bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic genome and transcriptome signatures in colorectal cancers
Authors: Nunes Luís , Li Fuqiang , Wu Meizhen , Luo Tian , Hammarström Klara , Torell Emma , Ljuslinder Ingrid , Mezheyeuski Artur , Edqvist Per-Henrik , Löfgren-Burström Anna , Zingmark Carl , Edin Sofia , Larsson Chatarina , Mathot Lucy , Osterman Erik , Osterlund Emerik , Ljungström Viktor , Neves Inês , Yacoub Nicole , Guðnadóttir Unnur , Birgisson Helgi , Enblad Malin , Ponten Fredrik , Palmqvist Richard , Xu Xun , Uhlén Mathias , Wu Kui , Glimelius Bengt , Lin Cong , Sjöblom Tobias 
Published: August 2024

AbstractColorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.
PTER is a N-acetyltaurine hydrolase that regulates feeding and obesity
Authors: Wei Wei , Lyu Xuchao , Markhard Andrew L. , Fu Sipei , Mardjuki Rachel E. , Cavanagh Peter E. , Zeng Xianfeng , Rajniak Jakub , Lu Nannan , Xiao Shuke , Zhao Meng , Moya-Garzon Maria Dolores , Truong Steven D. , Chou Jonathan Chiu‐Chun , Wat Lianna W. , Chidambaranathan-Reghupaty Saranya , Coassolo Laetitia , Xu Duo , Shen Fangfang , Huang Wentao , Ramirez Cuauhtemoc B. , Jang Cholsoon , Li Lingyin , Svensson Katrin J. , Fischbach Michael A. , Long Jonathan Z. 
Published: August 2024

AbstractTaurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans1–3. In endogenous taurine metabolism, dedicated enzymes are involved in the biosynthesis of taurine from cysteine and in the downstream metabolism of secondary taurine metabolites4,5. One taurine metabolite is N-acetyltaurine6. Levels of N-acetyltaurine are dynamically regulated by stimuli that alter taurine or acetate flux, including endurance exercise7, dietary taurine supplementation8 and alcohol consumption6,9. So far, the identities of the enzymes involved in N-acetyltaurine metabolism, and the potential functions of N-acetyltaurine itself, have remained unknown. Here we show that the body mass index associated orphan enzyme phosphotriesterase-related (PTER)10 is a physiological N-acetyltaurine hydrolase. In vitro, PTER catalyses the hydrolysis of N-acetyltaurine to taurine and acetate. In mice, PTER is expressed in the kidney, liver and brainstem. Genetic ablation of Pter in mice results in complete loss of tissue N-acetyltaurine hydrolysis activity and a systemic increase in N-acetyltaurine levels. After stimuli that increase taurine levels, Pter knockout mice exhibit reduced food intake, resistance to diet-induced obesity and improved glucose homeostasis. Administration of N-acetyltaurine to obese wild-type mice also reduces food intake and body weight in a GFRAL-dependent manner. These data place PTER into a central enzymatic node of secondary taurine metabolism and uncover a role for PTER and N-acetyltaurine in body weight control and energy balance.
Age-related epithelial defects limit thymic function and regeneration
Authors: Kousa Anastasia I. , Jahn Lorenz , Zhao Kelin , Flores Angel E. , Acenas Dante , Lederer Emma , Argyropoulos Kimon V. , Lemarquis Andri L. , Granadier David , Cooper Kirsten , D’Andrea Michael , Sheridan Julie M. , Tsai Jennifer , Sikkema Lisa , Lazrak Amina , Nichols Katherine , Lee Nichole , Ghale Romina , Malard Florent , Andrlova Hana , Velardi Enrico , Youssef Salma , Burgos da Silva Marina , Docampo Melissa , Sharma Roshan , Mazutis Linas , Wimmer Verena C. , Rogers Kelly L. , DeWolf Susan , Gipson Brianna , Gomes Antonio L. C. , Setty Manu , Pe’er Dana , Hale Laura , Manley Nancy R. , Gray Daniel H. D. , van den Brink Marcel R. M. , Dudakov Jarrod A. 
Published: August 2024

AbstractThe thymus is essential for establishing adaptive immunity yet undergoes age-related involution that leads to compromised immune responsiveness. The thymus is also extremely sensitive to acute insult and although capable of regeneration, this capacity declines with age for unknown reasons. We applied single-cell and spatial transcriptomics, lineage-tracing and advanced imaging to define age-related changes in nonhematopoietic stromal cells and discovered the emergence of two atypical thymic epithelial cell (TEC) states. These age-associated TECs (aaTECs) formed high-density peri-medullary epithelial clusters that were devoid of thymocytes; an accretion of nonproductive thymic tissue that worsened with age, exhibited features of epithelial-to-mesenchymal transition and was associated with downregulation of FOXN1. Interaction analysis revealed that the emergence of aaTECs drew tonic signals from other functional TEC populations at baseline acting as a sink for TEC growth factors. Following acute injury, aaTECs expanded substantially, further perturbing trophic regeneration pathways and correlating with defective repair of the involuted thymus. These findings therefore define a unique feature of thymic involution linked to immune aging and could have implications for developing immune-boosting therapies in older individuals.
Experimental validation of a low-cost maximum power point tracking technique based on artificial neural network for photovoltaic systems
Authors: Abouzeid Ahmed Fathy , Eleraky Hadeer , Kalas Ahmed , Rizk Rawya , Elsakka Mohamed Mohamed , Refaat Ahmed 
Published: August 2024

AbstractMaximum power point tracking (MPPT) is a technique involved in photovoltaic (PV) systems for optimizing the output power of solar panels. Traditional solutions like perturb and observe (P&O) and Incremental Conductance (IC) are commonly utilized to follow the MPP under various environmental circumstances. However, these algorithms suffer from slow tracking speed and low dynamics under fast-changing environment conditions. To cope with these demerits, a data-driven artificial neural network (ANN) algorithm for MPPT is proposed in this paper. By leveraging the learning capabilities of the ANN, the PV operating point can be adapted to dynamic changes in solar irradiation and temperature. Consequently, it offers promising solutions for MPPT in fast-changing environments as well as overcoming the limitations of traditional MPPT techniques. In this paper, simulations verification and experimental validation of a proposed data-driven ANN-MPPT technique are presented. Additionally, the proposed technique is analyzed and compared to traditional MPPT methods. The numerical and experimental findings indicate that, of the examined MPPT methods, the proposed ANN-MPPT approach achieves the highest MPPT efficiency at 98.16% and the shortest tracking time of 1.3 s.
Three-dimensional iodine mapping quantified by dual-energy CT for predicting programmed death-ligand 1 expression in invasive pulmonary adenocarcinoma
Authors: Yamagata Kazuki , Yanagawa Masahiro , Hata Akinori , Ogawa Ryo , Kikuchi Noriko , Doi Shuhei , Ninomiya Keisuke , Tokuda Yukiko , Tomiyama Noriyuki 
Published: August 2024

AbstractWe examined the association between texture features using three-dimensional (3D) io-dine density histogram on delayed phase of dual-energy CT (DECT) and expression of programmed death-ligand 1 (PD-L1) using immunostaining methods in non-small cell lung cancer. Consecutive 37 patients were scanned by DECT. Unenhanced and enhanced (3 min delay) images were obtained. 3D texture analysis was performed for each nodule to obtain 7 features (max, min, median, mean, standard deviation, skewness, and kurtosis) from iodine density mapping and extracellular volume (ECV). A pathologist evaluated a tumor proportion score (TPS, %) using PD-L1 immunostaining: PD-L1 high (TPS ≥ 50%) and low or negative expression (TPS < 50%). Associations between PD-L1 expression and each 8 parameter were evaluated using logistic regression analysis. The multivariate logistic regression analysis revealed that skewness and ECV were independent indicators associated with high PD-L1 expression (skewness: odds ratio [OR]  7.1 [95% CI 1.1, 45.6], p = 0.039; ECV: OR 6.6 [95% CI 1.1, 38.4], p = 0.037). In the receiver-operating characteristic analysis, the area under the curve of the combination of skewness and ECV was 0.83 (95% CI 0.67, 0.93) with sensitivity of 64% and specificity of 96%. Skewness from 3D iodine density histogram and ECV on dual energy CT were significant factors for predicting PD-L1 expression.
A Case Study of Suspected Childhood Apraxia of Sign
Authors: Jackson Christyn , Hagstrom Lauren , Emmorey Karen 
Published: August 2024

Purpose:
We provide a case report of “Zoe,” a 4-year-old deaf child from a deaf signing family, who presented with a possible case of Childhood Apraxia of Sign (CASign).

Method:
The description is based on reports from the child's speech-language pathologist, her Individualized Education Program report, and a clinician-created sign imitation task.

Results:
Zoe's sign articulation errors in American Sign Language differed from those reported for typically developing deaf children and were parallel to the types of errors observed for hearing children with childhood apraxia of speech. Specifically, Zoe produced inconsistent errors across signs, substituted more complex handshapes for simple handshapes, made errors on both unmarked (common) and marked (less common) forms, produced articulatory distortions (rather than substitutions), and exhibited “groping” behaviors (a sequence of attempts to move her hands into the correct position). In addition, Zoe sometimes self-corrected her errors by manipulating her own hands, for example, using her left hand to move the thumb of her right hand into the correct position.

Conclusion:
Zoe's pattern of sign errors is consistent with an underlying deficit in motor planning and/or programming and may constitute the first reported case of CASign.
Search of extended emission from HESS J1702-420 with eROSITA
Authors: Malyshev Denys , Chernyakova Maria , Aharonian Felix , Santangelo Andrea 
Published: August 2024

Context. HESS J1702-420 is a peculiar TeV complex with a morphology changing from a diffuse source (HESS J1702-420B) at ≲2 TeV to a point-like one (HESS J1702-420A) at ≳10 TeV energies. The morphology and spectral properties of HESS J1702-420 could be understood in terms of (diffusive) hadronic or leptonic models in which the observed TeV emission arises correpondingly from proton-proton or IC-radiation of relativistic particles present in the region.
Aims. In this work, we perform searches of the X-ray counterpart of the HESS J1702-420B source originating from the synchrotron emission of the primary or secondary relativistic electrons produced within leptonic or hadronic models. Such an emission can be extended and remain beyond the detection capabilities of narrow field-of-view instruments such as XMM-Newton.
Methods. We utilised the publicly available first-6-months eROSITA dataset (DR1) fully covering the selected analysis region of > 5°-radius around HESS J1702-420. We discuss biases connected to variable plasma temperature or neutral hydrogen column density in the region and present results based on the background modelling approach.
Results. The performed analysis does not allow us to detect the extended X-ray counterpart of HESS J1702-420 of 0.07° −3°-radii sizes. The derived upper limits are significantly higher than the expected hadronic model flux of the X-ray counterpart. For the leptonic model, the derived limits indicate the magnetic field in the region B ≲ 2 μG. We argue that further advances in the diffuse X-ray counterpart searches could be achieved with either next-generation missions or Msec-long observational campaigns using currently operating instruments.
Revealing faint compact radio jets at redshifts above 5 with very long baseline interferometry
Authors: Krezinger M. , Baldini G. , Giroletti M. , Sbarrato T. , Ghisellini G. , Giovannini G. , An T. , Gabányi K. É. , Frey S. 
Published: August 2024

Context. Over the past two decades, our knowledge of the high-redshift (z > 5) radio quasars has expanded, thanks to dedicated high-resolution very long baseline interferometry (VLBI) observations. Distant quasars provide unique information about the formation and evolution of the first galaxies and supermassive black holes in the Universe. Powerful relativistic jets are likely to have played an essential role in these processes. However, the sample of VLBI-observed radio quasars is still too small to allow meaningful statistical conclusions.
Aims. We extend the list of the VLBI observed radio quasars to investigate how the source structure and physical parameters are related to radio loudness.
Methods. We assembled a sample of ten faint radio quasars located at 5 < z < 6 with their radio-loudness indices spanning between 0.9 − 76. We observed the selected targets with the European VLBI Network (EVN) at 1.7 GHz. The milliarcsecond-scale resolution of VLBI at this frequency allowed us to probe the compact innermost parts of radio-emitting relativistic jets. In addition to the single-band VLBI observations, we collected single-dish and low-resolution radio interferometric data to investigate the spectral properties and variability of our sources.
Results. The detection rate of this high-redshift, low-flux-density sample is 90%, with only one target (J0306+1853) remaining undetected. The other nine sources appear core-dominated and show a single, faint and compact radio core on this angular scale. The derived radio powers are typical of Fanaroff-Riley II radio galaxies and quasars. By extending our sample with other VLBI-detected z > 5 sources from the literature, we found that the core brightness temperatures and monochromatic radio powers tend to increase with radio loudness.
Grey-box modeling of Air Handling Units for Analysis and Virtual Sensing
Authors: Fjerbæk Esben Visby , Smith Kevin Michael , Hviid Christian Anker 
Published: August 2024

The optimization of control sequences in air handling units (AHUs) presents a significant opportunity for energy savings within HVAC systems. However, many building owners and operators require quantifiable estimates of potential energy savings before committing to retrofitting control systems. Valid estimates of energy savings require system models that consider capacity and limitations of the AHU, but in existing systems, scarce information hinders such modeling efforts. This lack of information complicates AHU modeling and the assessment of alternative control strategies.
This paper demonstrates an approach that leverages time-series data from a newly constructed Danish AHU, equipped with multiple sensors for temperature, flow, and pressure, to construct a grey-box model of the unit, including component properties.
The estimated parameters for the components are validated against data sheet information, and shows that the estimation procedure is accurate for parameter estimation. To analyze the energy-efficiency of the cooling coil, the model is used to estimate the latent cooling in the cooling coil, as Danish conditions rarely require dehumidification of supply air.
Institutionelle und patient*innenbezogene Einflussfaktoren auf die
Häufigkeit von Fixiermaßnahmen auf einer allgemeinpsychiatrischen
Akutstation
Authors: Paetzold Miriam , Kuhr Kathrin , Lehnhardt Fritz-Georg 
Published: August 2024

Zusammenfassung
Ziel Valide Kenntnisse über eine Risikostratifizierung sind essenziell für
die Entwicklung präventiver Ansätze zur Reduktion von Zwangsmaßnahmen.
Methodik In dieser retrospektiven, monozentrischen Untersuchung wurden
alle 248 Fixiermaßnahmen an 79 Patient*innen einer universitären
Abteilungspsychiatrie im Jahr 2015 untersucht. Acht institutionelle und sieben
patient*innenbezogene Einflussfaktoren wurden statistisch mittels logistischer
Regressionsanalyse und „matched pairs“ berechnet.
Ergebnisse Eine statistisch signifikant erhöhte Fixierwahrscheinlichkeit
zeigte sich bei den institutionellen Einflussfaktoren für eine geringere Anzahl
Pflegekräfte pro Patient*innen, eine höhere Anzahl gesetzlich untergebrachter
Patient*innen, eine geringere Berufserfahrung der Pflegekräfte, im pflegerischen
Spätdienst, sowie bei den patient*innenbezogenen Einflussfaktoren lediglich für
den Zugangsweg über den Rettungsdienst.
Schlussfolgerung Auf Basis der Ergebnisse werden Möglichkeiten präventiver
organisatorischer Maßnahmen abgeleitet und Voraussetzungen für eine prospektive
Evaluation der komplexen, insbesondere patient*innenbezogenen Einflussfaktoren
auf Zwangsmaßnahmen diskutiert.
Predicting ERCP procedure time – the SWedish Estimation of ERCP Time (SWEET) tool
Authors: Waldthaler Alexander , Warnqvist Anna , Waldthaler Josefine , Vujasinovic Miroslav , Ghorbani Poya , von Seth Erik , Arnelo Urban , Lohr Mathias , Bergquist Annika 
Published: August 2024

Abstract
Background: The duration of an endoscopic retrograde cholangiopancreatography (ERCP) is influenced by a multitude of factors. The aim of this study was to describe the factors influencing ERCP time and to create a tool for preintervention estimation of ERCP time.
Methods: Data from 74 248 ERCPs performed from 2010 to 2019 were extracted from the Swedish National Quality Registry (GallRiks) to identify variables predictive for ERCP time using linear regression analyses and root mean squared error (RMSE) as a loss function. Ten variables were combined to create an estimation tool for ERCP duration. The tool was externally validated using 9472 ERCPs from 2020 to 2021.
Results: Mean (SD) ERCP time was 36.8 (25.3) minutes. Indications with the strongest influence on ERCP time were primary sclerosing cholangitis and chronic pancreatitis. Hilar and intrahepatic biliary strictures and interventions on the pancreatic duct were the anatomic features that most strongly affected ERCP time. The procedure steps with most influence were intraductal endoscopy, lithotripsy, dilation, and papillectomy. Based on these results, we built and validated the Swedish Estimation of ERCP Time (SWEET) tool, which is based on a 10-factor scoring system (e.g. 5 minutes for bile duct cannulation and 15 minutes for pancreatic duct cannulation) and predicted ERCP time with an average difference between actual and predicted duration of 17.5 minutes during external validation.
Conclusions: Based on new insights into the factors affecting ERCP time, we created the SWEET tool, the first specific tool for preintervention estimation of ERCP time, which is easy-to-apply in everyday clinical practice, to guide efficient ERCP scheduling.
Nickel-Catalyzed Radical Hydroalkylative Dearomatization of Indoles with Alkyl Bromides
Authors: Cheng Yuan-Zheng , You Shu-Li , Dai Hao-Tian , Huang Xu-Lun 
Published: August 2024

AbstractDearomatization of indole derivatives offers a straightforward approach to accessing the indoline framework. However, highly efficient dearomatization of indoles bearing electron-deficient groups remains underdeveloped. Herein, a nickel-catalyzed intermolecular hydroalkylative dearomatization reaction of indoles with simple alkyl bromides through a single-electron-transfer process is reported. A wide variety of indole derivatives bearing various functional groups were compatible with this protocol and reacted with primary, secondary, or tertiary alkyl bromides to afford a series of indolines in good yields (up to 82%) and with excellent diastereoselectivity (up to >20:1). Notably, a nickel-mediated hydrogen-atom-transfer process was observed when terminal alkyl bromides were employed as the radical precursors, which resulted in branched products.
Iron(III) Triflate and γ-Cyclodextrin-Catalyzed Hydroarylation of Alkenes with 1-Naphthols and 2-Naphthols
Authors: Hu Meng-Xue , Chen Peng , Jiang Yi-Jun , Miao Le-Wei , Shi Jianghuan 
Published: August 2024

AbstractA Fe(OTf)3 and γ-cyclodextrin-catalyzed hydroarylation of alkenes with 1-naphthols or 2-naphthols is demonstrated. This efficient and general method delivers a wide range of benzylic naphthols from readily available starting materials with high chemo- and regioselectivity in up to 99% yield, with no need for a strong base or additive.
Serendipity as a Driving Force in the Synthesis of Isatins Substituted with Electron-Donating Groups
Authors: Ryabukhin Serhiy V. , Bondarenko Semen S. , Fedorchenko Anatolii M. , Druzhenko Tetiana V. , Melnykov Kostiantyn P. , Volovenko Yulian M. , Volochnyuk Dmytro M. 
Published: August 2024

AbstractAn efficient synthetic procedure for the synthesis of isatins was found after careful analysis of the serendipitous results of the unexpected products obtained by aromatic nucleophilic substitution when it was attempted to introduce 6-fluoroisatins to the classic Pfitzinger reaction. Attentive analysis of these results led to elaborating a methodology for synthesizing electron-enriched isatins, including those with hydroxy-, alkoxy-, alkylthio-, and dialkylamino-substituted aromatic rings. Limitations of the method were established. The reaction conditions were optimized according to the understanding of water’s role. Finally, the classic Pfitzinger reaction procedure was modified to yield the expected 2-substituted 7-fluoroquinoline-4-carboxylic acids.