bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between the tumor immune microenvironments and clinical outcome in low‐grade, early‐stage endometrial cancer patients
Authors: López‐Janeiro Álvaro , Villalba‐Esparza María , Brizzi María Emilia , Jiménez‐Sánchez Daniel , Ruz‐Caracuel Ignacio , Kadioglu Ece , Masetto Ivan , Goubert Virginie , Garcia‐Ros David , Melero Ignacio , Peláez‐García Alberto , Hardisson David , de Andrea Carlos E 
Published: September 2022

AbstractEndometrial tumors show substantial heterogeneity in their immune microenvironment. This heterogeneity could be used to improve the accuracy of current outcome prediction tools. We assessed the immune microenvironment of 235 patients diagnosed with low‐grade, early‐stage endometrial cancer. Multiplex quantitative immunofluorescence was carried out to measure CD8, CD68, FOXP3, PD‐1, and PD‐L1 markers, as well as cytokeratin (CK), on tissue microarrays. Clustering results revealed five robust immune response patterns, each associated with specific immune populations, cell phenotypes, and cell spatial clustering. Most samples (69%) belonged to the immune‐desert subtype, characterized by low immune cell densities. Tumor‐infiltrating lymphocyte (TIL)‐rich samples (4%) displayed high CD8+ T‐cell infiltration, as well as a high percentage of CD8/PD‐1+ cells. Immune‐exclusion samples (19%) displayed the lowest CD8+ infiltration combined with high PD‐L1 expression levels in CK+ tumor cells. In addition, they demonstrated high tumor cell spatial clustering as well as increased spatial proximity of CD8+/PD‐1+ and CK/PD‐L1+ cells. FOXP3 and macrophage‐rich phenotypes (3% and 4% of total samples) displayed relatively high levels of FOXP3+ regulatory T‐cells and CD68+ macrophages, respectively. These phenotypes correlated with clinical outcomes, with immune‐exclusion tumors showing an association with tumor relapse. When compared with prediction models built using routine pathological variables, models optimized with immune variables showed increased outcome prediction capacity (AUC = 0.89 versus 0.78) and stratification potential. The improved prediction capacity was independent of mismatch repair protein status and adjuvant radiotherapy treatment. Further, immunofluorescence results could be partially recapitulated using single‐marker immunohistochemistry (IHC) performed on whole tissue sections. TIL‐rich tumors demonstrated increased CD8+ T‐cells by IHC, while immune‐exclusion tumors displayed a lack of CD8+ T‐cells and frequent expression of PD‐L1 in tumor cells. Our results demonstrate the capability of the immune microenvironment to improve standard prediction tools in low‐grade, early‐stage endometrial carcinomas. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Inside the Michelangelo effect: The role of art and aesthetic attractiveness on perceived fatigue and hand kinematics in virtual painting
Authors: Iosa Marco , Bini Fabiano , Marinozzi Franco , Antonucci Gabriella , Pascucci Simona , Baghini Giulia , Guarino Valeria , Paolucci Stefano , Morone Giovanni , Tieri Gaetano 
Published: September 2022

AbstractIt has recently been discovered that during a virtual reality task of painting, if the subjects have the illusion of recreating an artistic masterpiece, they improve their performances and perceive less fatigue compared to simply coloring a virtual canvas. This phenomenon has been called the Michelangelo effect. However, it was unclear if this effect was related to the aesthetic experience of beauty or if it was specific to artistic stimuli. To clarify this point, 26 healthy subjects performed the virtual task of erasing a blank sheet on the canvas, revealing an image that could be a painting or a photo, classified as beautiful or not. Beautiful paintings were famous artistic portraits, non‐beautiful paintings were rough reproductions of them. Photos of popular people were matched with paintings according to their similarity for somatic traits, posture, and clothes. Beautiful and non‐beautiful photos were classified according to whether the pictured person was famous or not for their beauty. For each stimulus the objective beauty, subjective beauty, and effort to complete the task perceived by the subject were self‐assessed on a numerical rating scale, recorded and analyzed. Furthermore, the hand kinematic trajectory was instrumentally recorded and its spatiotemporal parameters were computed. Less fatigue was perceived for the paintings than for the photos (p = .020), but not for beautiful versus non‐beautiful stimuli (p = .325). Only in the artistic stimuli, subjective beauty was found to be negatively correlated with perceived fatigue (p = .030) and performed errors (p = .005). The kinematic parameters were found to be affected by the interactions between the gender of the participant and that of the person in the photo. These results supported the idea that the Michelangelo effect was stronger when subjects interacted with artefacts, modulated by the perceived beauty of the artistic stimulus.
Gut microbiome health and dysbiosis: A clinical primer
Authors: Bidell Monique R. , Hobbs Athena L. V. , Lodise Thomas P. 
Published: September 2022

AbstractThe gut microbiome has been referred to as the “forgotten organ.” Although much about the gut microbiome remains incompletely understood, data on its clinical importance is emerging at rapid speed. Many practicing clinicians may be unaware of the essential role that the microbiome plays in both health and disease. This review aims to improve clinical understanding of the gut microbiome by discussing key terminology and foundational concepts. The role of a healthy microbiome in normal host function is described, as well as the consequences of a disrupted microbiome (i.e., dysbiosis). Management strategies to restore the gut microbiome from a disrupted to a healthy state are also briefly discussed. Lastly, we review emerging areas for therapeutic potential and opportunity to bring determinants of microbiome health from the bench to bedside.
Systematic evaluation of plasma signaling cascades by functional proteomics approaches: SARS‐CoV‐2 infection as model
Authors: Juanes‐Velasco Pablo , García‐Vaquero Marina L. , Landeira‐Viñuela Alicia , Lopez‐Campos José Luis , Marín Carmen , Lecrevisse Quentin , Arias‐Hidalgo Carlota , Montalvillo Enrique , Góngora Rafael , Hernández Ángela‐Patricia , Fuentes Manuel 
Published: September 2022

AbstractPurposeAcute phase reactants (APRs) play a critical role in inflammation. The difference in their physiological functions or the different dynamic ranges of these proteins in plasma makes it difficult to detect them simultaneously and to use several of these proteins as a tool in clinical practice.Experimental DesignA novel multiplex assay has been designed and optimized to carry out a high‐throughput and simultaneous screening of APRs, allowing the detection of each of them at the same time and in their corresponding dynamic range.ResultsUsing Sars‐CoV‐2 infection as a model, it has been possible to profile different patterns of acute phase proteins that vary significantly between healthy and infected patients. In addition, severity profiles (acute respiratory distress syndrome and sepsis) have been established.Conclusions and Clinical RelevanceDifferential profiles in acute phase proteins can serve as a diagnostic and prognostic tool, among patient stratification. The design of this new platform for their simultaneous detection paves the way for them to be more extensive use in clinical practice.
PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education
Authors: Varadi Mihaly , Anyango Stephen , Appasamy Sri Devan , Armstrong David , Bage Marcus , Berrisford John , Choudhary Preeti , Bertoni Damian , Deshpande Mandar , Leines Grisell Diaz , Ellaway Joseph , Evans Genevieve , Gaborova Romana , Gupta Deepti , Gutmanas Aleksandras , Harrus Deborah , Kleywegt Gerard J. , Bueno Weslley Morellato , Nadzirin Nurul , Nair Sreenath , Pravda Lukas , Afonso Marcelo Querino Lima , Sehnal David , Tanweer Ahsan , Tolchard James , Abrams Charlotte , Dunlop Roisin , Velankar Sameer 
Published: September 2022

AbstractThe archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe‐KB; pdbekb.org), we provide data, data‐access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.
Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid
Authors: Wu Kuan‐Lin , Moore Joshua A. , Miller Mitchell D. , Chen Yuda , Lee Catherine , Xu Weijun , Peng Zane , Duan Qinghui , Phillips George N. , Uribe Rosa A. , Xiao Han 
Published: September 2022

AbstractGenetic code expansion technology allows for the use of noncanonical amino acids (ncAAs) to create semisynthetic organisms for both biochemical and biomedical applications. However, exogenous feeding of chemically synthesized ncAAs at high concentrations is required to compensate for the inefficient cellular uptake and incorporation of these components into proteins, especially in the case of eukaryotic cells and multicellular organisms. To generate organisms capable of autonomously biosynthesizing an ncAA and incorporating it into proteins, we have engineered a metabolic pathway for the synthesis of O‐methyltyrosine (OMeY). Specifically, we endowed organisms with a marformycins biosynthetic pathway‐derived methyltransferase that efficiently converts tyrosine to OMeY in the presence of the co‐factor S‐adenosylmethionine. The resulting cells can produce and site‐specifically incorporate OMeY into proteins at much higher levels than cells exogenously fed OMeY. To understand the structural basis for the substrate selectivity of the transferase, we solved the X‐ray crystal structures of the ligand‐free and tyrosine‐bound enzymes. Most importantly, we have extended this OMeY biosynthetic system to both mammalian cells and the zebrafish model to enhance the utility of genetic code expansion. The creation of autonomous eukaryotes using a 21st amino acid will make genetic code expansion technology more applicable to multicellular organisms, providing valuable vertebrate models for biological and biomedical research.
Three‐Point Functions of Higher‐Spin Supercurrents in 4D N=1${{\cal N}}=1$ Superconformal Field Theory
Authors: Buchbinder Evgeny I. , Hutomo Jessica , Tartaglino‐Mazzucchelli Gabriele 
Published: September 2022

AbstractWe develop a general formalism to study the three‐point correlation functions of conserved higher‐spin supercurrent multiplets in 4D superconformal theory. All the constraints imposed by superconformal symmetry on the three‐point function are systematically derived for arbitrary , thus reducing the problem mostly to computational and combinatorial. As an illustrative example, we explicitly work out the allowed tensor structures contained in , where is the supercurrent. We find that this three‐point function depends on two independent tensor structures, though the precise form of the correlator depends on whether r is even or odd. The case reproduces the three‐point function of the ordinary supercurrent derived by Osborn. Additionally, we present the most general structure of mixed correlators of the form and , where L is the flavour current multiplet.
Shallow artificial networks with morphokinetic time‐lapse parameters coupled to ART data allow to predict live birth
Authors: Benchaib Mehdi , Labrune Elsa , Giscard d'Estaing Sandrine , Salle Bruno , Lornage Jacqueline 
Published: September 2022

AbstractPurposeThe purpose of this work was to construct shallow neural networks (SNN) using time‐lapse technology (TLT) from morphokinetic parameters coupled to assisted reproductive technology (ART) parameters in order to assist the choice of embryo(s) to be transferred with the highest probability of achieving a live birth (LB).MethodsA retrospective observational single‐center study was performed, 654 cycles were included. Three SNN: multilayers perceptron (MLP), simple recurrent neuronal network (simple RNN) and long short term memory RNN (LSTM‐RNN) were trained with K‐fold cross‐validation to avoid sampling bias. The predictive power of SNNs was measured using performance scores as AUC (area under curve), accuracy, precision, Recall and F1 score.ResultsIn the training data group, MLP and simple RNN provide the best performance scores; however, all AUCs were above 0.8. In the validating data group, all networks were equivalent with no performance scores difference and all AUC values were above 0.8.ConclusionCoupling morphokinetic parameters with ART parameters allows to SNNs to predict the probability of LB, and all SNNs seems to be efficient according to the performance scores. An automatic time recognition system coupled to one of these SNNs could allow a complete automation to choose the blastocyst(s) to be transferred.
Robust tracking control of a robot arm actuated by permanent magnet synchronous motors
Authors: Borisov Oleg , Isidori Alberto , Kakanov Mikhail , Pyrkin Anton 
Published: September 2022

AbstractIn this article, we show the use of the recently developed enhanced extended observer design technique in tracking time‐dependent references by a PMSM‐actuated robot arm. It is proven that this robust control framework guarantees achievement of semiglobal practical stability and makes trajectories of the system arbitrarily close to those that would had been obtained by the non‐robust nominal feedback‐linearizing control if there were no plant uncertainties.
Internet‐of‐things architectures for secure cyber–physical spaces: The VISOR experience report
Authors: De Pascale Daniel , Cascavilla Giuseppe , Sangiovanni Mirella , Tamburri Damian A. , van den Heuvel Willem‐Jan 
Published: September 2022

AbstractInternet of things (IoT) technologies are becoming a more and more widespread part of civilian life in common urban spaces, which are rapidly turning into cyber–physical spaces. Simultaneously, the fear of terrorism and crime in such public spaces is ever‐increasing. Due to the resulting increased demand for security, video‐based IoT surveillance systems have become an important area for research. Considering the large number of devices involved in the illicit recognition task, we conducted a field study in a Dutch Easter music festival in a national interest project called VISOR to select the most appropriate device configuration in terms of performance and results. We iteratively architected solutions for the security of cyber–physical spaces using IoT devices. We tested the performance of multiple federated devices encompassing drones, closed‐circuit television, smart phone cameras, and smart glasses to detect real‐case scenarios of potentially malicious activities such as mosh pits and pick‐pocketing. Our results pave the way to select optimal IoT architecture configurations—that is, a mix of CCTV, drones, smart glasses, and camera phones in our case—to make safer cyber–physical spaces' a reality.
Emergency department care transition barriers: A qualitative study of care partners of older adults with cognitive impairment
Authors: Gettel Cameron J. , Serina Peter T. , Uzamere Ivie , Hernandez‐Bigos Kizzy , Venkatesh Arjun K. , Cohen Andrew B. , Monin Joan K. , Feder Shelli L. , Fried Terri R. , Hwang Ula 
Published: September 2022

AbstractINTRODUCTIONAfter emergency department (ED) discharge, persons living with cognitive impairment (PLWCI) and their care partners are particularly at risk for adverse outcomes. We sought to identify the barriers experienced by care partners of PLWCI during ED discharge care transitions.METHODSWe conducted a qualitative study of 25 care partners of PLWCI discharged from four EDs. We used the validated 4AT and care partner‐completed AD8 screening tools, respectively, to exclude care partners of older adults with concern for delirium and include care partners of older adults with cognitive impairment. We conducted recorded, semi‐structured interviews using a standardized guide, and two team members coded and analyzed all professional transcriptions to identify emerging themes and representative quotations.RESULTSCare partners’ mean age was 56.7 years, 80% were female, and 24% identified as African American. We identified four major barriers regarding ED discharge care transitions among care partners of PLWCI: (1) unique care considerations while in the ED setting impact the perceived success of the care transition, (2) poor communication and lack of care partner engagement was a commonplace during the ED discharge process, (3) care partners experienced challenges and additional responsibilities when aiding during acute illness and recovery phases, and (4) navigating the health care system after an ED encounter was perceived as difficult by care partners.DISCUSSIONOur findings demonstrate critical barriers faced during ED discharge care transitions among care partners of PLWCI. Findings from this work may inform the development of novel care partner‐reported outcome measures as well as ED discharge care transition interventions targeting care partners.
Development of a vadose zone advanced monitoring system: Tools to assess groundwater vulnerability
Authors: Linneman Dorothy C. , Strickland Christopher E. , Appriou Delphine , Rockhold Mark L. , Thomle Jonathan N. , Szecsody James E. , Martin Paul F. , Vermeul Vince R. , Mackley Rob D. , Freedman Vicky L. 
Published: September 2022

AbstractPerforming repeat pore‐fluid sampling over long time‐scales can provide valuable information on unsaturated zone contaminants and their potential flux to ground water. This information can be used to manage groundwater remedies and identify contaminants that need to be sequestered in the vadose zone to minimize flux to ground water. Pore‐water samples are commonly used to obtain contaminant concentrations within the vadose zone, but existing methods are limited as they only provide a single sample at one location and time. The vadose zone advanced monitoring system (VZAMS) has been designed to integrate multiple technologies into a single down‐borehole system that allows for sampling of pore fluids (liquid and gas) to provide information about contamination and hydraulic conditions at multiple depths (∼0.3‐m intervals) within a cased borehole. Testing has been completed at the laboratory scale to verify the sampling elements of VZAMS, including geochemical testing for representative contaminants known to exist at the Hanford Site, located in southeastern Washington State. Physical tests focused on the ability of the sampler to draw fluid under unsaturated conditions. Initial geochemical testing showed that the stainless steel material used with the porous cuff may affect the sampled concentrations of redox‐sensitive contaminants under very dry conditions. Additional laboratory testing demonstrated that the VZAMS components are able to collect representative samples for substances of interest under expected field conditions. In this paper, the design and functionality of a novel instrument are demonstrated in support of subsequent testing in the field.
Evolution of precision oncology‐guided treatment paradigms
Authors: DasGupta Ramanuj , Yap Aixin , Yaqing Elena Yong , Chia Shumei 
Published: September 2022

AbstractCancer treatment is gradually evolving from the classical use of nonspecific cytotoxic drugs targeting generic mechanisms of cell growth and proliferation. Instead, new “patient‐specific treatment paradigms” that are based on an individual patient's tumor‐specific molecular features are emerging, and these include “druggable” genomic alterations such as oncogenic driver mutations, downstream activities of cancer‐signaling pathways, and the expression of specific genes involved in tumorigenesis and cancer progression. This evolving landscape of making evidence‐based treatment decisions forms the foundation of precision oncology, which aims to deliver “the right drug, to the right patient and at the right time”. The long‐term vision for this approach is to maximize the treatment efficacy while minimizing exposure to ineffective therapy and reducing co‐morbidity‐related side effects. Successful clinical translation and implementation of this vision have the potential to revolutionize treatment paradigms from predominantly reactive, to more evidence‐based, proactive and predictive care. In this article, we review the past and current approaches in precision oncology, and describe their remarkable power and limitations. We also speculate on the evolution of newly emerging methodologies of the future that can be used to address some of the key challenges associated with the existing paradigms.This article is categorized under:
Cancer > Genetics/Genomics/Epigenetics
Cancer > Molecular and Cellular Physiology
Cancer > Computational Models
β‐Diketiminate Aluminum Dihydride is a Valuable Precursor for the Preparation of Acyclic and Cyclic Systems
Authors: Huo Shuai‐Cong , Li Yao , Ji Peng‐Fei , Zhang De‐Xiang , Zhang Zhi‐Jiao , Yang Ying , Roesky Herbert W. 
Published: September 2022

AbstractTreatments of β‐diketiminate aluminum dihydride LAlH2 (L=HC[C(Me)N(Ar)]2, Ar=2,6‐iPr2C6H3) with (2‐chlorophenyl)methanol, 2,3‐dimethylbutane‐2,3‐diol, 2,2‐dimethylpropane‐1,3‐diol, 2,2‐bis(bromomethyl)propane‐1,3‐diol, and p‐diphenol resulted in the formation of compounds containing the C−O−Al−O−C linkages, including the acyclic LAl[(μ‐O)CH2(o‐Cl−C6H4)2]2 (1), the five‐membered ring LAl[(μ‐O)CMe2]2 (2), the six‐membered ring LAl[(μ‐O)CH2]2CMe2 (3) and LAl[(μ‐O)CH2]2C(CH2Br)2 (4), and the macrocyclic [LAl(μ‐O)2(p‐C6H4)]4 (5), respectively. These practices prove that β‐diketiminate aluminum dihydride is a valuable precursor for the preparation of acyclic and cyclic systems. 1–5 were characterized by melting point, 1H and 13C NMR, FT‐IR, and single‐crystal X‐ray diffraction studies.