bluuebunny/crossref_metadata_2025_split huggingface dataset:
A practical guide to adopting Bayesian analyses in clinical research
Authors: Gunn-Sandell Lauren B. , Bedrick Edward J. , Hutchins Jacob L. , Berg Aaron A. , Kaizer Alexander M. , Carlson Nichole E. 
Published: December 2023

Abstract

Background:
Bayesian statistical approaches are extensively used in new statistical methods but have not been adopted at the same rate in clinical and translational (C&T) research. The goal of this paper is to accelerate the transition of new methods into practice by improving the C&T researcher’s ability to gain confidence in interpreting and implementing Bayesian analyses.

Methods:
We developed a Bayesian data analysis plan and implemented that plan for a two-arm clinical trial comparing the effectiveness of a new opioid in reducing time to discharge from the post-operative anesthesia unit and nerve block usage in surgery. Through this application, we offer a brief tutorial on Bayesian methods and exhibit how to apply four Bayesian statistical packages from STATA, SAS, and RStan to conduct linear and logistic regression analyses in clinical research.

Results:
The analysis results in our application were robust to statistical package and consistent across a wide range of prior distributions. STATA was the most approachable package for linear regression but was more limited in the models that could be fitted and easily summarized. SAS and R offered more straightforward documentation and data management for the posteriors. They also offered direct programming of the likelihood making them more easily extendable to complex problems.

Conclusion:
Bayesian analysis is now accessible to a broad range of data analysts and should be considered in more C&T research analyses. This will allow C&T research teams the ability to adopt and interpret Bayesian methodology in more complex problems where Bayesian approaches are often needed.
The Key to Authentic Pre-Columbian Fakes: The Racial Myth of the Natural Man and Its Mise-en-Scène
Authors: Balán Laura 
Published: December 2023

AbstractSince the end of the nineteenth century, the Alzate family, of Medellín, Colombia, grasped the magnetism of the Natural Man (a malleable myth with porous edges that combines both the Edenic and the cannibalistic visions of indigenous peoples) and its economic potential and orchestrated a family craft business of fake pre-Columbian pottery. They created pieces that would engage in dialogue with collectors’, anthropologists’, museums’, and tourists’ desires and imaginaries, as well as authenticity criteria, about indigenous pre-Columbian peoples. This article shows the relationship between these forgeries’ production, circulation, and consumption and the ways Latin American indigenous peoples have been conceived of by others. Moreover, this research stresses how authentic fakes, together with official and popular discourses and images, certain exhibition and validation rhetorics, and other mises-en-scène construct what is sacralized as uncontaminated, original, and traditional. Such fakes operate politically by undermining social hierarchies linked to essentialized race and identity.
Posjudaísmo en Buenos Aires: Deconstruir comunidad para consumir identidad
Authors: Peña Jiménez Lorena 
Published: December 2023

ResumenEste artículo analiza la propuesta teórica del posjudaísmo articulada por el proyecto YOK en respuesta a la crisis del judaísmo institucionalizado en Buenos Aires, Argentina. Contrario a cualquier forma de pensar lo judío en términos tradicionales y normativos, el proyecto posjudío se planteó como una deconstrucción capaz de derribar los muros del judaísmo tradicional y, con el mismo movimiento, dar voz a aquellos judíos que no encuentran acomodo en las infraestructuras institucionales de la comunidad. Nuestra hipótesis es que su arquitectura conceptual, cuyo objetivo es conseguir la total liberación de las formas identitarias judías, termina legitimando una nueva servidumbre, esta es: la adaptación de lo identitario a la fluidez del mercado. Para demostrarlo, me detendré en reflexionar sobre cómo el posjudaísmo repiensa, desde el andamiaje de las filosofías posmodernas, la comunidad tradicional con el fin de proponer un judaísmo en las antípodas de este, un judaísmo basado en un trabajo de autocreación incesante que apele a lo plural, a lo abierto y a lo emancipado de toda norma y de todo dogma. Esto me permitirá demostrar cómo la autocreación es fruto de las dinámicas posmodernas de transformación de la subjetividad cimentadas sobre la emoción y la individualidad creadora.
The Barthlott effect
Authors: Vonna Laurent 
Published: December 2023

Abstract
In 1997, Barthlott and Neinhuis published a groundbreaking article entitled "Purity of the sacred lotus, or escape from contamination in biological surfaces" that caused a true paradigm shift in surface science. In this article, they explained the water-repellent and self-cleaning properties of plants, attributing the superhydrophobicity to nano- and micrometric wax textures on the surface of the leaves. This became known as the "Lotus Effect". In the late 1980s, Barthlott already demonstrated the microtexture of plant surfaces and its effect on wetting. However, this knowledge remained confined to botany until the 1997 article popularized it. The dissemination of this knowledge to the materials science community led to the development of countless synthetic superhydrophobic surfaces and a better understanding of wetting mechanisms. The story of this discovery and its consequences demonstrates the relevance of atypical approaches and emphasizes the urgency of respecting biodiversity.
Unbundling the State: Legal Development in an Era of Global, Private Governance
Authors: Allen Michael O. 
Published: December 2023

AbstractWhat happens to a public, domestic institution when its authority is delegated to a privately run, transnational institution? I argue that outsourcing traditionally national legal responsibilities to transnational bodies can lead to the stagnation of domestic institutional capacity. I examine this through a study of international commercial arbitration (ICA), a widely used system of cross-border commercial dispute resolution. I argue that ICA provides commercial actors an “exit option” from weak public institutions, reducing pressure on the state to invest in capacity-enhancing reform. I find that the enactment of strong protections for ICA leads to the gradual erosion of the capacity of domestic legal institutions, particularly in countries with already weak legal systems. I test the mechanism driving this dynamic using dispute data from the International Chamber of Commerce. I find that pro-arbitration laws increase the use of international arbitration by national firms, suggesting that firms use ICA as an escape from domestic institutions. This article contributes to debates on globalization and development as well as work on the second-order effects of global governance institutions.
Improving otitis externa management in secondary care through a standardised treatment algorithm
Authors: Hasan Waseem , Kennett Jessica , Bentounsi Zineb , Amir-Ghasemi Aria , Jones Huw , Biggs Timothy 
Published: December 2023

AbstractObjectiveOtitis externa is a common condition managed by junior doctor-led ENT clinics in secondary/tertiary care, but no national guidelines exist for presentations in these settings. The aim of this study was to implement a treatment algorithm to support junior doctors and improve otitis externa management.MethodsBaseline data were retrospectively collected for 16 weeks. A standardised otitis externa treatment algorithm was then implemented, and 16 weeks of data prospectively gathered. A second improvement cycle was completed thereafter focusing on topical antibiotics and water precaution advice.ResultsOverall, 202 cases of otitis externa managed between November 2021 to October 2022 were reviewed. Following the interventions, topical antibiotic prescribing improved (p = 0.01) as well as the provision of water precaution advice (p < 0.01). Junior doctors trended towards reviewing patients more frequently but required less senior support.ConclusionOur treatment algorithm empowers junior doctors to become more independent in their management of otitis externa and improves overall otitis externa treatment.
Jupiter's Multi‐Year Cycles of Temperature and Aerosol Variability From Ground‐Based Mid‐Infrared Imaging
Authors: Antuñano Arrate , Fletcher Leigh N. , Orton Glenn S. , Melin Henrik , Donnelly Padraig T. , Roman Michael T. , Sinclair James A. , Kasaba Yasumasa , Momary Thomas , Fujiyoshi Takuya 
Published: December 2023

AbstractWe use a long‐term record of ground‐based mid‐infrared (7.9–24.5 μm) observations, captured between 1984 and late 2019 from 3‐m and 8‐m class observatories (mainly NASA's Infrared Telescope Facility, ESO's Very Large Telescope, and the Subaru Telescope), to characterize the long‐term, multi‐decade variability of the thermal and aerosol structure in Jupiter's atmosphere. In this study, spectral cubes assembled from images in multiple filters are inverted to provide estimations of stratospheric and tropospheric temperatures and tropospheric aerosol opacity. We find evidence of non‐seasonal and quasi‐seasonal variations of the stratospheric temperatures at 10 mbar, with a permanent hemispherical asymmetry at mid‐latitudes, where the northern mid‐latitudes are overall warmer than southern mid‐latitudes. A correlation analysis between stratospheric and tropospheric temperature variations reveals a moderate anticorrelation between the 10‐mbar and 330‐mbar temperatures at the equator, revealing that upper‐tropospheric equatorial temperatures are coupled to Jupiter’s Equatorial Stratospheric Oscillation. The North and South Equatorial Belts show temporal variability in their aerosol opacity and tropospheric temperatures that are in approximate antiphase with one another, with moderate negative correlations in the North Equatorial Belt and South Equatorial Belt changes between conjugate latitudes at 10°–16°. This long‐term anticorrelation between belts separated by ∼15° is still not understood. Finally we characterize the lag between thermal and aerosol opacity changes at a number of latitudes, finding that aerosol variations tend to lag after thermal variations by around 6 months at multiple latitudes.
Transport of Anthropogenic Carbon From the Antarctic Shelf to Deep Southern Ocean Triggers Acidification
Authors: Zhang Shuang , Wu Yingxu , Cai Wei‐Jun , Cai Wenju , Feely Richard A. , Wang Zhaomin , Tanhua Toste , Wang Yanmin , Liu Chengyan , Li Xichen , Yang Qinghua , Ding Minghu , Xu Zhongsheng , Kerr Rodrigo , Luo Yiming , Cheng Xiao , Chen Liqi , Qi Di 
Published: December 2023

AbstractFlow of dense shelf water provide an efficient mechanism for pumping CO2 to the deep ocean along the continental shelf slope, particularly around the Antarctic bottom water (AABW) formation areas where much of the global bottom water is formed. However, the contribution of the formation of AABW to sequestering anthropogenic carbon (Cant) and its consequences remain unclear. Here, we show prominent transport of Cant (25.0 ± 4.7 Tg C yr−1) into the deep ocean (>2,000 m) in four AABW formation regions around Antarctica based on an integrated observational data set (1974–2018). This maintains a lower Cant in the upper waters than that of other open oceans to sustain a stronger CO2 uptake capacity (16.9 ± 3.8 Tg C yr−1). Nevertheless, the accumulation of Cant can further trigger acidification of AABW at a rate of −0.0006 ± 0.0001 pH unit yr−1. Our findings elucidate the prominent role of AABW in controlling the Southern Ocean carbon uptake and storage to mitigate climate change, whereas its side effects (e.g., acidification) could also spread to other ocean basins via the global ocean conveyor belt.
Adult dental epithelial stem cell-derived organoids deposit hydroxylapatite biomineral
Authors: Kim Hyun-Yi , Cooley Victoria , Kim Eun-Jung , Li Shujin , Lee Jong-Min , Sheyfer Dina , Liu Wenjun , Klein Ophir D. , Joester Derk , Jung Han-Sung 
Published: December 2023

AbstractAmeloblasts are specialized cells derived from the dental epithelium that produce enamel, a hierarchically structured tissue comprised of highly elongated hydroxylapatite (OHAp) crystallites. The unique function of the epithelial cells synthesizing crystallites and assembling them in a mechanically robust structure is not fully elucidated yet, partly due to limitations with in vitro experimental models. Herein, we demonstrate the ability to generate mineralizing dental epithelial organoids (DEOs) from adult dental epithelial stem cells (aDESCs) isolated from mouse incisor tissues. DEOs expressed ameloblast markers, could be maintained for more than five months (11 passages) in vitro in media containing modulators of Wnt, Egf, Bmp, Fgf and Notch signaling pathways, and were amenable to cryostorage. When transplanted underneath murine kidney capsules, organoids produced OHAp crystallites similar in composition, size, and shape to mineralized dental tissues, including some enamel-like elongated crystals. DEOs are thus a powerful in vitro model to study mineralization process by dental epithelium, which can pave the way to understanding amelogenesis and developing regenerative therapy of enamel.
Targeting the E2F1/Rb/HDAC1 axis with the small molecule HR488B effectively inhibits colorectal cancer growth
Authors: Duan Namin , Hu Xiaohui , Qiu Huiran , Zhou Rui , Li Yuru , Lu Wenxia , Zhu Yamin , Shen Shuang , Wu Wenhui , Yang Feifei , Liu Ning 
Published: December 2023

AbstractColorectal cancer (CRC), the third most common cancer worldwide, remains highly lethal as the disease only becomes symptomatic at an advanced stage. Growing evidence suggests that histone deacetylases (HDACs), a group of epigenetic enzymes overexpressed in precancerous lesions of CRC, may represent promising molecular targets for CRC treatment. Histone deacetylase inhibitors (HDACis) have gradually become powerful anti-cancer agents targeting epigenetic modulation and have been widely used in the clinical treatment of hematologic malignancies, while only few studies on the benefit of HDACis in the treatment of CRC. In the present study, we designed a series of small-molecule Thiazole-based HDACis, among which HR488B bound to HDAC1 with a high affinity and exerted effective anti-CRC activity both in vitro and in vivo. Moreover, we revealed that HR488B specifically suppressed the growth of CRC cells by inducing cell cycle G0/G1 arrest and apoptosis via causing mitochondrial dysfunction, reactive oxygen species (ROS) generation, and DNA damage accumulation. Importantly, we noticed that HR488B significantly decreased the expression of the E2F transcription factor 1 (E2F1), which was crucial for the inhibitory effect of HR488B on CRC. Mechanistically, HR488B obviously decreased the phosphorylation level of the retinoblastoma protein (Rb), and subsequently prevented the release of E2F1 from the E2F1/Rb/HDAC1 complex, which ultimately suppressed the growth of CRC cells. Overall, our study suggests that HR488B, a novel and efficient HDAC1 inhibitor, may be a potential candidate for CRC therapy in the future. Furthermore, targeting the E2F1/Rb/HDAC1 axis with HR488B provides a promising therapeutic avenue for CRC.
POU5F1 promotes the proliferation, migration, and invasion of gastric cancer cells by reducing the ubiquitination level of TRAF6
Authors: Yang Wenshuo , Cui Xiaohan , Sun Danping , Sun Guorui , Yan Zhibo , Wei Meng , Wang Zuoyang , Yu Wenbin 
Published: December 2023

AbstractPOU5F1 plays an important role in maintaining the cancer stem cell (CSC) -like properties of gastric cancer (GC) cells. The impact of POU5F1 on the proliferation and metastasis of GC was examined, along with the potential of ATRA as a specific therapeutic agent for GC. The dysregulation of POU5F1 expression in GC tissues was analyzed using public databases and bioinformatics techniques, and the disparity in POU5F1 expression between normal gastric tissues and GC tissues was further assessed through western blot, RT-qPCR, and immunohistochemistry. The present study aimed to investigate the impact of POU5F1 on the proliferation, migration, and invasion of GC cells through both in vivo and in vitro experiments. Additionally, the effects of ATRA on the proliferation, migration, and invasion of GC cells were examined using in vivo and in vitro approaches. Our findings revealed a significant upregulation of POU5F1 in GC tissues, which was found to be associated with a poorer prognosis in patients with GC. Moreover, POU5F1 was observed to enhance the proliferation, migration, and invasion of GC cells in vitro, as well as promote subcutaneous tumor growth and lung metastasis of GC cells in vivo. The overexpression of POU5F1 mechanistically triggers the process of Epithelial-mesenchymal transition (EMT) by down-regulating E-Cadherin and up-regulating N-Cadherin and VIM. POU5F1 hinders the ubiquitination of TRAF6 through negative regulation of TRIM59, thereby facilitating the activation of the NF-κB pathway. Furthermore, the administration of ATRA effectively impedes the proliferation, migration, and invasion of GC cells by suppressing the expression of POU5F1. The upregulation of POU5F1 elicits EMT, fosters the initiation of the NF-κB signaling pathway in GC cells, and stimulates the proliferation, invasion, and metastasis of GC cells. All-trans retinoic acid (ATRA) can impede these POU5F1-induced effects, thereby potentially serving as an adjunctive therapeutic approach for GC.
ALOX5 deficiency contributes to bladder cancer progression by mediating ferroptosis escape
Authors: Liu Tianyao , Xu Xinyan , Li Jiazheng , Bai Ming , Zhu Wenjie , Liu Yanqing , Liu Siyang , Zhao Zihan , Li Tianhang , Jiang Ning , Bai Yuhao , Jin Qingyang , Zhang Yulin , Zheng Yufeng , Zhou Shengkai , Zhan Shoubin , Sun Ying , Liang Gaoli , Luo Yang , Chen Xi , Guo Hongqian , Yang Rong 
Published: December 2023

AbstractFerroptosis is an iron-dependent form of regulated cell death driven by the lethal lipid peroxides. Previous studies have demonstrated that inducing ferroptosis holds great potential in cancer therapy, especially for patients with traditional therapy failure. However, cancer cells can acquire ferroptosis evasion during progression. To date, the therapeutic potential of inducing ferroptosis in bladder cancer (BCa) remains unclear, and whether a ferroptosis escape mechanism exists in BCa needs further investigation. This study verified that low pathological stage BCa cells were highly sensitive to RSL3-induced ferroptosis, whereas high pathological stage BCa cells exhibited obviously ferroptosis resistance. RNA-seq, RNAi-mediated loss-of-function, and CRISPR/Cas9 experiments demonstrated that ALOX5 deficiency was the crucial factor of BCa resistance to ferroptosis in vitro and in vivo. Mechanistically, we found that ALOX5 deficiency was regulated by EGR1 at the transcriptional level. Clinically, ALOX5 expression was decreased in BCa tissues, and its low expression was associated with poor survival. Collectively, this study uncovers a novel mechanism for BCa ferroptosis escape and proposes that ALOX5 may be a valuable therapeutic target and prognostic biomarker in BCa treatment.
In vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub
Authors: Liu Fang , Chen Ziying , Zhang Shuo , Wu Kejing , Bei Cheng , Wang Chuan , Chao Yanjie 
Published: December 2023

AbstractSmall noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3’UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
SEMA6A drives GnRH neuron-dependent puberty onset by tuning median eminence vascular permeability
Authors: Lettieri Antonella , Oleari Roberto , van den Munkhof Marleen Hester , van Battum Eljo Yvette , Verhagen Marieke Geerte , Tacconi Carlotta , Spreafico Marco , Paganoni Alyssa Julia Jennifer , Azzarelli Roberta , Andre’ Valentina , Amoruso Federica , Palazzolo Luca , Eberini Ivano , Dunkel Leo , Howard Sasha Rose , Fantin Alessandro , Pasterkamp Ronald Jeroen , Cariboni Anna 
Published: December 2023

AbstractInnervation of the hypothalamic median eminence by Gonadotropin-Releasing Hormone (GnRH) neurons is vital to ensure puberty onset and successful reproduction. However, the molecular and cellular mechanisms underlying median eminence development and pubertal timing are incompletely understood. Here we show that Semaphorin-6A is strongly expressed by median eminence-resident oligodendrocytes positioned adjacent to GnRH neuron projections and fenestrated capillaries, and that Semaphorin-6A is required for GnRH neuron innervation and puberty onset. In vitro and in vivo experiments reveal an unexpected function for Semaphorin-6A, via its receptor Plexin-A2, in the control of median eminence vascular permeability to maintain neuroendocrine homeostasis. To support the significance of these findings in humans, we identify patients with delayed puberty carrying a novel pathogenic variant of SEMA6A. In all, our data reveal a role for Semaphorin-6A in regulating GnRH neuron patterning by tuning the median eminence vascular barrier and thereby controlling puberty onset.
TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
Authors: Okhovat Mariam , VanCampen Jake , Nevonen Kimberly A. , Harshman Lana , Li Weiyu , Layman Cora E. , Ward Samantha , Herrera Jarod , Wells Jackson , Sheng Rory R. , Mao Yafei , Ndjamen Blaise , Lima Ana C. , Vigh-Conrad Katinka A. , Stendahl Alexandra M. , Yang Ran , Fedorov Lev , Matthews Ian R. , Easow Sarah A. , Chan Dylan K. , Jan Taha A. , Eichler Evan E. , Rugonyi Sandra , Conrad Donald F. , Ahituv Nadav , Carbone Lucia 
Published: December 2023

AbstractTopological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons compared to species-specific boundaries. CRISPR-Cas9 knockouts of an ultraconserved boundary in a mouse model lead to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in the upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations and showcases the functional importance of TAD evolution.