bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding contextual influences on auditory perception from primary auditory cortex
Authors: Englitz B. , Akram S. , Elhilali M. , Shamma S. 
Published: December 2023

AbstractPerception can be highly dependent on stimulus context, but whether and how sensory areas encode the context remains uncertain. We used an ambiguous auditory stimulus - a tritone pair - to investigate the neural activity associated with a preceding contextual stimulus that strongly influenced the tritone pair’s perception: either as an ascending or a descending step in pitch.We recorded single-unit responses from a population of auditory cortical cells in awake ferrets listening to the tritone pairs preceded by the contextual stimulus. We find that the responses adapt locally to the contextual stimulus, consistent with human MEG recordings from the auditory cortex under the same conditions. Decoding the population responses demonstrates that cells responding to pitch-class-changes are able to predict well the context-sensitive percept of the tritone pairs. Conversely, decoding the individual pitch-class representations and taking their distance in the circular Shepard tone space predicts theoppositeof the percept. The various percepts can be readily captured and explained by a neural model of cortical activity based on populations of adapting, pitch-class and pitch-class-direction cells, aligned with the neurophysiological responses.Together, these decoding and model results suggest that contextual influences on perception may well be already encoded at the level of the primary sensory cortices, reflecting basic neural response properties commonly found in these areas.
Structure and dynamics of secondary and mature rainforests: insights from South Asian long-term monitoring plots
Authors: Murali Akhil , Kasinathan Srinivasan , Bhat Kshama , Ratnam Jayashree , Sankaran Mahesh , Mudappa Divya , Raman T. R. Shankar , Osuri Anand M. 
Published: December 2023

AbstractWe assessed tree community and carbon dynamics over 5 years in two 1-ha long-term ecosystem monitoring plots, one each in mature tropical rainforests (MR) and 10-year post-agroforestry secondary rainforests (SR) in India’s Western Ghats mountains. Both plots were established in 2017 and monitored annually six times. We expected (1) higher tree diversity, distinct species composition, and greater carbon stock in MR; (2) higher carbon sequestration rates in SR; and (3) carbon dynamics shaped by growth and mortality in SR and MR, respectively. The SR plot had fewer species (67 vs. 84), stored substantially less carbon (76 vs. 193 Mg), and comprised a distinct community with fewer late-successional species than MR. SR gained 5.8 Mg carbon, due to tree growth exceeding losses from mortality, while in MR mortality exceeded growth and recruitment resulting in a 3.3 Mg carbon decline over five years. While MR had higher tree diversity, carbon stocks and relatively intact composition, the high rates of biodiversity and carbon accrual in SR highlight the conservation and climate significance of post-agroforestry secondary forests. Moderate carbon losses noted here in MR, as in other mature South Asian tropical forests, is a cause for concern under ongoing climate change.
Comprehensive characterization of the integrin family across 32 cancer types
Authors: Zou Cheng , Zhu Jinwei , Xiong Jiangling , Tian Yu , Peng Yousong , Cheung Edwin , Zhang Dingxiao 
Published: December 2023

ABSTRACTIntegrin genes widely involve in tumorigenesis. Yet, a comprehensive characterization of integrin family and their interactome on the pan-cancer level is lacking. Here, we systematically dissect integrin family in nearly 10000 tumors across 32 cancer types. Globally, integrins represent a frequently altered and misexpressed pathway, with alteration and dysregulation overall being protumorigenic. Expression dysregulation, better than mutational landscape, of integrin family successfully identifies a subgroup of aggressive tumors demonstrating a high level of proliferation and stemness. We identify that several molecular mechanisms jointly regulate integrin expression in a context-dependent manner. For potential clinical usage, we construct a weighted score, integrinScore, to measure integrin signaling patterns in individual tumors. Remarkably, integrinScore consistently correlates with predefined molecular subtypes in multiple cancers, with integrinScore high tumors being more aggressive. Importantly, integrinScore is cancer-dependently and closely associated with proliferation, stemness, tumor microenvironment, metastasis, and immune signatures. IntegrinScore also predicts patient’s response to immunotherapy. By mining drug databases, we unravel an array of compounds that may serve as integrin signaling modulators. Finally, we build a user-friendly database to facilitate researchers to explore integrin-related knowledge. Collectively, we provide a comprehensive characterization of integrins across cancers, which offers gene- and cancer-specific rationales for developing integrin-targeted therapy.
MINI-EX version 2: cell-type-specific gene regulatory network inference using an integrative single-cell transcriptomics approach
Authors: Staut Jasper , Manosalva Pérez Nicolás , Depuydt Thomas , Vandepoele Klaas , Lukicheva Svitlana 
Published: December 2023

AbstractUnderstanding and predicting cell-type-specific gene regulatory networks (GRNs) is essential for unraveling the complex interactions between transcription factors (TFs) that modulate the expression of target genes and control diverse biological processes in multicellular organisms. MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data) is an integrative tool tailored for identifying cell-type-specific GRNs in plants. Leveraging single-cell transcriptomics data, MINI-EX constructs expression-based networks and integrates TF motif information to produce GRNs with increased accuracy. Furthermore, it assigns regulatory modules to distinct cell types and prioritizes candidate regulators by employing a strategy that encompasses network centrality measures, functional annotations, and expression specificity. Taken together, MINI-EX offers a powerful approach to identify cell-type-specific transcriptional cascades and enhance our understanding of TF functions in plant biology. Here, we discuss recent advancements in the tool’s latest version and explain how single-cell GRNs can be identified for non-model species lacking TF motif information. Additionally, we provide a comprehensive guide to use MINI-EX, covering the entire pipeline from preparing input files starting from a single-cell experiment, over configuring parameters, to interpreting output data.
Mutual interplay of actin meshwork and stress fibers in cellular adaptive response: Insights from percolation dynamics
Authors: Ueda Yuika , Matsunaga Daiki , Deguchi Shinji 
Published: December 2023

AbstractCells dynamically remodel their internal structures by modulating the arrangement of actin filaments (AFs). In this process, individual AFs exhibit stochastic behavior without knowing macroscopic higher-order structures they are meant to create or disintegrate. Cellular adaptation to environmental cues is accompanied with this type of self-assembly and disassembly, but the mechanism allowing for the stochastic process-driven remodeling of the cell structure remains incompletely understood. Here we employ percolation theory to explore how AFs interacting only with neighboring ones without recognizing the overall configuration can nonetheless construct stress fibers (SFs) at particular locations. To achieve this, we determine the binding and unbinding probabilities of AFs undergoing cellular tensional homeostasis, a fundamental property maintaining intracellular tension. We showed that the duration required for the assembly of SFs is shortened by the amount of preexisting actin meshwork, while the disassembly occurs independently of the presence of actin meshwork. This asymmetry between the assembly and disassembly, consistently observed in actual cells, is explained by considering the nature of intracellular tension transmission. Thus, our percolation analysis provides insights into the role of coexisting higher-order actin structures in their flexible responses during cellular adaptation.
Interaction of the Immune System TIM-3 Protein with a Model Cellular Membrane Containing Phosphatidyl-Serine Lipids
Authors: Delova Anastasiia , Pasc Andreea , Monari Antonio 
Published: December 2023

AbstractT cell transmembrane, Immunoglobulin, and Mucin (TIM) are important immune system proteins which are especially present in T-cells and regulated the immune system by sensing cell engulfment and apoptotic processes. Their role is exerted by the capacity to detect the presence of phosphatidyl-serine lipid polar head in the outer leaflet of cellular membranes (correlated with apoptosis). In this contribution by using equilibrium and enhanced sampling molecular dynamics simulation we unravel the molecular bases and the thermodynamics of TIM, and in particular TIM-3, interaction with phosphatidyl serine in a lipid bilayer. Since TIM-3 deregulation is an important factor of pro-oncogenic tumor micro-environment understanding its functioning at a molecular level may pave the way to the development of original immunotherapeutic approaches.
Quo vadis, esthetic dentistry? Part II: Composite resin overtreatment and social media appeal
Authors: Hirata Ronaldo , Hilgert Leandro Augusto , Sampaio Camila S. , de Andrade Oswaldo Scopin , Melo Ginger , Ritter André V. 
Published: December 2023

AbstractObjectivesThis article presents case reports highlighting over‐treatments with resin composites, often misconceived as minimally invasive procedures.Clinical ConsiderationsTooth‐colored restorative materials, such as ceramics and composites, have found widespread application to correct problems related to tooth color, shape, and alignment. When composite resin is used, these procedures can be done in a very conservative, cost‐effective, and timely fashion. However, it is noteworthy that contemporary dental esthetic expectations are based on standards propagated by social media and other marketing and communications platforms. The abuse of and addiction to social media impacts can lead to unrealistic esthetic expectations and standards for both patients and dentists.ConclusionsAfter a critical discussion on ceramic veneers published in part I of this 2‐part series, this article directs attention towards what has become a trendy fashion, i.e., the use of direct composite resins as “non‐prep” veneers in clinical situations that arguably required no restorative intervention at all. We further explore how social media influences the decision‐making processes of both professionals and patients.
RHD‐negative red cells may be avoided for patients with ambiguous serologic typing for the RHD antigen
Authors: Juhl David , Luckner Kathrin , Brockmann Christian , Musiolik Ingrid , Bunge‐Philipowski Tina , Görg Siegfried , Ziemann Malte 
Published: December 2023

AbstractBackground and ObjectivesSerologic typing with monoclonal anti‐D is mandatory for RHD antigen determination before transfusion, but due to aberrant (weak or partial) variants of RHD, results may be ambiguous and molecular RHD‐typing is required. Before that, RHD‐negative (RHD –) red blood cells concentrates (RBCs) shall be transfused to avoid anti‐D formation, which probably leads to wastage of RHD ‐ RBCs.Study Design and MethodsAll patients with ambiguous results in serologic RHD‐typing and molecular RHD‐typing were assessed retrospectively. The proportions of patients at risk for anti‐D formation and the proportion of RHD ‐ RBCs transfused unnecessarily were evaluated for the following transfusion strategies: (1) RHD‐positive (RHD + )RBCs for all patients, (2) RHD + RBCs for patients with at least 2+ reaction with anti‐D, (3) RHD + RBCs for patients with C and/or E in their RHCE‐phenotype, (4) RHD + RBCs for patients with C and/or E and at least 2+ reaction, and (5) RHD ‐ RBCs for all patients.ResultsA total of 112 patients were included. Most had weak D type 1–3 and a minority had other, rare RHD variants. The risk of anti‐D formation was 4.5%, 2.9%, 1.8%, 1.0%, and 0% for strategies 1–5, respectively. The proportion of RHD ‐ RBCs transfused unnecessarily was 0%, 49.5%, 0.9%, 50.5%, and 95.5%.ConclusionTransfusing patients with a C and/or E in their RHCE‐phenotype with RHD + RBCs resulted in a very low risk of immunization while avoiding wastage of RHD ‐ RBCs. Therefore, this strategy should be used for some patients with ambiguous results in serologic RHD‐typing and pending results of molecular RHD‐typing.
Exspatiantur: Warum scheitert der ovidische Phaethon am Sternbild des Skorpions?
Authors: Hübner Wolfgang 
Published: December 2023

Abstract
The ride of the Ovidian Phaethon hitherto has not been explained sufficiently, in particular by J. Loos in Mnemosyne 2008 and 2012. Instead for the different motion of the sun one has to regard the particularities and position of the zodiacal signs, especially that of the Scorpion.
Vividness and Spatial Scenes
Authors: Winter Kathrin 
Published: December 2023

Abstract
Heraclitus’ fragments employ a powerful literary technique which is used to convey information without giving it directly: the texts appeal to sensation and bodily experience to evoke spatial scenes and so become intuitively comprehensible and display a surprisingly vivid quality. The means to bring this effect about can be analysed and explained with approaches from cognitive studies. This article presents three criteria to analyse vividness in spatial scenes and applies them to four fragments of Heraclitus in order to show how the text makes use of perceptual structures and exploits them to convey information without the recipient noticing it.
The Three Parts of Philosophy
Authors: Salerno Lorenzo 
Published: December 2023

Abstract
In Pl. 1.3, Apuleius provides an account of the genesis of the tripartition of philosophy, recalling its incorrect (but by then traditional) attribution to Plato. In doing so, Apuleius states that Plato showed that the three parts of philosophy do not fight each other, but on the contrary support each other with mutual aid. While the meaning of the passage is clear, the text has been long debated. The aim of this paper is to show that none of the texts printed so far is satisfactory, and to propose a new solution.
Unlocking the Riddles of Imperial Greek Melodies: The ‘Lydian’ Metamorphosis of the Classical Harmonic System
Authors: Lynch Tosca A.C. 
Published: December 2023

Abstract
Building upon Lynch 2022a and 2022b, this article offers the first account of the historical evolution of the Greek harmonic system and notation keys (tónoi) that bridges the gap between Classical and Imperial music. This new solution allows us to reconstruct, for the first time, a continuous, if evolving, tradition that stretches from Euripides’ Orestes to late antiquity, reconciling key theoretical insights provided by Ptolemy, Porphyry and others with documentary evidence that illustrates the structure of the Imperial harmonic system and its use in the Imperial musical documents (dDAGM). This approach also enables us to trace the gradual expansion of the Greek notation system from an initial set of symbols (–) to the full array recorded by Aristides and Alypius, mapping its development onto key historical milestones including the revolutionary innovations of the New Musicians and Damon of Oa’s inclusion of the Lydian mode into the Greek modulation system.
Research on textile-vamp punching based on punching point gradient phase and edge significance
Authors: Meng Zhuo , Zhang Hao , Chen Yujie , Sun Yize 
Published: December 2023

A visual technology to identify the punching points of a textile vamp to replace manual punching by machinery is proposed in this paper. This could solve several problems relating to the manual punching of textile vamp, such as high manual-punching strength, low efficiency, and poor punching accuracy. Unsharp mask guided filtering was adopted, to enhance the details of the textile-vamp punching points, considering the edge point position, gradient phase, and edge significance of the punching points, in building the template matching similarity measure function. A partial Hausdorff distance was proposed to sum and average values, to improve the degree of matching of punching point shape defects. A local search area of punching points to improve identification efficiency and punching evaluation criteria was established to evaluate the punching effects. The results showed that the matching similarity of the complete boundary was above 0.9. Positioning accuracy was 0.43 mm in the x-direction, 0.38 mm in the y-direction, and repeat positioning accuracy was 0.09 mm. The center average relative error was 5.03% and the relative error of the radius was 7.81%. Identification timeliness increased with the rotation angle, template size, and the number of punching points. When the rotation angle was between –180° and 180° and the number of punching points was 24, identification timeliness was 830 ms, which met productivity requirements. Textile-vamp punching grades A to D qualified, however, grades E and F were unqualified for punching.
Assessing the suitability of the Carer Support Needs Assessment Tool (CSNAT-Paediatric) for use with parents of children with a life-limiting condition: A qualitative secondary analysis
Authors: Fisher Victoria , Atkin Karl , Ewing Gail , Grande Gunn , Fraser Lorna K 
Published: December 2023

Background: The demands of caring for a child with a life-limiting condition can have a profound impact on parents’ health and wellbeing. Currently, there is no standard procedure for identifying and addressing the support needs of these parents. Aim: To assess the suitability of the Carer Support Needs Assessment Tool (CSNAT (Paediatric)) for use with parents of children with a life-limiting condition. Design: Secondary qualitative content analysis of two qualitative datasets exploring the health, wellbeing and experiences of support of mothers and fathers of children with a life-limiting condition. Setting: A total of 30 mothers and 12 fathers were recruited via four UK children’s hospices and social media. Results: Parental experiences of support mapped onto the existing domains of the CSNAT (Paediatric). One aspect of their experience, surrounding their child’s educational needs, went beyond the existing domains of the CSNAT. An adapted version of the tool CSNAT (Paediatric) should include this domain. Conclusion: The CSNAT (Paediatric) is a relevant tool for the assessment of parental support needs. Further research should assess the acceptability and feasibility of implementation of the broader intervention: CSNAT-I (Paediatric).
The use of CytoSorb in acute oral mercuric chloride poisoning at a potentially lethal dose
Authors: Krakowiak Anna , Janasik Beata , Sadowski Łukasz , Szwabe Katarzyna , Wiśniewski Tomasz , Anna Rak Małgorzata , Machała Waldemar 
Published: December 2023

Introduction: The study aims to present a case of acute mercuric chloride poisoning treated successfully with continuous renal replacement therapy using the CytoSorb filter. Case description: A 21-year-old female patient after a suicide attempt by intentional ingestion of mercuric chloride, was admitted to the hospital with features of multiple organ damage for specific treatment. The performed laboratory tests confirmed high levels of mercury in the blood (1051 μg/L) and urine (22,960 μg/L). Due to acute renal failure, continuous renal replacement therapy (CRRT) CVVHD Ci-Ca was initiated; the procedure was then converted to CVVHDF Ci-Ca with ultrafiltration to optimise therapy, and CytoSorb was added to the artificial kidney system on day 3. Specific antidote therapy (DMPS) was administered concurrently. The ongoing treatment resulted in a reduction in subjective complaints, a decrease in blood mercury levels to 580 μg/L, and an improvement in parenchymal organ function. Conclusion: In the event of poisoning with inorganic mercury compounds (mercuric chloride), continuous renal replacement therapy using the CytoSorb filter as an extracorporeal blood purification method may be considered.
Has the COVID-19 pandemic affected ureteral stone management in pregnant women? A retrospective single-center study
Authors: Haghpanah Abdolreza , Kamran Hooman , Irani Dariush , Kohansal Erfan , Rahmanian Mahdi , Defidio Lorenzo , Dehghani Anahita , Jahanabadi Zahra , Askarpour Mohammad Reza 
Published: December 2023

Introduction: This study aimed to evaluate the effect of coronavirus disease (COVID-19) on the patients’ referral in the pregnant population and also investigate each treatment approach’s advantages and disadvantages for acute renal colic in pregnancy. Methods: In this retrospective study, we included all pregnant women with ureteral stones referred to a referral center between January 2019 and March 2021. Results: Among 53 pregnant women, 18 (33.9%) were on conservative therapy, which passed the stone without any complications. Double J stent or nephrostomy tube insertion was done for 24 patients (45.2%). Seventeen of these patients (70.8%) presented post-surgical complications, including hematuria (29.2%), pyelonephritis (20.8%), and lower urinary tract symptoms (20.8%). Transurethral lithotripsy (TUL) was done in 11 patients (20.7%). Only one of these patients developed hematuria following TUL. Thus, in our population study, double J stent or nephrostomy insertion was associated with a higher chance of postoperative complications than TUL ( p-value = 0.001). Thirty-six patients were referred within 13 months before the entry of COVID-19, while 17 were referred during a similar approximate duration after the COVID-19 entry into the country. Only the initial presentation had a significant difference between these two periods ( p-value = 0.034). Conclusions: When conservative treatment fails, we recommend TUL as the second-line treatment over temporary procedures, such as double J stent or nephrostomy insertion. Of note, in a group of patients with an emergent clinical setting, including active infection, deteriorating renal function, signs of preterm labor, solitary kidney, etc., double J or nephrostomy tube insertion remains the preferred management method for its fast resolution of obstruction and infection. Besides, a decrease in visits with an increase in complicated cases after COVID-19 was observed, maybe due to a delay in referring.