bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining the Formalin Fixation Method for Maintaining High RNA Quality in Surgical Lung Specimens
Authors: Teishikata Takashi , Itoh Manabu , Okamoto Yusuke , Miyahara Naofumi , Nakashima Chiho , Takahashi Koichiro , Hiratsuka Masafumi , Kai Keita , Kamohara Keiji 
Published: January 2025

ABSTRACTBackgroundMultiplex genetic testing is recommended when treating nonsmall cell lung cancer. A certain percentage of test failures in RNA assays owing to poor surgical specimen quality have been documented, and fixation failure is a possible cause. At our institution, sheet‐like fixation is performed to reduce fixation time. This study aimed to compare the quality of RNA from resected lung cancer specimens following different fixation methods.MethodsSheet‐like fixation specimens (n = 15), conventional fixation specimens of the same resected lungs (n = 15), and other lung cancer specimens collected for conventional fixation and subjected to multiplex gene‐panel testing (n = 22) were retrospectively examined. RNA was extracted from each specimen. RNA quality and quantity were compared, and the success rate of multiplex gene‐panel testing was determined.ResultsThe DV200 value was significantly higher in RNA extracted from sheet‐like fixation samples (median 47.5%, interquartile range [IQR]:40.3–51.5) compared with RNA extracted from conventionally fixed samples or conventionally fixed samples of other patient specimens (median 21%, IQR:5.3–29.8 and median 16.3%, IQR:9.5–27.1, respectively). No significant difference was observed in nucleic acid concentration. The multiplex genetic analysis success rate was 95% with conventional methods (one failure); however, it was 100% with the sheet‐like fixation method.ConclusionSheet‐like fixation preserved RNA extracted from lung cancer specimens, resulting in lesser degradation than with conventional fixation.
Accounting for spatiotemporal patterns of long‐term recursion in estimating local‐scale step selection
Authors: Egan Michael E. , Gorman Nicole T. , Eichholz Michael W. , Skinner Dan , Schlichting Peter E. , Bastille‐Rousseau Guillaume 
Published: January 2025

Abstract

Step‐selection analysis (SSA) is ubiquitous for assessing local‐scale habitat selection by comparing relocations from telemetry data (used steps) to potential relocations given the movement of the animal (available steps). The case–control design of SSA is intended to estimate selection at the spatiotemporal scale of these steps. However, long‐term behaviour associated with recurring use of certain locations or resources may additionally impact movement decisions, potentially impacting the estimates produced by SSA.

To determine the impact of recursive behaviour on local selection, we simulated movement trajectories in which animals exhibited patterns of recursion. Based on these simulated trajectories, we evaluated the impact of long‐term behaviour on estimates of step‐selection. Then, we developed a new approach to identify recursion points based on a time‐dependent kernel density estimate including latitude, longitude and time of day. Based on this information, we accounted for recursive behaviour by including the relationship between available steps to recursion points or using recursion points to adjust our sample of available steps. Finally, we apply this approach to estimate the response of white‐tailed deer (Odocoileus virginianus) to sources of risk.

Recursive movement resulted in biased estimates of selection when using previously established step‐selection methods. However, we found that our correction models were able to produce accurate estimates across differing recursion scenarios. When applied to an empirical deer data set, these methods revealed a pattern of selection and avoidance for human modified areas that was masked by previous approaches.

Our results suggest that long‐term recursive behaviour may have unappreciated effects on estimates from SSA. Specifically, since the used and available steps in SSA are associated with specific places and times, covariates must account for variation in spatial and temporal patterns of long‐term behaviour. Unless properly accounted for, the effects of long‐term recursive behaviour will inhibit the ability of SSA to characterize fine‐scale behaviours such as predator response or foraging ecology.
Confidence and information usage: Evidence from soil testing in India
Authors: Gars Jared , Fishman Ram , Kishore Avinash , Rothler Yoav , Ward Patrick S. 
Published: January 2025

AbstractInformational barriers are often considered to be a major constraint to the adoption of improved farming practices, inputs, and technologies by smallholder farmers. In the Indian context, it is widely believed that farmers misapply chemical fertilizers because they lack scientific information on soil conditions and corresponding fertilizer recommendations, thus resulting in imbalanced and potentially detrimental fertilizer application. Policymakers are frequently interested in providing farmers with various streams of information to overcome these informational barriers to optimize farming activities. However, such informational interventions frequently fail either because generic recommendations may be ill‐suited for decision makers in highly heterogeneous agricultural environments or because farmers' beliefs may be so entrenched as to make them unresponsive to new information. We implemented a field experiment in Bihar, India to test whether plot‐specific fertilizer recommendations affect farmers' fertilizer use. We find little evidence for sizable impacts on fertilizer use in general, though impacts are more apparent for low cost or costless recommendations such as increasing the use of highly subsidized fertilizers or shifting the timing of application. Despite modest evidence of such effects, even those fall short of their potential magnitude. We show that treated farmers who are less confident in their subjective beliefs about optimal fertilizer application rates (i.e., with more disperse priors) are more responsive to the recommendations and have a higher ex ante willingness to pay for soil testing. These results suggest that heterogeneity in beliefs may constrain the overall effectiveness of information provision, even when the information is tailored to individual farms.
Development of a nomogram model to predict postoperative urinary retention risk after transabdominal preperitoneal inguinal hernia repair
Authors: Wang Jiwei , Li Kanghu , Wang Guangyuan , Liu Kai , Wu Yin , Zhang Tao , Xie Ming 
Published: January 2025

AbstractObjectiveTo explore independent risk factors and to establish a predictive model for postoperative urinary retention (POUR) following transabdominal preperitoneal inguinal hernia repair (TAPP).MethodsBetween January 2017 and December 2023, 598 patients with inguinal hernia who underwent TAPP at the General Surgery Department of Zunyi Medical University Affiliated Liupanshui Hospital were enrolled in the study. Participants were randomly divided into training and validation sets (7:3 ratio). The training set was further divided into POUR and non‐POUR groups (38 and 381 cases, respectively). Independent risk factors for POUR were screened by logistic regression analysis. A nomogram predictive model was established based on the independent risk factors. The model's predictive ability was evaluated.ResultsLogistic regression revealed recurrent hernia (P = 0.013, OR = 0.279, 95% confidence interval [CI]: 0.105–0.805), BPH (P = 0.002, OR = 5.09, 95% CI: 2.658–96.282), preoperative catheterization (P = 0.004, OR = 0.087, 95% CI: 0.012–0.370), operation time (P < 0.001, OR = 0.015, 95% CI: 1.006–1.023), and use of narcotic analgesics (P = 0.042, OR = 2.224, 95% CI: 1.021–5.222) as independent risk factors for POUR after TAPP. Discriminant analysis showed the training set AUC was 0.763 (95% CI: 0.684–0.842, P < 0.001) while that for the validation set was 0.812 (95% CI: 0.677–0.947, P < 0.001). The Hosmer–Lemeshow test was performed to assess calibration of the training (P = 0.696) and validation (P = 0.194) sets.ConclusionRecurrent hernia, BPH, preoperative catheterization, operation time, and use of narcotic analgesics were identified as independent risk factors for POUR after TAPP. The nomogram model for risk prediction based on these factors has strong predictive performance and application prospect.
Organoid Ethical Typology: varieties of three‐dimensional stem cell constructs and the many issues they raise in bioethics
Authors: Gaillard Maxence , Pence Charles H. , Botbol‐Baum Mylène 
Published: January 2025

AbstractThe advancement of and prospects for stem cell research raise a number of specific ethical issues. While navigating the ethical landscape of stem cell research is often challenging for biology researchers and biotechnology innovators, it is also difficult for the public and other persons of concern (from ethicists to policy‐makers) to grasp the technicalities of a burgeoning field that develops in many directions. Organoids are one of these new biotechnological constructs that are currently eliciting a rich debate in bioethics. In this guide, we argue that different types of organoids have different emerging properties with different ethical implications. Going from general properties to particular ones, we propose a typology of organoid technology and other associated biotechnology from a philosophical and ethical perspective. We point to relevant ethical issues and try to convey the sense of uncertainty peculiar to ongoing research and emerging technological objects.
Neutral lipids restrict the mobility of broken DNA molecules during comet assays
Authors: Soulet Caroline , Josa‐Castro Jordi , Moriel‐Carretero María 
Published: January 2025

AbstractOne widespread technique to assess in relative terms the amount of broken DNA present in the genome of individual cells consists of immobilizing the cell's nucleus under an agarose pad (called the nucleoid) and subjecting the whole genome to electrophoresis to force broken DNA molecules out of it. Since the migrating broken DNA molecules create a tail behind the nucleoid, this technique is named the comet assay. While performing comet assays regularly, we systematically observed circular regions devoid of DNA within the nucleoid region. We characterize here that these correspond to clusters of neutral (apolar) lipids, since they could be labeled with neutral lipid‐dying molecules, increased when cells were fed with oleic acid, and were irresponsive to the electrophoretic field. Of relevance, de‐lipidation assays, either in vivo, or in vitro using acetone, show that these neutral lipids (NL) within the nucleoid limit the ability of broken DNA molecules to migrate into the comet tail. From a technical point of view, we show that de‐lipidation permits a wider range for the detection of broken DNA molecules. Biologically, we put forward the notion that NL in contact with DNA may locally exert regulatory functions within the cell's nucleus.
Mineral Licks: An Overlooked Model System for Species Interactions
Authors: Griffiths Brian M. , Luther David C. , Pollock Henry S. 
Published: January 2025

ABSTRACTMineral licks are deposits of minerals, salts, and/or clays that attract animals and serve as keystone resources in terrestrial ecosystems worldwide. Previous research on natural mineral licks has focused largely on characterizing the soil properties of the licks and describing the species that consume the minerals. Yet mineral licks are also hubs of species interactions, where predators hunt prey, diseases are spread, and social information is transferred. Here, we argue that mineral licks are an overlooked model system with massive potential for both characterizing biodiversity and studying species interactions. We review the current state of knowledge and identify gaps related to predator–prey interactions, disease transfer, social information, and population dynamics and mineral licks. In each area, we propose future research directions, including how to leverage emerging technologies to more fully understand the ecology of mineral licks. We highlight that new conservation technologies may be particularly powerful in studying species at mineral licks, including telemetry and tracking, LiDAR, environmental DNA, and camera traps. We also note that experimental approaches to mineral licks are currently severely underutilized in ecosystems around the world and offer enormous potential in understanding species interactions in our four highlighted areas. This synthesis provides a framework for testing hypotheses about the ecological importance of mineral licks as a keystone resource and shifts the focus to include more emphasis on current knowledge gaps.
NOTCH3 Mutation Causes Glymphatic Impairment and Promotes Brain Senescence in CADASIL
Authors: Li Chunyi , Li Hui , Men Xuejiao , Wang Yuge , Kang Xinmei , Hu Mengyan , Su Xiaotao , Wang Shisi , Lu Danli , Shen Shishi , Huang Huipeng , Deng Xiaohui , Liu Yuxin , Zhang Lei , Cai Wei , Wu Aimin , Lu Zhengqi 
Published: January 2025

ABSTRACTAimsThe aim of this study is to investigate the role of glymphatic function of cerebral autosomal dominant arteriopathy, subcortical infarcts, and leukoencephalopathy (CADASIL), the most common monogenic small vessel disease caused by NOTCH3 mutation, and to explore potential therapeutic strategies to improve glymphatic function.MethodsWe assessed glymphatic influx and efflux function in CADASIL mouse models (Notch3R170C) and correlated these findings with brain atrophy in CADASIL patients. We also investigated the underlying mechanisms of glymphatic impairment, focusing the expression of AQP4 in astrocytic endfeet.ResultsCADASIL mouse exhibited both impaired glymphatic influx and efflux, which impedes waste clearance and promotes brain senescence. In accordance, brain atrophy in CADASIL patients is associated with perivascular space enlargement, indicating that glymphatic impairment contributes to advanced brain senescence in CADASIL. The glymphatic malfunction in CADASIL is attributed to diminished AQP4 expression in astrocytic endfeet, which is the core mediator of glymphatic activity. Mechanistically, AQP4 expression is regulated by NOTCH3‐RUNX1‐CMYB signaling. Reinforcing AQP4 expression in astrocytes by AAV‐based therapy resumes the glymphatic functions in CADASIL mice, which further prevents brain senescence.ConclusionWe propose that to improve glymphatic function by reinforcing AQP4 expression is a promising therapeutic strategy in CADASIL.
Deep‐Learning Generated Synthetic Material Decomposition Images Based on Single‐Energy CT to Differentiate Intracranial Hemorrhage and Contrast Staining Within 24 Hours After Endovascular Thrombectomy
Authors: Wang Tianyu , Jiang Caiwen , Ding Weili , Chen Qing , Shen Dinggang , Ding Zhongxiang 
Published: January 2025

ABSTRACTAimsTo develop a transformer‐based generative adversarial network (trans‐GAN) that can generate synthetic material decomposition images from single‐energy CT (SECT) for real‐time detection of intracranial hemorrhage (ICH) after endovascular thrombectomy.MaterialsWe retrospectively collected data from two hospitals, consisting of 237 dual‐energy CT (DECT) scans, including matched iodine overlay maps, virtual noncontrast, and simulated SECT images. These scans were randomly divided into a training set (n = 190) and an internal validation set (n = 47) in a 4:1 ratio based on the proportion of ICH. Additionally, 26 SECT scans were included as an external validation set. We compared our trans‐GAN with state‐of‐the‐art generation methods using several physical metrics of the generated images and evaluated the diagnostic efficacy of the generated images for differentiating ICH from contrast staining.ResultsIn comparison with other generation methods, the images generated by trans‐GAN exhibited superior quantitative performance. Meanwhile, in terms of ICH detection, the use of generated images from both the internal and external validation sets resulted in a higher area under the receiver operating characteristic curve (0.88 vs. 0.68 and 0.69 vs. 0.54, respectively) and kappa values (0.83 vs. 0.56 and 0.51 vs. 0.31, respectively) compared with input SECT images.ConclusionOur proposed trans‐GAN provides a new approach based on SECT for real‐time differentiation of ICH and contrast staining in hospitals without DECT conditions.
Effect of reserve protection level and governance on tree cover loss and gain
Authors: Stoudmann Natasha , Byrne Jason , Adams Vanessa 
Published: January 2025

AbstractTerrestrial protected areas are essential for biodiversity conservation, yet it is not fully understood when and how different types of protected areas are most effective in achieving specific conservation objectives. We assessed the impact of reserves on tree cover loss and gain through a case study in Tasmania, Australia. We considered varying protection levels (strict, where human activities are restricted, and multiple use) and governance types (public and private). We used a counterfactual matching approach to compare tree cover loss and gain between reserves and matched unprotected areas from 2004 to 2021. We accounted for forest policy changes, environmental covariates, and human pressures to reduce placement bias. We also characterized reserves by size, governance, management, and vegetation and compared covariates inside and outside reserves to define baseline conditions. Reserves established from 2004 to 2016 were overall 75.4% less likely to have lost tree cover and 16.0% more likely to have had tree cover gain compared with controls. Patterns of loss and gain varied by protection level and governance type. Multiple‐use reserves were as effective as reserves in which human activities were more restricted. Privately managed reserves contributed to tree cover growth, and public reserves helped avoid loss. This highlights reserves’ distinct contributions to conservation targets, with private reserves allowing for growth and restoration and public reserves acting as stable anchor points. Our results emphasize the importance of having a diverse array of protected areas to enhance the resilience of reserve networks. We advocate for adaptive regional measures and robust monitoring to achieve global ecological targets.
The Songdo consensus: Development of minimum reporting standards for studies of intervention in idiopathic anal fistula using a modified nominal group technique
Authors: Joshi Shivani , Hanna Luke , Cho Dong Ho , Garg Pankaj , Glyn Tamara , Gurland Brooke , Hwang Do‐Yeon , Kim Kiduk , Kotze Paulo Gustavo , Lee Jong Kyun , Lightner Amy L. , Matzel Klaus E. , Sahnan Kapil , Seow‐Choen Francis , Shafik Ali , Won Daeyoun , Zimmerman David D. E. , Tozer Phil J. 
Published: January 2025

AbstractAimCryptoglandular anal fistulas carry a substantial burden to quality of life. Surgery is the only effective curative treatment but requires balancing fistula healing against pain, wounds and continence impairment. Sphincter‐preserving procedures do exist but demonstrate variable rates of success. A lack of consistency and precision in outcome reporting and methodological quality hinders effective evidence‐based decision‐making. We aimed to establish a series of minimum reporting standards for interventional studies in idiopathic anal fistula, to eradicate low‐quality studies, thus providing a consistent baseline of useful evidence.MethodsAn international group of 16 experts participated in a modified nominal group technique consensus. The nominal question was: ‘What should be the minimum set of reporting standards for studies of intervention in idiopathic anal fistula?’ The process was conducted between May and June 2023, culminating in a hybrid in‐person/virtual meeting that took place at the Songdo International Proctology Symposium in June 2023.ResultsInitial idea generation resulted in 37 statements within the first round. Themes included variable reporting of follow‐up and incontinence. Participants indicated their agreement via a 9‐point Likert scale. Any statement achieving >70% consensus was retained. Subsequent group discussion condensed the list to 11 statements for further voting and a final minimum set of 12 reporting standards was created.ConclusionTo date, this is the first study dedicated to developing minimum reporting standards for interventional studies in idiopathic anal fistula using a modified nominal group technique. These standards will instruct researchers in producing meticulous, high‐quality studies that are accurate, transparent and reproducible.
Ivermectin and Neem residues in cattle dung: Effects on dung beetle attraction and ecological functions in Brazilian pastures
Authors: Souza Agnis C. , Correa César M. A. , Ferreira Ronara Souza , Louzada Julio 
Published: January 2025

AbstractIdentification of veterinary medical products carrying reduced risks to dung beetles remains a critical objective for the sustainable management of livestock parasites. Despite the essential role dung beetles play in tropical pasturelands, our understanding of the impact of alternative parasiticides, such as Neem plant extract, on dung beetle attraction and dung use is still limited. This study assessed the effects of dung from cattle exposed to Ivermectin (known to be harmful to dung beetles), Neem, and non‐exposed animals (control) on dung beetle assemblage and their ecological functions (dung removal and soil bioturbation), in introduced and native pastures in the Brazilian Cerrado. Our findings revealed similar patterns of dung beetle attraction to Ivermectin, Neem, and control dung in introduced pastures. However, in native pastures, dung beetles exhibited greater attraction to dung from Ivermectin and Neem‐treated cattle compared with the control. Telecoprid beetles displayed an increased attraction to Neem‐treated dung in native pastures, with two species demonstrating a preference for this dung type. Ecological function performance was higher in Neem‐treated dung compared with control, yet no significant difference was noted between Neem and Ivermectin in both pasture types. These results underscore the compelling attractiveness of cattle dung from Neem‐treated animals to dung beetles, concurrently ensuring the preservation of dung beetle ecological functions in both pasture settings. This highlights the need for a rigorous evaluation of novel protocols incorporating natural parasiticides, which emerge as important tools in the conservation of dung beetle biodiversity and their ecological functions in tropical pasturelands.
Exploring Emergency Distance Education in Higher Education: A Systematic Review
Authors: Battal Bahadır 
Published: January 2025

ABSTRACTThe aim of this article is to explore the advantages and disadvantages experienced in higher education institutions during the period of emergency distance education, based on the qualitative findings of qualitative and mixed‐methods research conducted. In pursuit of this objective, a compilation of mixed‐methods and qualitative research conducted on higher education institutions during the COVID‐19 period from 2020 to 2023 has been gathered from the English language and Web of Science database. Thematic analysis of the classified data reveals that emergency distance education leads to significant disadvantages in countries with low economic indicators. Considering the potential use of emergency distance education in future crises, the importance of preparatory measures becomes evident. Focusing on the disparity among various geographical and economic regions during the period of emergency distance education is a distinguishing feature of this research. Based on the results obtained, recommendations have been provided to international organisations, regulatory bodies in higher education, and higher education institutions.