bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distilling large language models for matching patients to clinical trials
Authors: Nievas Mauro , Basu Aditya , Wang Yanshan , Singh Hrituraj 
Published: April 2024

Abstract

Objective
The objective of this study is to systematically examine the efficacy of both proprietary (GPT-3.5, GPT-4) and open-source large language models (LLMs) (LLAMA 7B, 13B, 70B) in the context of matching patients to clinical trials in healthcare.

Materials and methods
The study employs a multifaceted evaluation framework, incorporating extensive automated and human-centric assessments along with a detailed error analysis for each model, and assesses LLMs’ capabilities in analyzing patient eligibility against clinical trial’s inclusion and exclusion criteria. To improve the adaptability of open-source LLMs, a specialized synthetic dataset was created using GPT-4, facilitating effective fine-tuning under constrained data conditions.

Results
The findings indicate that open-source LLMs, when fine-tuned on this limited and synthetic dataset, achieve performance parity with their proprietary counterparts, such as GPT-3.5.

Discussion
This study highlights the recent success of LLMs in the high-stakes domain of healthcare, specifically in patient-trial matching. The research demonstrates the potential of open-source models to match the performance of proprietary models when fine-tuned appropriately, addressing challenges like cost, privacy, and reproducibility concerns associated with closed-source proprietary LLMs.

Conclusion
The study underscores the opportunity for open-source LLMs in patient-trial matching. To encourage further research and applications in this field, the annotated evaluation dataset and the fine-tuned LLM, Trial-LLAMA, are released for public use.
Introduction and establishment of Euwallacea fornicatus (Coleoptera: Curculionidae: Scolytinae) in Brazil
Authors: Covre Luana S , Atkinson Thomas H , Johnson Andrew J , Flechtmann Carlos A H 
Published: April 2024

Abstract
Euwallacea fornicatus is an invasive tree pest able to infest healthy plants and cause damage to many host plants. This beetle has become established in several countries where it was introduced. It has now become established in Brazil, and while the original introduction site remains uncertain, there is a possibility of multiple introductions. We report the first evidence for the establishment of E. fornicatus with molecular confirmation, as well as its distribution, and host plants in Brazil. Euwallacea fornicatus has spread to main commercial avocado groves, other monocultures, and native vegetation in the country, and its pest status puts it as a threat, mainly to Brazilian avocado producers.
Anisotropic Bayesian linearized stochastic seismic inversion with multi-parameter decoupling
Authors: Yu Bo , Shi Ying , Tian Yukun , Zhou Hui , Yu Zhanqing , Zhang Yuanpeng , Wang Weihong 
Published: April 2024

AbstractThe shale-oil reservoir emerges as a significant unconventional energy source, commonly predicted by anisotropic seismic inversion. Considering the intricate nature of shale-oil reservoirs, it becomes imperative to consider uncertainties during anisotropic inversion. An effective approach to address this involves stochastic inversion, specifically the anisotropic Bayesian linearized inversion (ABLI), which characterizes statistical and spatial correlations of subsurface parameters through a crucial multivariate correlation matrix constructed through geostatistics. However, an inevitable challenge in stochastic inversion arises from interference during the calibration of statistical and spatial correlations of subsurface parameters. This challenge becomes particularly pronounced in anisotropic inversion, heightened by the multitude of involved model parameters. Existing decorrelation approaches primarily address statistical correlation, neglecting the impact of spatial correlation. To tackle this issue, a novel multi-parameter decoupling strategy is proposed, formulating decoupling-ABLI (D-ABLI). D-ABLI introduces an advanced decorrelation approach, and uses principal component analysis (PCA) to simultaneously eliminate impact of statistical and spatial correlations on ABLI. The decoupling enhances the inversion accuracy of model parameters in ABLI, particularly for density and anisotropic parameters. The theoretical underpinnings of the decoupling strategy are demonstrated to be reasonable, and the effectiveness of D-ABLI is proved through a theoretical data test and a field data test regarding shale-oil reservoirs. The D-ABLI results offer the capability to estimate fracture density accurately and unveil the distribution of shale oil.
Microhabitat selection by the Oscura Mountains Colorado Chipmunk (Neotamias quadrivittatus oscuraensis): an old-growth pinyon–juniper woodland specialist
Authors: O’Connell Clare N , Frey Jennifer K 
Published: April 2024

Abstract
Habitat specialists have been largely overlooked in old-growth pinyon–juniper woodlands, despite specialists exhibiting heightened sensitivity to anthropogenic habitat loss. Furthermore, small mammal relationships within pinyon–juniper woodlands have most commonly been investigated via species abundance or habitat use, rather than habitat selection, thereby providing limited management metrics. We used the Oscura Mountains Colorado Chipmunk (Neotamias quadrivittatus oscuraensis) as a model organism to evaluate whether old-growth conditions drive resource selection by small mammals associated with pinyon–juniper woodlands. The goal of our study was to determine resources important to the chipmunk to inform management decisions. We evaluated microhabitat selection by testing a priori predictions based on natural history characteristics of the chipmunk and the woodlands. We grouped predictions into habitat characteristics affiliated with or not affiliated with old growth. We tested predictions under a multistage modeling framework using generalized linear mixed models with a binomial response variable of use versus availability. Probability of selection by chipmunks increased with increasing mean juniper diameter and increasing variation of pinyon diameter and decreased with increased distance to rocky escape terrain and increased mean percent grass cover. Our findings support the classification of the Oscura Mountains Colorado chipmunk as an old-growth pinyon–juniper specialist, as the chipmunk displayed disproportionate preference for old-growth microhabitat conditions. We recommend management policies that conserve old-growth multiage stands of pinyons and junipers. Old-growth conditions near outcroppings, escarpments, and large boulders are of particular conservation concern. Further, thinning resulting in increased grass cover may be detrimental to this old-growth pinyon–juniper specialist.
Philosophical Acts of Wonder in Bioethics
Authors: Zhang Alexander 
Published: April 2024

AbstractTwo sources of possible disagreement in bioethics may be associated with pessimism about what bioethics can achieve. First, pluralism implies that bioethics engages with interlocutors who hold divergent moral beliefs. Pessimists might believe that these disagreements significantly limit the extent to which bioethics can provide normatively robust guidance in relevant areas. Second, the interdisciplinary nature of bioethics suggests that interlocutors may hold divergent views on the nature of bioethics itself—particularly its practicality. Pessimists may suppose that interdisciplinary disagreements could frustrate the goals of bioethics. In this article, I explore how wonder may alleviate the concerns of the first group of pessimists regarding problems associated with pluralism, provided that we are willing to accept some interdisciplinary frustrations. Then, I invite readers of this issue of The Journal of Medicine & Philosophy to test these intuitions by considering the role of wonder in these articles.
The combination of elevated CO2 and warmer temperature reduces photosynthetic capacity without diluting leaf N concentration in Amur linden (Tilia amurensis)
Authors: Wang Lei , Zheng Jinping , Wang Gerong , Dang Qing-Lai 
Published: April 2024

Abstract
Elevated CO2 and warmer temperatures represent the future environmental conditions in the context of global change. A good understanding of plant response to their combined effects is, therefore, critically important for predicting future plant performance. This study investigated the photosynthetic acclimation of Amur linden (Tilia amurensis) seedlings (current year, about 60 cm tall), a shade-tolerant tree species in the temperate broadleaf deciduous forest, to the combination of current CO2 concentration and temperature (CC) and the combination of the predicted future CO2 concentration and temperature (FC). The results show that FC promoted aboveground growth, but reduced photosynthetic capacity (Vcmax: maximum rate of RuBP carboxylation and Jmax: maximum photosynthetic electron transport rate). However, the photosynthetic rate measured under the corresponding growth CO2 concentration was still higher under FC than under CC. FC depressed the photosynthetic limiting transition point (Ci-t, An-t) from Rubisco carboxylation to RuBP regeneration, i.e. An-t decreased without a change in Ci-t. FC did not change leaf N concentration but increased the total leaf N content per tree and photosynthetic nitrogen utilization efficiency. This suggests that N utilization, rather than photosynthetic capacity, may play an important role in the acclimation of the species to future climatic conditions. This study provides new insights into the photosynthetic acclimation of Amur linden and can be used to predict its possible performance under future climatic conditions.
Redox regulation of epigenetic and epitranscriptomic gene regulatory pathways in plants
Authors: Auverlot Juline , Dard Avilien , Sáez-Vásquez Julio , Reichheld Jean-Philippe 
Published: April 2024

Abstract
Developmental and environmental constraints influence genome expression through complex networks of regulatory mechanisms. Epigenetic modifications and remodelling of chromatin are some of the major actors regulating the dynamic of gene expression. Unravelling the factors relaying environmental signals that induce gene expression reprogramming under stress conditions is an important and fundamental question. Indeed, many enzymes involved in epigenetic and chromatin modifications are regulated by redox pathways, through post-translational modifications of proteins or by modifications of the flux of metabolic intermediates. Such modifications are potential hubs to relay developmental and environmental changes for gene expression reprogramming. In this review, we provide an update on the interaction between major redox mediators, such as reactive oxygen and nitrogen species and antioxidants, and epigenetic changes in plants. We detail how redox status alters post-translational modifications of proteins, intracellular epigenetic and epitranscriptional modifications, and how redox regulation interplays with DNA methylation, histone acetylation and methylation, miRNA biogenesis, and chromatin structure and remodelling to reprogram genome expression under environmental constraints.
Sugar sensing in C4 source leaves: a gap that needs to be filled
Authors: Chen Lily , Ghannoum Oula , Furbank Robert T 
Published: April 2024

Abstract
Plant growth depends on sugar production and export by photosynthesizing source leaves and sugar allocation and import by sink tissues (grains, roots, stems, and young leaves). Photosynthesis and sink demand are tightly coordinated through metabolic (substrate, allosteric) feedback and signalling (sugar, hormones) mechanisms. Sugar signalling integrates sugar production with plant development and environmental cues. In C3 plants (e.g. wheat and rice), it is well documented that sugar accumulation in source leaves, due to source–sink imbalance, negatively feeds back on photosynthesis and plant productivity. However, we have a limited understanding about the molecular mechanisms underlying those feedback regulations, especially in C4 plants (e.g. maize, sorghum, and sugarcane). Recent work with the C4 model plant Setaria viridis suggested that C4 leaves have different sugar sensing thresholds and behaviours relative to C3 counterparts. Addressing this research priority is critical because improving crop yield requires a better understanding of how plants coordinate source activity with sink demand. Here we review the literature, present a model of action for sugar sensing in C4 source leaves, and suggest ways forward.
Evolution of FLOWERING LOCUS T-like genes in angiosperms: a core Lamiales-specific diversification
Authors: Zhao Jiu-Xia , Wang Shu , Wen Jing , Zhou Shi-Zhao , Jiang Xiao-Dong , Zhong Mi-Cai , Liu Jie , Dong Xue , Deng Yunfei , Hu Jin-Yong , Li De-Zhu 
Published: April 2024

Abstract
Plant life history is determined by two transitions, germination and flowering time, in which the phosphatidylethanolamine-binding proteins (PEBPs) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) play key regulatory roles. Compared with the highly conserved TFL1-like genes, FT-like genes vary significantly in copy numbers in gymnosperms, and monocots within the angiosperms, while sporadic duplications can be observed in eudicots. Here, via a systematic analysis of the PEBPs in angiosperms with a special focus on 12 representative species featuring high-quality genomes in the order Lamiales, we identified a successive lineage-specific but systematic expansion of FT-like genes in the families of core Lamiales. The first expansion event generated FT1-like genes mainly via a core Lamiales-specific whole-genome duplication (cL-WGD), while a likely random duplication produced the FT2-like genes in the lineages containing Scrophulariaceae and the rest of the core Lamiales. Both FT1- and FT2-like genes were further amplified tandemly in some families. These expanded FT-like genes featured highly diverged expression patterns and structural variation, indicating functional diversification. Intriguingly, some core Lamiales contained the relict MOTHER OF FT AND TFL1 like 2 (MFT2) that probably expanded in the common ancestor of angiosperms. Our data showcase the highly dynamic lineage-specific expansion of the FT-like genes, and thus provide important and fresh evolutionary insights into the gene regulatory network underpinning flowering time diversity in Lamiales and, more generally, in angiosperms.
Redox regulation of gene expression: proteomics reveals multiple previously undescribed redox-sensitive cysteines in transcription complexes and chromatin modifiers
Authors: Dard Avilien , Van Breusegem Frank , Mhamdi Amna 
Published: April 2024

Abstract
Redox signalling is crucial for regulating plant development and adaptation to environmental changes. Proteins with redox-sensitive cysteines can sense oxidative stress and modulate their functions. Recent proteomics efforts have comprehensively mapped the proteins targeted by oxidative modifications. The nucleus, the epicentre of transcriptional reprogramming, contains a large number of proteins that control gene expression. Specific redox-sensitive transcription factors have long been recognized as key players in decoding redox signals in the nucleus and thus in regulating transcriptional responses. Consequently, the redox regulation of the nuclear transcription machinery and its cofactors has received less attention. In this review, we screened proteomic datasets for redox-sensitive cysteines on proteins of the core transcription complexes and chromatin modifiers in Arabidopsis thaliana. Our analysis indicates that redox regulation affects every step of gene transcription, from initiation to elongation and termination. We report previously undescribed redox-sensitive subunits in transcription complexes and discuss the emerging challenges in unravelling the landscape of redox-regulated processes involved in nuclear gene transcription.
Discovery of a new IW And-type dwarf nova with both tilted disc and tidal instability
Authors: Sun Yongkang , Li Xin , Ao Qige , Cui Wenyuan , Zhang Bowen , Huang Yang , Shi Jianrong , Li Linlin , Liu Jifeng 
Published: April 2024

ABSTRACT
IW And-type dwarf novae are anomalous Z Cam stars featured with outbursts happening during standstill states, which are not expected in the standard disc instability model. The physical mechanisms for these variations remain unclear. In this study, we report the discovery of a new candidate IW And-type dwarf nova J0652+2436, identified with its frequent outbursts from the slowly rising standstill states. Luckily, the Transiting Exoplanet Survey Satellite observations during a long standstill state and the earlier K2 observations give a chance to find the orbital and negative superhump period in the light curve of J0652+2436, allowing the measurement of its mass ratio of 0.366. This mass ratio is marginally possible for the tidal instability to set in according to previous smoothed particle hydrodynamics simulations. Thus, we propose that the outbursts in J0652+2436 are likely to be caused by the growing accretion disc during standstills, in favour of the previous hypothesis of the mechanisms lying in all IW And stars. We conclude that J0652+2436 might be the first IW And star with both a precessing tilted disc and tidal instability, which will be an important laboratory for studying the accretion disc dynamics and help understand the IW And phenomenon.
Gas-phase hydrogenation of large, astronomically relevant PAH cations
Authors: Hua Lijun , Hu Xiaoyi , Zhen Junfeng , Yang Xuejuan 
Published: April 2024

ABSTRACT
To investigate the gas-phase hydrogenation processes of large, astronomically relevant cationic polycyclic aromatic hydrocarbon (PAH) molecules under the interstellar environments, the ion–molecule collision reaction between six PAH cations and H-atoms is studied. The experimental results show that the hydrogenated PAH cations are efficiently formed, and no even–odd hydrogenated mass patterns are observed in the hydrogenation processes. The structure of newly formed hydrogenated PAH cations and the bonding energy for the hydrogenation reaction pathways are investigated with quantum theoretical calculations. The exothermic energy for each reaction pathway is relatively high, and the competition between hydrogenation and dehydrogenation is confirmed. From the theoretical calculation, the bonding ability plays an important role in the gas-phase hydrogenation processes. The factors that affect the hydrogenation chemical reactivity are discussed, including the effect of carbon skeleton structure, the side-edged structure, the molecular size, the five- and six-membered C-ring structure, the bay region structure, and the neighbouring hydrogenation. The infrared spectra of hydrogenated PAH cations are also calculated. These results we obtain once again validate the complexity of hydrogenated PAH molecules, and provide the direction for the simulations and observations under the co-evolution interstellar chemistry network. We infer that if we do not consider other chemical evolution processes (e.g. photoevolution), then the hydrogenation states and forms of PAH compounds are intricate and complex in the interstellar medium.
Limited capability of MRI radiomics to predict primary tumor histology of brain metastases in external validation
Authors: Strotzer Quirin D , Wagner Thomas , Angstwurm Pia , Hense Katharina , Scheuermeyer Lucca , Noeva Ekaterina , Dinkel Johannes , Stroszczynski Christian , Fellner Claudia , Riemenschneider Markus J , Rosengarth Katharina , Pukrop Tobias , Wiesinger Isabel , Wendl Christina , Schicho Andreas 
Published: April 2024

Abstract

Background
Growing research demonstrates the ability to predict histology or genetic information of various malignancies using radiomic features extracted from imaging data. This study aimed to investigate MRI-based radiomics in predicting the primary tumor of brain metastases through internal and external validation, using oversampling techniques to address the class imbalance.

Methods
This IRB-approved retrospective multicenter study included brain metastases from lung cancer, melanoma, breast cancer, colorectal cancer, and a combined heterogenous group of other primary entities (5-class classification). Local data were acquired between 2003 and 2021 from 231 patients (545 metastases). External validation was performed with 82 patients (280 metastases) and 258 patients (809 metastases) from the publicly available Stanford BrainMetShare and the University of California San Francisco Brain Metastases Stereotactic Radiosurgery datasets, respectively. Preprocessing included brain extraction, bias correction, coregistration, intensity normalization, and semi-manual binary tumor segmentation. Two-thousand five hundred and twenty-eight radiomic features were extracted from T1w (± contrast), fluid-attenuated inversion recovery (FLAIR), and wavelet transforms for each sequence (8 decompositions). Random forest classifiers were trained with selected features on original and oversampled data (5-fold cross-validation) and evaluated on internal/external holdout test sets using accuracy, precision, recall, F1 score, and area under the receiver-operating characteristic curve (AUC).

Results
Oversampling did not improve the overall unsatisfactory performance on the internal and external test sets. Incorrect data partitioning (oversampling before train/validation/test split) leads to a massive overestimation of model performance.

Conclusions
Radiomics models’ capability to predict histologic or genomic data from imaging should be critically assessed; external validation is essential.
Internal sexual harassment among police personnel: Insights from a Birmingham, UK cross-sectional survey
Authors: Magsi Lali , Ariel Barak 
Published: April 2024

Abstract
Internal sexual harassment by and between police officers is understudied. We report on a perversive, damaging, and underreported phenomenon through an anonymous survey in Birmingham, UK. Overall, internal sexual harassment affects one in every five employees, with 8.3% of males and 43% of females victimized, particularly in small police units. More than two-thirds of officers who experience physical sexual harassment and half who experience non-physical sexual harassment are serial victims (three or more), indicating that some staff members are routinely targeted by their peers—especially female officers. Victims reported long-term adverse effects, including stress, anxiety, isolation, and anger, and a quarter considered leaving the organization. One in ten observe internal sexual harassment; however, bystanders refrain from reporting incidents due to the perception that such conduct constitutes banter or the desire to protect the harasser’s reputation. In light of the responses, policy implications are discussed.