bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cross-sectional study on Campylobacter fetus subsp. venerealis prevalence and associated factors in Brazilian southern cattle farms
Authors: Siqueira Franciele Maboni , Breyer Gabriela Merker , De Carli Silvia , Lopes Cassiane E. , Dias Maria Eduarda , da Silva Maria Eduarda Rocha Jacques , Moni Camila , Zitelli Larissa Caló , Borsato Márcio , Gomes Rogers , Lopes Francisco Paulo Nunes , Moraes Rosane Collares , Cattáneo Milton , Sosa Ruben , Pessoa Gilson Antonio , de Freitas Costa Eduardo 
Published: September 2023

AbstractCattle farming is a major livestock activity with economic relevance in Rio Grande do Sul (RS), Brazil. However, this activity is still considered of intermediate to low technological level, and in this region, there are few epidemiologic reports of Campylobacter fetus subsp. venerealis (Cfv), the causative agent of bovine genital campylobacteriosis (BGC). Thus, we designed a cross-sectional study to assess the prevalence and Cfv-associated factors in cattle farms in RS, Brazil. In total, 99 farms were randomly selected to participate in the survey. Preputial mucus samples from selected bulls were collected twice (within a 15-day interval) and subjected to Cfv molecular detection. A farm was considered positive when at least one sample was positive for Cfv. Our findings indicate that the farm-level Cfv prevalence in RS is 67.67%. On average, the chance of a farm using natural service to be Cfv-positive increased approximately twice compared to farms that do not use natural service. We also determined that Cfv routine tests reduce the chance of a farm being positive by 92%. Therefore, both Cfv detection tests and the reduction of natural services decrease the chance of a farm being positive for Cfv. Finally, we conclude that Cfv is widely spread in Southern Brazil cattle farms and it is urgent the implementation of control measures to reduce Cfv prevalence in the target population.
Reliability and Performance of the Online Literature Database CAMbase after Changing from a Semantic Search to a Score Ranking Algorithm
Authors: Unger Sebastian , Raak Christa K. , Ostermann Thomas 
Published: September 2023

AbstractDespite the increase in scientific publications in the field of integrative medicine over the past decades, a valid overview of published evidence remains challenging to get. The online literature database CAMbase (available at https://cambase.de) is one of the established databases designed to provide such an overview. In 2020, the database was migrated from a 32-bit to a 64-bit operating system, which resulted in unexpected, technical issues and forced the replacement of the semantic search algorithm with Solr, an open-source platform that uses a score ranking algorithm. Although semantic search was replaced, the goal was to create a literature database that is essentially no different from the legacy system. Therefore, a before-after analysis was conducted to compare first the number of retrieved documents and then their titles, while the titles were syntactically compared using two Sentence-Bidirectional Encoder Representations from Transformers (SBERT) models. Analysis with a paired t-test revealed no significant overall differences between the legacy system and the final system in the number of documents (t =− 1.41, df = 35, p = 0.17), but an increase in performance (t = 4.13, df = 35, p < 0.01). Analysis with a t-test for independent samples of the values from the models also revealed a high degree of consistency between the retrieved documents. The results show that an equivalent search can be provided by using Solr, while improving the performance, making this technical report a viable blueprint for projects with similar contexts.
Lessons Learned from Assessing Trustworthy AI in Practice
Authors: Vetter Dennis , Amann Julia , Bruneault Frédérick , Coffee Megan , Düdder Boris , Gallucci Alessio , Gilbert Thomas Krendl , Hagendorff Thilo , van Halem Irmhild , Hickman Eleanore , Hildt Elisabeth , Holm Sune , Kararigas Georgios , Kringen Pedro , Madai Vince I. , Wiinblad Mathez Emilie , Tithi Jesmin Jahan , Westerlund Magnus , Wurth Renee , Zicari Roberto V. ,   Z-Inspection® initiative (2022)
Published: September 2023

AbstractBuilding artificial intelligence (AI) systems that adhere to ethical standards is a complex problem. Even though a multitude of guidelines for the design and development of such trustworthy AI systems exist, these guidelines focus on high-level and abstract requirements for AI systems, and it is often very difficult to assess if a specific system fulfills these requirements. The Z-Inspection® process provides a holistic and dynamic framework to evaluate the trustworthiness of specific AI systems at different stages of the AI lifecycle, including intended use, design, and development. It focuses, in particular, on the discussion and identification of ethical issues and tensions through the analysis of socio-technical scenarios and a requirement-based framework for ethical and trustworthy AI. This article is a methodological reflection on the Z-Inspection® process. We illustrate how high-level guidelines for ethical and trustworthy AI can be applied in practice and provide insights for both AI researchers and AI practitioners. We share the lessons learned from conducting a series of independent assessments to evaluate the trustworthiness of real-world AI systems, as well as key recommendations and practical suggestions on how to ensure a rigorous trustworthiness assessment throughout the lifecycle of an AI system. The results presented in this article are based on our assessments of AI systems in the healthcare sector and environmental monitoring, where we used the framework for trustworthy AI proposed in the Ethics Guidelines for Trustworthy AI by the European Commission’s High-Level Expert Group on AI. However, the assessment process and the lessons learned can be adapted to other domains and include additional frameworks.
Thermo‐Kinematic Constraints on Restoration of the Eastern Sichuan Fold‐And‐Thrust Belt, South China
Authors: Feng Qianqian , Qiu Nansheng , Wu Hang , Koyi Hemin 
Published: September 2023

AbstractKinematic restoration of the eastern Sichuan fold‐and‐thrust belt (ESFTB) in South China is calibrated with a new thermo‐kinematic model combining analog models, discrete element method, and thermochronology data. Thermo‐kinematic analysis provides constraints on the onset, rate, and lateral variation of deformation and exhumation. Results show that the ESFTB experienced a northwestward thrusting and periodic exhumation. Its evolution was characterized by five major stages based on the deformation characteristics; (a) Shortening above a basal decollement and formation of large imbricates separated by narrow synclines during 170–130 Ma; (b) Transition stage during 130–100 Ma; (c) Stepping up of deformation to shallow decollement levels and shaping of the thick‐skinned domain during 100–70 Ma; (d) Shaping of the thin‐skinned domain during 70–20 Ma; and (e) Continuous exhumation and structural modification from 20 Ma to present. The changes in the exhumation rate have been tectonic responses to the subduction retreat of the Paleo‐Pacific Plate and the eastward growth of the Tibetan Plateau. The westward subduction of the Paleo‐Pacific Plate resulted in northwestward shortening across South China, progressive deformation of the ESFTB, and rapid exhumation from the Late Jurassic to the Late Cretaceous. The crustal extension associated with the rollback of the Paleo‐Pacific slab accounted for the Mesozoic exhumation rate decrease until the Miocene. The accelerated cooling of the thin‐skinned domain of the ESFTB since the Miocene was a response to the eastward growth of the Tibetan Plateau, while the continuous slow exhumation in the thick‐skinned domain was related to the continuous crustal extension in South China.
Seismic Ocean Thermometry Using CTBTO Hydrophones
Authors: Wu Wenbo , Shen Zhichao , Peng Shirui , Zhan Zhongwen , Callies Jörn 
Published: September 2023

AbstractDue to limited observational coverage, monitoring the warming of the global ocean, especially the deep ocean, remains a challenging sampling problem. Seismic ocean thermometry (SOT) complements existing point measurements by inferring large‐scale averaged ocean temperature changes using the sound waves generated by submarine earthquakes, called T waves. We demonstrate here that Comprehensive Nuclear‐Test‐Ban Treaty Organization (CTBTO) hydrophones can record T waves with a higher signal‐to‐noise ratio compared to a previously used land‐based T‐wave station. This allows us to use small earthquakes (magnitude <4.0), which occur much more frequently than large events, dramatically improving the resulting temporal resolution of SOT. We also find that the travel time changes of T waves at the land‐based T‐wave station and the CTBTO hydrophone show small but systematic differences, although the two stations are only about 20 km apart. We attribute this feature to their different acoustic mode components sampling different parts of the ocean. Applying SOT to two CTBTO hydrophones in the East Indian Ocean reveals signals from decadal warming, seasonal variations, and mesoscale eddies, some of which are missing or underestimated in previously available temperature reconstructions. This application demonstrates the great advantage of hydrophone stations for global SOT, especially in regions with a low seismicity level.
Induced Polarization of Metal Grains: Simulations of Three‐Dimensional Electric Fields
Authors: Izumoto Satoshi 
Published: September 2023

AbstractInduced polarization (IP) method is one of the geophysical methods that utilizes polarization of subsurface materials. This method is very sensitive to the presence of (semi) conducting materials. Previous studies revealed the underlying mechanisms of metal polarization in simple geometry. However, there is a gap between such studies and the conditions in geological materials. To fill the gap, I have established the simulation method for studying the polarization of metal grains in a three‐dimensional field using the open‐source computational‐fluid‐dynamic software OpenFOAM. The three‐dimensional view of the surface potential distribution on a metal grain clarified how polarization is induced while varying geometrical constrictions. I varied the channel size, the orientation of the anisotropic grain, the elongation of the grain, and the distance of two grains. The results include: (a) a less decay of imaginary potential over distance for shorter or narrower channel, enhanced polarization in narrower channel and reduced polarization in shorter channel, (b) shift of the position of maximum imaginary potential over frequency on the surface of the oriented anisotropic grains, (c) higher peak frequency and larger polarization locally at the edge of the grains for elongated grains, and (d) enhancement of polarization by interaction of nearby grains. The underlying mechanisms were examined for each case. In addition, relationships between each scenario in my simulation and the subsurface environment were discussed. My successful implementation of the simulation for metal grains may be applied to improve the modeling, interpretation, and laboratory experimental setup.
Gentle Perseverance Lifts the Veil on Martian Dust
Authors: Lorenz Ralph D. 
Published: September 2023

AbstractObservations with sensitive photodiode detectors on the Perseverance rover (Hueso et al., 2023, https://doi.org/10.1029/2022JE007516; Vicente‐Retortillo et al., 2023, https://doi.org/10.1029/2022je007672) to detect dust devils and track formation, and movies of the Ingenuity helicopter's downwash impingement on the Martian surface (Lemmon et al., 2022a, https://doi.org/10.1029/2022je007605; Lemmon et al., 2022b, https://doi.org/10.1029/2022gl100126), together with in‐situ meteorological data, give new insights into the important problem of dust‐lifting on Mars, a phenomenon which influenced the lifetime of recent rovers and landers. These results, together with new low‐gravity wind tunnel experiments on parabolic flights and interpretation of the large blast pattern from lander retrorockets, indicate that particle motion and visible darkening on Mars can result from aerodynamic pressures of only 1–5 Pa, considerably less than previously thought.
Minnelide combined with anti-ANGPTL3-FLD monoclonal antibody completely protects mice with adriamycin nephropathy by promoting autophagy and inhibiting apoptosis
Authors: Ji Baowei , Liu Junchao , Yin Ye , Xu Hong , Shen Qian , Yu Jian 
Published: September 2023

AbstractMinimal change disease (MCD) is the common type of nephrotic syndrome (NS) in children. Currently, there is an urgent need to explore new treatments because of the significant side effects of long-term use of glucocorticoids and immunosuppressive drugs and the failure to reduce proteinuria in some patients. Angiopoietin-like protein 3 (Angptl3) is an essential target of NS, and anti-ANGPTL3-FLD monoclonal antibody (mAb) significantly reduces proteinuria in mice with adriamycin nephropathy (AN). However, some proteinuria is persistent. Minnelide, a water-soluble prodrug of triptolide, has been used for the treatment of glomerular disease. Therefore, the present study aimed to investigate whether minnelide combined with mAb could further protect mice with AN and the underlying mechanisms. 8-week-old C57BL/6 female mice were injected with 25 mg/kg of Adriamycin (ADR) by tail vein to establish the AN model. A dose of 200 μg/kg of minnelide or 20 mg/kg of mAb was administered intraperitoneally for the treatment. In vitro, the podocytes were treated with 0.4 μg/mL of ADR for 24 h to induce podocyte injury, and pretreatment with 10 ng/mL of triptolide for 30 min or 100 ng/mL of mAb for 1 h before ADR exposure was used to treat. The results showed that minnelide combined with mAb almost completely ameliorates proteinuria and restores the ultrastructure of the podocytes in mice with AN. In addition, minnelide combined with mAb restores the distribution of Nephrin, Podocin, and CD2AP and reduces the level of inflammatory factors in mice with AN. Mechanistically, minnelide combined with mAb could further alleviate apoptosis and promote autophagy in mice with AN by inhibiting the mTOR signaling pathway. In vitro, triptolide combined with mAb increases the expression of Nephrin, Podocin, and CD2AP, alleviates apoptosis, and promotes autophagy. Overall, minnelide combined with mAb completely protects the mice with AN by promoting autophagy and inhibiting apoptosis.
YAP is required for prostate development, regeneration, and prostate stem cell function
Authors: Xie Hui , Guo Linpei , Ma Qianwang , Zhang Wenyi , Yang Zhao , Wang Zhun , Peng Shuanghe , Wang Keruo , Wen Simeng , Shang Zhiqun , Niu Yuanjie 
Published: September 2023

AbstractProstate development and regeneration depend on prostate stem cell function, the delicate balance of stem cell self-renewal and differentiation. However, mechanisms modulating prostate stem cell function remain poorly identified. Here, we explored the roles of Yes-associated protein 1 (YAP) in prostate stem cells, prostate development and regeneration. Using YAPfl/fl, CD133-CreER mice, we found that stem cell-specific YAP-deficient mice had compromised branching morphogenesis and epithelial differentiation, resulting in damaged prostate development. YAP inhibition also significantly affected the regeneration process of mice prostate, leading to impaired regenerated prostate. Furthermore, YAP ablation in prostate stem cells significantly reduced its self-renewal activity in vitro, and attenuated prostate regeneration of prostate grafts in vivo. Further analysis revealed a decrease in Notch and Hedgehog pathways expression in YAP inhibition cells, and treatment with exogenous Shh partially restored the self-renewal ability of prostate sphere cells. Taken together, our results revealed the roles of YAP in prostate stem cell function and prostate development and regeneration through regulation of the Notch and Hedgehog signaling pathways.
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms
Authors: Pividori Milton , Lu Sumei , Li Binglan , Su Chun , Johnson Matthew E. , Wei Wei-Qi , Feng Qiping , Namjou Bahram , Kiryluk Krzysztof , Kullo Iftikhar J. , Luo Yuan , Sullivan Blair D. , Voight Benjamin F. , Skarke Carsten , Ritchie Marylyn D. , Grant Struan F. A. ,   eMERGE Consortium, Greene Casey S. 
Published: September 2023

AbstractGenes act in concert with each other in specific contexts to perform their functions. Determining how these genes influence complex traits requires a mechanistic understanding of expression regulation across different conditions. It has been shown that this insight is critical for developing new therapies. Transcriptome-wide association studies have helped uncover the role of individual genes in disease-relevant mechanisms. However, modern models of the architecture of complex traits predict that gene-gene interactions play a crucial role in disease origin and progression. Here we introduce PhenoPLIER, a computational approach that maps gene-trait associations and pharmacological perturbation data into a common latent representation for a joint analysis. This representation is based on modules of genes with similar expression patterns across the same conditions. We observe that diseases are significantly associated with gene modules expressed in relevant cell types, and our approach is accurate in predicting known drug-disease pairs and inferring mechanisms of action. Furthermore, using a CRISPR screen to analyze lipid regulation, we find that functionally important players lack associations but are prioritized in trait-associated modules by PhenoPLIER. By incorporating groups of co-expressed genes, PhenoPLIER can contextualize genetic associations and reveal potential targets missed by single-gene strategies.
Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles
Authors: Xie Xuan , Sun Xia , Wang Yuheng , Lehner Ben , Li Xianghua 
Published: September 2023

AbstractAn important challenge in genetics, evolution and biotechnology is to understand and predict how mutations combine to alter phenotypes, including molecular activities, fitness and disease. In diploids, mutations in a gene can combine on the same chromosome or on different chromosomes as a “heteroallelic combination”. However, a direct comparison of the extent, sign, and stability of the genetic interactions between variants within and between alleles is lacking. Here we use thermodynamic models of protein folding and ligand-binding to show that interactions between mutations within and between alleles are expected in even very simple biophysical systems. Protein folding alone generates within-allele interactions and a single molecular interaction is sufficient to cause between-allele interactions and dominance. These interactions change differently, quantitatively and qualitatively as a system becomes more complex. Altering the concentration of a ligand can, for example, switch alleles from dominant to recessive. Our results show that intra-molecular epistasis and dominance should be widely expected in even the simplest biological systems but also reinforce the view that they are plastic system properties and so a formidable challenge to predict. Accurate prediction of both intra-molecular epistasis and dominance will require either detailed mechanistic understanding and experimental parameterization or brute-force measurement and learning.
Transfer Learning with Kernel Methods
Authors: Radhakrishnan Adityanarayanan , Ruiz Luyten Max , Prasad Neha , Uhler Caroline 
Published: September 2023

AbstractTransfer learning refers to the process of adapting a model trained on a source task to a target task. While kernel methods are conceptually and computationally simple models that are competitive on a variety of tasks, it has been unclear how to develop scalable kernel-based transfer learning methods across general source and target tasks with possibly differing label dimensions. In this work, we propose a transfer learning framework for kernel methods by projecting and translating the source model to the target task. We demonstrate the effectiveness of our framework in applications to image classification and virtual drug screening. For both applications, we identify simple scaling laws that characterize the performance of transfer-learned kernels as a function of the number of target examples. We explain this phenomenon in a simplified linear setting, where we are able to derive the exact scaling laws.
Coupled reaction equilibria enable the light-driven formation of metal-functionalized molecular vanadium oxides
Authors: Repp Stefan , Remmers Moritz , Rein Alexandra Stefanie Jessica , Sorsche Dieter , Gao Dandan , Anjass Montaha , Mondeshki Mihail , Carrella Luca M. , Rentschler Eva , Streb Carsten 
Published: September 2023

AbstractThe introduction of metal sites into molecular metal oxides, so-called polyoxometalates, is key for tuning their structure and reactivity. The complex mechanisms which govern metal-functionalization of polyoxometalates are still poorly understood. Here, we report a coupled set of light-dependent and light-independent reaction equilibria controlling the mono- and di-metal-functionalization of a prototype molecular vanadium oxide cluster. Comprehensive mechanistic analyses show that coordination of a Mg2+ ion to the species {(NMe2H2)2[VV12O32Cl]}3- results in formation of the mono-functionalized {(NMe2H2)[(MgCl)VV12O32Cl]}3- with simultaneous release of a NMe2H2+ placeholder cation. Irradiation of this species with visible light results in one-electron reduction of the vanadate, exchange of the second NMe2H2+ with Mg2+, and formation/crystallization of the di-metal-functionalized [(MgCl)2VIVVV11O32Cl]4-. Mechanistic studies show how stimuli such as light or competing cations affect the coupled equilibria. Transfer of this synthetic concept to other metal cations is also demonstrated, highlighting the versatility of the approach.
Cell diversity and plasticity during atrioventricular heart valve EMTs
Authors: Lotto Jeremy , Cullum Rebecca , Drissler Sibyl , Arostegui Martin , Garside Victoria C. , Fuglerud Bettina M. , Clement-Ranney Makenna , Thakur Avinash , Underhill T. Michael , Hoodless Pamela A. 
Published: September 2023

AbstractEpithelial-to-mesenchymal transitions (EMTs) of both endocardium and epicardium guide atrioventricular heart valve formation, but the cellular complexity and small scale of this tissue have restricted analyses. To circumvent these issues, we analyzed over 50,000 murine single-cell transcriptomes from embryonic day (E)7.75 hearts to E12.5 atrioventricular canals. We delineate mesenchymal and endocardial bifurcation during endocardial EMT, identify a distinct, transdifferentiating epicardial population during epicardial EMT, and reveal the activation of epithelial-mesenchymal plasticity during both processes. In Sox9-deficient valves, we observe increased epithelial-mesenchymal plasticity, indicating a role for SOX9 in promoting endothelial and mesenchymal cell fate decisions. Lastly, we deconvolve cell interactions guiding the initiation and progression of cardiac valve EMTs. Overall, these data reveal mechanisms of emergence of mesenchyme from endocardium or epicardium at single-cell resolution and will serve as an atlas of EMT initiation and progression with broad implications in regenerative medicine and cancer biology.