bluuebunny/crossref_metadata_2025_split huggingface dataset:
An open-source framework for end-to-end analysis of electronic health record data
Authors: Heumos Lukas , Ehmele Philipp , Treis Tim , Upmeier zu Belzen Julius , Roellin Eljas , May Lilly , Namsaraeva Altana , Horlava Nastassya , Shitov Vladimir A. , Zhang Xinyue , Zappia Luke , Knoll Rainer , Lang Niklas J. , Hetzel Leon , Virshup Isaac , Sikkema Lisa , Curion Fabiola , Eils Roland , Schiller Herbert B. , Hilgendorff Anne , Theis Fabian J. 
Published: September 2024

AbstractWith progressive digitalization of healthcare systems worldwide, large-scale collection of electronic health records (EHRs) has become commonplace. However, an extensible framework for comprehensive exploratory analysis that accounts for data heterogeneity is missing. Here we introduce ehrapy, a modular open-source Python framework designed for exploratory analysis of heterogeneous epidemiology and EHR data. ehrapy incorporates a series of analytical steps, from data extraction and quality control to the generation of low-dimensional representations. Complemented by rich statistical modules, ehrapy facilitates associating patients with disease states, differential comparison between patient clusters, survival analysis, trajectory inference, causal inference and more. Leveraging ontologies, ehrapy further enables data sharing and training EHR deep learning models, paving the way for foundational models in biomedical research. We demonstrate ehrapy’s features in six distinct examples. We applied ehrapy to stratify patients affected by unspecified pneumonia into finer-grained phenotypes. Furthermore, we reveal biomarkers for significant differences in survival among these groups. Additionally, we quantify medication-class effects of pneumonia medications on length of stay. We further leveraged ehrapy to analyze cardiovascular risks across different data modalities. We reconstructed disease state trajectories in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on imaging data. Finally, we conducted a case study to demonstrate how ehrapy can detect and mitigate biases in EHR data. ehrapy, thus, provides a framework that we envision will standardize analysis pipelines on EHR data and serve as a cornerstone for the community.
Tonic and burst-like locus coeruleus stimulation distinctly shift network activity across the cortical hierarchy
Authors: Grimm Christina , Duss Sian N. , Privitera Mattia , Munn Brandon R. , Karalis Nikolaos , Frässle Stefan , Wilhelm Maria , Patriarchi Tommaso , Razansky Daniel , Wenderoth Nicole , Shine James M. , Bohacek Johannes , Zerbi Valerio 
Published: September 2024

AbstractNoradrenaline (NA) release from the locus coeruleus (LC) changes activity and connectivity in neuronal networks across the brain, modulating multiple behavioral states. NA release is mediated by both tonic and burst-like LC activity. However, it is unknown whether the functional changes in target areas depend on these firing patterns. Using optogenetics, photometry, electrophysiology and functional magnetic resonance imaging in mice, we show that tonic and burst-like LC firing patterns elicit brain responses that hinge on their distinct NA release dynamics. During moderate tonic LC activation, NA release engages regions associated with associative processing, while burst-like stimulation biases the brain toward sensory processing. These activation patterns locally couple with increased astrocytic and inhibitory activity and change the brain’s topological configuration in line with the hierarchical organization of the cerebral cortex. Together, these findings reveal how the LC–NA system achieves a nuanced regulation of global circuit operations.
Comprehensive battery aging dataset: capacity and impedance fade measurements of a lithium-ion NMC/C-SiO cell
Authors: Luh Matthias , Blank Thomas 
Published: September 2024

AbstractBattery degradation is critical to the cost-effectiveness and usability of battery-powered products. Aging studies help to better understand and model degradation and to optimize the operating strategy. Nevertheless, there are only a few comprehensive and freely available aging datasets for these applications. To our knowledge, the dataset1 presented in the following is one of the largest published to date. It contains over 3 billion data points from 228 commercial NMC/C+SiO lithium-ion cells aged for more than a year under a wide range of operating conditions. We investigate calendar and cyclic aging and also apply different driving cycles to cells. The dataset1 includes result data (such as the remaining usable capacity or impedance measured in check-ups) and raw data (i.e., measurement logs with two-second resolution). The data can be used in a wide range of applications, for example, to model battery degradation, gain insight into lithium plating, optimize operating strategies, or test battery impedance or state estimation algorithms using machine learning or Kalman filtering.
Performance analysis of partially shaded high-efficiency mono PERC/mono crystalline PV module under indoor and environmental conditions
Authors: Kumari Neha , Singh Sanjay Kumar , Kumar Sanjay , Jadoun Vinay Kumar 
Published: September 2024

AbstractThe ever-increasing demand for sustainable energy has drawn attention towards photovoltaic efficiency and reliability. In this context, the shading and associated hotpot degradation within PV modules has become an important area of research and development. The experimental approach of this paper aims to investigate single cell shading in high efficiency monocrystalline silicon PV PERC modules. Prior to the outdoor experiment, the PV module underwent experimental testing under STC to determine variation in electrical and thermal behaviour due to partial shading. The indoor experiments are performed using Sun-simulator and the I–V and P–V curves are analysed. Further, the outdoor experiments were performed under realistic conditions. In both cases, results showed that during 40–60% shading in single cell leads to critical shading scenario causing significant drop in power output in comparison with their unshaded conditions. The maximum power loss of 36.34% and 42% is recorded for indoor and outdoor experiments. The outdoor experiments recorded hotspot temperature of 85–90.1 °C under respective 40% and 60% critical shading scenarios. The efficiency recorded in the time interval of 11:00:00 and 11:30:00 was highest for the solar radiations between 940 and 990 W/m2. The maximum drop in efficiency is recorded from noon till 13:30:00 time of the day. Development of hotspot is directly related to the failure or malfunction of protecting system. Hence the importance of type of PV technology, amount of shading, and critical shading scenario is presented in the study. This study is important for researcher and manufacture to consider single cell shading in PV technology.
IF1 is a cold-regulated switch of ATP synthase hydrolytic activity to support thermogenesis in brown fat
Authors: Brunetta Henver S , Jung Anna S , Valdivieso-Rivera Fernando , de Campos Zani Stepheny C , Guerra Joel , Furino Vanessa O , Francisco Annelise , Berçot Marcelo , Moraes-Vieira Pedro M , Keipert Susanne , Jastroch Martin , Martinez Laurent O , Sponton Carlos H , Castilho Roger F , Mori Marcelo A , Bartelt Alexander 
Published: September 2024

AbstractWhile mechanisms controlling uncoupling protein-1 (UCP1) in thermogenic adipocytes play a pivotal role in non-shivering thermogenesis, it remains unclear whether F1Fo-ATP synthase function is also regulated in brown adipose tissue (BAT). Here, we show that inhibitory factor 1 (IF1, encoded by Atp5if1), an inhibitor of ATP synthase hydrolytic activity, is a critical negative regulator of brown adipocyte energy metabolism. In vivo, IF1 levels are diminished in BAT of cold-adapted mice compared to controls. Additionally, the capacity of ATP synthase to generate mitochondrial membrane potential (MMP) through ATP hydrolysis (the so-called “reverse mode” of ATP synthase) is increased in brown fat. In cultured brown adipocytes, IF1 overexpression results in an inability of mitochondria to sustain the MMP upon adrenergic stimulation, leading to a quiescent-like phenotype in brown adipocytes. In mice, adeno-associated virus-mediated IF1 overexpression in BAT suppresses adrenergic-stimulated thermogenesis and decreases mitochondrial respiration in BAT. Taken together, our work identifies downregulation of IF1 upon cold as a critical event for the facilitation of the reverse mode of ATP synthase as well as to enable energetic adaptation of BAT to effectively support non-shivering thermogenesis.
RNA fine-tunes estrogen receptor-alpha binding on low-affinity DNA motifs for transcriptional regulation
Authors: Soota Deepanshu , Saravanan Bharath , Mann Rajat , Kharbanda Tripti , Notani Dimple 
Published: September 2024

AbstractTranscription factors (TFs) regulate gene expression by binding with varying strengths to DNA via their DNA-binding domain. Additionally, some TFs also interact with RNA, which modulates transcription factor binding to chromatin. However, whether RNA-mediated TF binding results in differential transcriptional outcomes remains unknown. In this study, we demonstrate that estrogen receptor α (ERα), a ligand-activated TF, interacts with RNA in a ligand-dependent manner. Defects in RNA binding lead to genome-wide loss of ERα recruitment, particularly at weaker ERα-motifs. Furthermore, ERα mobility in the nucleus increases in the absence of its RNA-binding capacity. Unexpectedly, this increased mobility coincides with robust polymerase loading and transcription of ERα-regulated genes that harbor low-strength motifs. However, highly stable binding of ERα on chromatin negatively impacts ligand-dependent transcription. Collectively, our results suggest that RNA interactions spatially confine ERα on low-affinity sites to fine-tune gene transcription.
Non-autophagic Golgi-LC3 lipidation facilitates TFE3 stress response against Golgi dysfunction
Authors: Kang Jaemin , Li Cathena Meiling , Kim Namhoon , Baek Jongyeon , Jung Yong-Keun 
Published: September 2024

AbstractLipidated ATG8/LC3 proteins are recruited to single membrane compartments as well as autophagosomes, supporting their functions. Although recent studies have shown that Golgi-LC3 lipidation follows Golgi damage, its molecular mechanism and function under Golgi stress remain unknown. Here, by combining DLK1 overexpression as a new strategy for induction of Golgi-specific LC3 lipidation, and the application of Golgi-damaging reagents, we unravel the mechanism and role of Golgi-LC3 lipidation. Upon DLK1 overexpression, LC3 is lipidated on the Golgi apparatus in an ATG12-ATG5-ATG16L1 complex-dependent manner; a post-Golgi trafficking blockade is the primary cause of this lipidation. During Golgi stress, ATG16L1 is recruited through its interaction with V-ATPase for Golgi-LC3 lipidation. After post-Golgi trafficking inhibition, TFE3, a key regulator of the Golgi stress response, is translocated to the nucleus. Defects in LC3 lipidation disrupt this translocation, leading to an attenuation of the Golgi stress response. Together, our results reveal the mechanism and unexplored function of Golgi-LC3 lipidation in the Golgi stress response.
Amplified centrosomes—more than just a threat
Authors: Kiermaier Eva , Stötzel Isabel , Schapfl Marina A , Villunger Andreas 
Published: September 2024

AbstractCentrosomes are major organizing components of the tubulin-based cytoskeleton. In recent years, we have gained extensive knowledge about their structure, biogenesis, and function from single cells, cell–cell interactions to tissue homeostasis, including their role in human diseases. Centrosome abnormalities are linked to, among others primary microcephaly, birth defects, ciliopathies, and tumorigenesis. Centrosome amplification, a state where two or more centrosomes are present in the G1 phase of the cell cycle, correlates in cancer with karyotype alterations, clinical aggressiveness, and lymph node metastasis. However, amplified centrosomes also appear in healthy tissues and, independent of their established role, in multi-ciliation. One example is the liver where hepatocytes carry amplified centrosomes owing to whole-genome duplication events during organogenesis. More recently, amplified centrosomes have been found in neuronal progenitors and several cell types of hematopoietic origin in which they enhance cellular effector functions. These findings suggest that extra centrosomes do not necessarily pose a risk for genome integrity and are harnessed for physiological processes. Here, we compare established and emerging ‘non-canonical functions’ of amplified centrosomes in cancerous and somatic cells and discuss their role in cellular physiology.
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases
Authors: Argov Chanan M , Shneyour Ariel , Jubran Juman , Sabag Eric , Mansbach Avigdor , Sepunaru Yair , Filtzer Emmi , Gruber Gil , Volozhinsky Miri , Yogev Yuval , Birk Ohad , Chalifa-Caspi Vered , Rokach Lior , Yeger-Lotem Esti 
Published: September 2024

AbstractPathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a few tissues and organs. However, variant effect prediction tools that aim to identify pathogenic variants are typically oblivious to tissue contexts. Here we report a machine-learning framework, denoted “Tissue Risk Assessment of Causality by Expression for variants” (TRACEvar, https://netbio.bgu.ac.il/TRACEvar/), that offers two advancements. First, TRACEvar predicts pathogenic variants that disrupt the normal physiology of specific tissues. This was achieved by creating 14 tissue-specific models that were trained on over 14,000 variants and combined 84 attributes of genetic variants with 495 attributes derived from tissue omics. TRACEvar outperformed 10 well-established and tissue-oblivious variant effect prediction tools. Second, the resulting models are interpretable, thereby illuminating variants’ mode of action. Application of TRACEvar to variants of 52 rare-disease patients highlighted pathogenicity mechanisms and relevant disease processes. Lastly, the interpretation of all tissue models revealed that top-ranking determinants of pathogenicity included attributes of disease-affected tissues, particularly cellular process activities. Collectively, these results show that tissue contexts and interpretable machine-learning models can greatly enhance the etiology of rare diseases.
Identifying mitigating strategies for endothelial cell dysfunction and hypertension in response to VEGF receptor inhibitors
Authors: Camarda Nicholas D. , Lu Qing , Meola Dawn M. , Man Joshua J. , Song Zeyuan , Travers Richard J. , Lopez Katherine E. , Powers Sarah N. , Papanastasiou Malvina , DeRuff Katherine C. , Mullahoo James , Egri Shawn B. , Davison Desiree , Sebastiani Paola , Eblen Scott T. , Buchsbaum Rachel , Huggins Gordon S. , London Cheryl A. , Jaffe Jacob D. , Upshaw Jenica N. , Yang Vicky K. , Jaffe Iris Z. 
Published: September 2024

Abstract
Vascular endothelial growth factor receptor inhibitors (VEGFRis) improve cancer survival but are associated with treatment-limiting hypertension, often attributed to endothelial cell (EC) dysfunction. Using phosphoproteomic profiling of VEGFRi-treated ECs, drugs were screened for mitigators of VEGFRi-induced EC dysfunction and validated in primary aortic ECs, mice, and canine cancer patients. VEGFRi treatment significantly raised systolic blood pressure (SBP) and increased markers of endothelial and renal dysfunction in mice and canine cancer patients. α-Adrenergic-antagonists were identified as drugs that most oppose the VEGFRi proteomic signature. Doxazosin, one such α-antagonist, prevented EC dysfunction in murine, canine, and human aortic ECs. In mice with sorafenib-induced-hypertension, doxazosin mitigated EC dysfunction but not hypertension or glomerular endotheliosis, while lisinopril mitigated hypertension and glomerular endotheliosis without impacting EC function. Hence, reversing EC dysfunction was insufficient to mitigate VEGFRi-induced-hypertension in this mouse model. Canine cancer patients with VEGFRi-induced-hypertension were randomized to doxazosin or lisinopril and both agents significantly decreased SBP. The canine clinical trial supports safety and efficacy of doxazosin and lisinopril as antihypertensives for VEGFRi-induced-hypertension and the potential of trials in canines with spontaneous cancer to accelerate translation. The overall findings demonstrate the utility of phosphoproteomics to identify EC-protective agents to mitigate cardio-oncology side effects.
Infrared surface brightness technique applied to RR Lyrae stars from the solar neighborhood
Authors: Zgirski Bartłomiej , Gieren Wolfgang , Pietrzyński Grzegorz , Górski Marek , Wielgórski Piotr , Storm Jesper , Bras Garance , Kervella Pierre , Nardetto Nicolas , Hajdu Gergely , Chini Rolf , Haas Martin 
Published: September 2024

Context. The Baade-Wesselink (BW) method, also known as the pulsation parallax method, allows us to estimate distances to individual pulsating stars. Accurate geometric parallaxes obtained by the Gaia mission serve us in the calibration of the method and in the determination of its precision. This method also provides a way of determining mean radii of pulsating stars.
Aims. The main aim of this work is to determine the scatter and possible dependence of p-factors of RR Lyrae stars on their pulsation periods. The secondary objective is to determine the mean radius-period relations for these stars.
Methods. Our calibrations for RR Lyrae stars are based on photometric data gathered at the Cerro Murphy Observatory and parallaxes from the Data Release 3 of the Gaia space mission. We obtained spectroscopic data specifically for this project using high-resolution spectrographs. We used the infrared surface brightness (IRSB) version of the method that relies on a surface brightness-color relation that is dependent on the (V − K) color. It allows us to estimate stellar angular diameters, while tracing variations of the stellar radius using measurements of the stellar radial velocity obtained from spectroscopy. We present results based on four different empirical surface brightness-color relations, with three relations for dwarfs and subgiants and one for classical Cepheids.
Results. We present our calibration of projection factors and determination of the mean radii for nine Galactic RR Lyrae stars. We obtained a spread of p-factors of around 0.07–0.08 for our sample of RR Lyrae stars from the solar neighborhood. However, depending on a given SBCR, we also found relations between the p-factor and the pulsation period for RRab stars with a root mean square (rms) scatter around the relation of around 0.05, but with relatively large uncertainty on the relation parameters. We also present relations between the mean radius and period for RR Lyrae pulsating in the fundamental mode with an rms scatter around the relation of 0.012 R⊙. We observe a clear offset between p-factors obtained using the IRSB technique (with a mean p value between 1.39 and 1.45) and values inferred using the SPIPS tool. This confirms that different implementations of the BW method are sensitive to various components of the p-factor. On the other hand, we obtain a similar scatter for p, as observed in a previous study based on the SPIPS tool. Our period-radius relations are in a good agreement with both the inference based on SPIPS and theoretical predictions.
A versatile steel belt casting equipment for in situ synchrotron radiation x-ray scattering measurement of polymer films
Authors: Liu Shenghui , Cheng Shichao , Luo Yu , Zhu Jianhe , Liu Liangbao , Guo Hang , Cui Kunpeng , An Minfang , Li Liangbin 
Published: September 2024

A steel belt casting equipment, weighing approximately ∼6–7 tons and measuring ∼5 m in length, has been designed and developed for simulating the industrial processing of polymer films and being combined with synchrotron radiation in situ x-ray scattering measurements. Through modification of its modules, it is feasible to implement two distinct film casting modes, namely the wet and the dry casting processes. The speed of a steel belt can span from 0.5 to 8 m/min. The highest experimental temperature and drying wind speed are 300 °C and 6 m/s, respectively. All film casting parameters, such as extrusion speed, distance between die and steel belt, casting speed, temperature, and wind speed, can be adjusted independently. Especially, the control accuracy of the temperature and casting rate can reach ±0.1 °C and ±0.01 m/min, respectively. The feasibility of this equipment has been validated through in situ x-ray scattering tests at the BL10U1 industrial beamline of the Shanghai synchrotron radiation facility. With the assistance of this equipment, the understanding of the physical mechanism behind the film casting process should be improved so that the development of advanced functional polymer films.
Compact metal nano-powder generator of 273 MW average power and synthesis of copper nano-powder
Authors: Dubey A. K. , Shukla R. , Sagar K. , Dey P. , Sharma A. 
Published: September 2024

The synthesis of metal nanoparticles holds significant promise for various applications ranging from electronics to catalysis. Their high specific surface area makes them more applicable in the form of lubricant and sorbent. Some of the metal nano-powders, such as silver, copper, and zinc, possess anti-microbial properties; hence, they are very useful in medical sciences. This paper presents a novel approach to the design and implementation of a compact metal nano-powder generator of 273 MW average power through the electrical explosion of wire method. The design focuses on achieving the automatic and repetitive operation of a compact metal nano-powder generator and minimizing its geometric inductance to achieve a fast rise time current across the exploding wire load. Copper nano-powder is produced with a copper wire of 450 μm thickness and 30 mm length at charging voltages of 8.5, 9.0, and 9.5 kV and achieving a superheat of 1.75, 1.92, and 2.06, respectively. The synthesis process is characterized by a detailed analysis of the copper nano-powder’s structural, morphological, and chemical composition using techniques such as x-ray diffraction, scanning electron microscopy, and energy-dispersive x-ray spectroscopy. The particle size distribution studies are performed by adopting the log-normal probability distribution. The results demonstrate the effectiveness of the proposed compact nano-powder generator in producing copper nano-powder with tailored properties suitable for diverse applications.