥ 1%) was positive in 14 patients (63.6%). Regarding the genomic alterations, 16 patients (88.9%) had some clinically relevant genomic alterations. TP53, TERT, CDKN2A, PIK3CA, NOTCH1, and CDKN2B loss were identified in 66.7%, 50%, 50%, 33.3%, 27.8%, and 22.2% of the patients, respectively. No MSI or TMB high (≥10 mutations/MB) cases were identified. NOTCH1 mutation was identified only in HPV-negative patients and it was associated with worse OS (yes: 5.5 vs no: 12.8 months, P = .049) and progression-free survival (yes: 5.5 vs no: 11.7 months, P = .032).

Conclusion
This study demonstrated that molecular alterations in mPSCC from developing countries are similar to those from developed countries. Predictive biomarkers for immunotherapy response such as TMB high or MSI were not identified. Specific gene mutations may identify patients with worse prognoses and open new avenues for therapeutic development.
The system building perspective for building sustainable system configurations using the German energy transition as an example
Authors: Olbrich Sarah , Bauknecht Dierk 
Published: September 2024

Abstract
An increasing number of countries employ net-zero decarbonization targets in their climate policies, which requires decarbonizing socio-technical systems like the energy system by mid-century. While there is a high level of agreement about net-zero targets, there remains great uncertainty as to how to meet them. At the same time, the challenges of building a new system that fulfils systemic targets such as net-zero are insufficiently reflected on in the sustainability transitions literature. With the help of a literature review building on theories of socio-technical transitions, this paper introduces system building dimensions that account for the difficulties of net-zero transitions. We identify four such dimensions: (1) competing potential system configurations with different sustainability implications; (2) a broad range of complementary system elements needed; (3) lock-ins and path dependencies in the system building process; and (4) the politics of system building. We offer the German energy transition as an empirical case study to illustrate the relevance of these system building dimensions.
An investigation of the relationship between tropical monsoon precipitation changes and stratospheric sulfate aerosol optical depth
Authors: Xavier Anu , Bala Govindasamy , Roose Shinto , KH Usha 
Published: September 2024

Abstract
Stratospheric aerosol geoengineering (SAG) is one of the several solar geoengineering options that have been proposed to counteract climate change. In the case of SAG, reflective aerosols injected into the stratosphere would reflect more sunlight and cool the planet. When assessing the potential efficacy and risks of SAG, the sensitivity of tropical monsoon precipitation changes should be also considered. Using a climate model, we perform several stylized simulations with different meridional distributions and amounts of volcanic sulfate aerosols in the stratosphere. Because tropical monsoon precipitation responds to global mean and interhemispheric difference in radiative forcing or temperature, we quantify the sensitivity of tropical monsoon precipitation to SAG in terms of two parameters: global mean aerosol optical depth (GMAOD) and interhemispheric AOD difference (IHAODD). For instance, we find that the simulated northern hemisphere monsoon precipitation has a sensitivity of −1.33 ± 0.95% per 0.1 increase in GMAOD and −7.62 ± 0.27% per 0.1 increase in IHAODD. Our estimated precipitation changes in terms of the two sensitivity parameters for the global mean precipitation and for the indices of tropical, northern hemisphere, southern hemisphere and Indian summer monsoon precipitation are in good agreement with the model simulated precipitation changes. Similar sensitivity estimates are also made for unit changes in global mean and interhemispheric differences in effective radiative forcing and surface temperature. Our study based on planetary energetics provides a simpler framework for understanding the tropical monsoon precipitation response to external forcing agents.
Diurnal.plant.tools in 2024: Expanding to Marchantia polymorpha and Four Angiosperms
Authors: Tan Qiao Wen , Tan Emmanuel , Mutwil Marek 
Published: September 2024

Abstract
Diurnal gene expression is a pervasive phenomenon occurring across all kingdoms of life, orchestrating adaptive responses to daily environmental fluctuations and thus enhancing organismal fitness. Our understanding of the plant circadian clock is primarily derived from studies in Arabidopsis, and direct comparisons are difficult due to differences in gene family sizes. To this end, the identification of functional orthologs based on diurnal and tissue expression is necessary. The diurnal.plant.tools database constitutes a repository of gene expression profiles from 17 members of the Archaeplastida lineage, with built-in tools facilitating cross-species comparisons. In this database update, we expand the dataset with diurnal gene expression from four agriculturally significant crop species and Marchantia, a plant of evolutionary significance. Notably, the inclusion of diurnal gene expression data for Marchantia enables researchers to glean insights into the evolutionary trajectories of the circadian clock and other biological processes spanning from algae to angiosperms. Moreover, integrating diurnal gene expression data with datasets from related gene co-expression databases, such as CoNekt-Plants and CoNekt-Stress, which contain gene expression data for tissue and perturbation experiments, provides a comprehensive overview of gene functions across diverse biological contexts. This expanded database serves as a valuable resource for elucidating the intricacies of diurnal gene regulation and its evolutionary underpinnings in plant biology.
N6-methyladenosine transcriptome-wide profiles of maize kernel development
Authors: Wu Jia Wen , Zheng Guang Ming , Zhang Lin , Zhao Ya Jie , Yan Ru Yu , Ren Ru Chang , Wei Yi Ming , Li Kunpeng , Zhang Xian Sheng , Zhao Xiang Yu 
Published: September 2024

Abstract
Maize (Zea mays L.) kernel development is a complex and dynamic process involving cell division and differentiation, into a variety of cell types. Epigenetic modifications, including DNA methylation, play a pivotal role in regulating this process. N6-methyladenosine modification is a universal and dynamic posttranscriptional epigenetic modification that is involved in the regulation of plant development. However, the role of N6-methyladenosine in maize kernel development remains unknown. In this study, we have constructed transcriptome-wide profiles for maize kernels at various stages of early development. Utilizing a combination of MeRIP-seq and RNA-seq analyses, we identified a total of 11,170, 10,973, 11,094, 11,990, 12,203, and 10,893 N6-methyladenosine peaks in maize kernels at 0, 2, 4, 6, 8, and 12 days after pollination, respectively. These N6-methyladenosine modifications were primarily deposited at the 3′-UTRs and were associated with the conserved motif-UGUACA. Additionally, we found that conserved N6-methyladenosine modification is involved in the regulation of genes that are ubiquitously expressed during kernel development. Further analysis revealed that N6-methyladenosine peak intensity was negatively correlated with the mRNA abundance of these ubiquitously expressed genes. Meanwhile, we employed phylogenetic analysis to predict potential regulatory proteins involved in maize kernel development and identified several that participate in the regulation of N6-methyladenosine modifications. Collectively, our results suggest the existence of a novel posttranscriptional epigenetic modification mechanism involved in the regulation of maize kernel development, thereby providing a novel perspective for maize molecular breeding.