bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a Standardization of Learning Curve Assessment in Minimally Invasive Liver Surgery
Authors: Kuemmerli Christoph , Toti Johannes M.A. , Haak Fabian , Billeter Adrian T. , Nickel Felix , Guidetti Cristiano , Santibanes Martin , Vigano Luca , Lavanchy Joël L. , Kollmar Otto , Seehofer Daniel , Abu Hilal Mohammed , Di Benedetto Fabrizio , Clavien Pierre-Alain , Dutkowski Philipp , Müller Beat P. , Müller Philip C. 
Published: June 2024

Objective:
The aim was to analyze the learning curves of minimal invasive liver surgery (MILS) and propose standardized reporting.

Background:
MILS offers benefits compared with open resections. For a safe introduction along the learning curve, formal training is recommended. However, definitions of learning curves and methods to assess it lack standardization.

Methods:
A systematic review of PubMed, Web of Science, and CENTRAL databases identified studies on learning curves in MILS. The primary outcome was the number needed to overcome the learning curve. Secondary outcomes included endpoints defining learning curves and characterization of different learning phases (competency, proficiency, and mastery).

Results:
Sixty articles with 12,241 patients and 102 learning curve analyses were included. The laparoscopic and robotic approach was evaluated in 71 and 18 analyses and both approaches combined in 13 analyses. Sixty-one analyses (60%) based the learning curve on statistical calculations. The most often used parameters to define learning curves were operative time (n=64), blood loss (n=54), conversion (n=42), and postoperative complications (n=38). Overall competency, proficiency, and mastery were reached after 34 [interquartile range (IQR) 19–56], 50 (IQR 24–74), and 58 (IQR 24–100) procedures, respectively. Intraoperative parameters improved earlier (operative time: competency to proficiency to mastery: −13%, 2%; blood loss: competency to proficiency to mastery: –33%, 0%; conversion rate (competency to proficiency to mastery; −21%, −29%), whereas postoperative complications improved later (competency to proficiency to mastery: −25%, −41%).

Conclusions:
This review summarizes the highest evidence on learning curves in MILS taking into account different definitions and confounding factors. A standardized 3-phase reporting of learning phases (competency, proficiency, and mastery) is proposed and should be followed.
Association of Daily Step Count and Postoperative Complication among All of Us Research Participants
Authors: Gehl Carson J , Verhagen Nathaniel B , Shaik Tahseen J , Nimmer Kaitlyn , Yang Xin , Xing Yun , Taylor Bradley W , Nataliansyah Mochamad M , Kerns Sarah L , Kothari Anai N 
Published: June 2024

BACKGROUND:
The association between preoperative wearable device step counts and surgical outcomes has not been examined using commercial devices linked to electronic health records (EHRs). This study measured the association between daily preoperative step counts and postoperative complications.

STUDY DESIGN:
Data were obtained using the All of Us (AOU) Research program, a nationwide initiative to collect EHR and health-related data from the population. Patients who underwent a surgical procedure included in the NSQIP-targeted procedures dataset were included. Patients who did not have available physical activity FitBit data were excluded. Primary outcome was the development of a postoperative complication. All analyses were performed in the AOU researcher workbench.

RESULTS:
Of 27,150 patients who underwent a surgical procedure, 475 participants with preoperative wearable data were included: 74.7% were female and 85.2% were White. The average age was 57.2 years. The overall rate of postoperative complications was 12.6%. Patients averaging less than 7,500 daily steps were at increased odds for developing a postoperative complication (odds ratio 1.83, 95% CI 1.01 to 3.31). After adjustment for age, sex, race, comorbid disease, BMI, and relative procedure risk, patients with a baseline average steps per day less than 7,500 were at increased odds for postoperative complication (adjusted odds ratio 2.06, 95% CI 1.05 to 4.06).

CONCLUSIONS:
This study found an increase in overall postoperative complication rate in patients recording lower average preoperative step counts. Patients with a baseline of less than 7,500 steps per day had increased odds of postoperative complications in this cohort. These data support the use of wearable devices for surgical risk stratification and suggest step count may measure preoperative fitness.
Multi-talker speech comprehension at different temporal scales in listeners with normal and impaired hearing
Authors: Li Jixing , Wang Qixuan , Zhou Qian , Yang Lu , Shen Yutong , Huang Shujian , Wang Shaonan , Pylkkänen Liina , Huang Zhiwu 
Published: June 2024

AbstractComprehending speech requires deciphering a range of linguistic representations, from phonemes to narratives. Prior research suggests that in single-talker scenarios, the neural encoding of linguistic units follows a hierarchy of increasing temporal receptive windows. Shorter temporal units like phonemes and syllables are encoded by lower-level sensory brain regions, whereas longer units such as sentences and paragraphs are processed by higher-level perceptual and cognitive areas. However, the brain’s representation of these linguistic units under challenging listening conditions, such as a cocktail party situation, remains unclear. In this study, we recorded electroencephalogram (EEG) responses from both normal-hearing and hearing-impaired participants as they listened to individual and dual speakers narrating different parts of a story. The inclusion of hearing-impaired listeners allowed us to examine how hierarchically organized linguistic units in competing speech streams affect comprehension abilities. We leveraged a hierarchical language model to extract linguistic information at multiple levels—phoneme, syllable, word, phrase, and sentence—and aligned these model activations with the EEG data. Our findings showed distinct neural responses to dual-speaker speech between the two groups. Specifically, compared to normal-hearing listeners, hearing-impaired listeners exhibited poorer model fits at the acoustic, phoneme, and syllable levels as well as the sentence levels, but not at the word and phrase levels. These results suggest that hearing-impaired listeners experience disruptions at both shorter and longer temporal scales, while their processing at medium temporal scales remains unaffected.
ClearFinder: a Python GUI for annotating cells in cleared mouse brain
Authors: Pastore Stefan , Hillenbrand Philipp , Molnar Nils , Kovlyagina Irina , Chongtham Monika Chanu , Sys Stanislav , Lutz Beat , Tevosian Margarita , Gerber Susanne 
Published: June 2024

ABSTRACTBackgroundTissue clearing combined with light-sheet microscopy is gaining popularity among neuroscientists interested in unbiased assessment of their samples in 3D volume. However, the analysis of such data remains a challenge. ClearMap and CellFinder are tools for analyzing neuronal activity maps in an intact volume of cleared mouse brains. However, these tools lack a user interface, restricting accessibility primarily to scientists proficient in advanced Python programming. The application presented here aims to bridge this gap and make data analysis accessible to a wider scientific community.ResultsWe developed an easy-to-adopt graphical user interface for cell quantification and group analysis of whole-cleared adult mouse brains. Fundamental statistical analysis, such as PCA and box plots, and additional visualization features allow for quick data evaluation and quality checks. Furthermore, we report significant differences in total cell counts between CellFinder and ClearMap when cross-analyzing the same samples, underscoring the need for optimizing reproducibility within the field.ConclusionsOur easily accessible tool allows more researchers to implement the methodology, troubleshoot arising issues, and develop quality checks, benchmarking, and standardized analysis pipelines for cell detection and region annotation in whole volumes of cleared brains.
Information transmission in a cell monolayer: A numerical study
Authors: Nałęcz-Jawecki Paweł , Szyc Przemysław , Grabowski Frederic , Kochańczyk Marek , Lipniacki Tomasz 
Published: June 2024

AbstractMotivated by the spatiotemporal waves of MAPK/ERK activity, crucial for long-range communication in regenerating tissues, we investigated stochastic homoclinic fronts propagating through channels formed by directly interacting cells. We evaluated the efficiency of long-range communication in these channels by examining the rate of information transmission. Our study identified the stochastic phenomena that reduce this rate: front propagation failure, new front spawning, and variability in the front velocity. We found that a trade-off between the frequencies of propagation failures and new front spawning determines the optimal channel width (which geometrically determines the front length). The optimal frequency of initiating new waves is determined by a trade-off between the input information rate (higher with more frequent initiation) and the fidelity of information transmission (lower with more frequent initiation). Our analysis provides insight into the relative timescales of intra- and intercellular processes necessary for successful wave propagation.Author SummaryIn biological tissues, traveling waves of cellular activity are observed in the process of wound healing when they coordinate cell replication and collective migration. These waves can carry information over long distances. However, random effects on the single-cell level can affect wave propagation and disrupt information flow. In this paper, using a numerical model we classified these stochastic events and quantified the maximum range and frequency of such waves and their capacity to carry information. We discovered that most effective transmission occurs in relatively narrow channels (formed by directly interacting cells), and that the refractory time, in which a cell is resistant to activation by neighboring cells, must be long with respect to the time needed for cell activation. The optimal time intervals between the initiated waves are of order of few refractory times (depending on channel length).
High-resolution quantification of the rhizosphere effect along a soil-to-root gradient shows selection-driven convergence of rhizosphere microbiomes
Authors: Poppeliers Sanne W.M. , Sánchez-Gil Juan José , López José Luis , Dutilh Bas E. , Pieterse Corné M. J. , de Jonge Ronnie 
Published: June 2024

AbstractPlants secrete a complex array of organic compounds, constituting about a third of their photosynthetic products, into the surrounding soil. As a result, concentration gradients are established from the roots into the bulk soil, known as the rhizosphere. Soil microbes benefit from these root exudates for their survival and propagation, and consequently, the composition of the rhizosphere microbial community follows the gradient of available compounds, a phenomenon oftentimes referred to as the rhizosphere effect. However, the fine-grained changes in the microbial community along this soil-root gradient have not been well described. Yet such insights would enable us to underpin the ecological rules underlying root microbial community assembly. Therefore, here we harvested the roots of individualArabidopsis thalianaplants grown in three different natural soils at high-resolution, such that we could interrogate community assembly and predict microbial growth rate across consecutive, fine-grained, rhizosphere ‘compartments’. We found that the strength of the rhizosphere effect depends on root proximity and that microbial communities closer to the roots harbour related microbes. Closer to the roots, microbial community assembly became less random and more driven by selection-based processes. Intriguingly, we observed priority effects, where related microbes that arrive first are more likely to establish, and that microbes might use different ecological growth strategies to colonise the rhizosphere. All effects appeared to be independent from starting conditions as microbial community composition converged on the root despite different soil ‘microbial seed banks’. Together, our results provide a high-resolution view of the microbiome changes across the soil-root gradient.
AML patient blasts exhibit polarization defect upon interaction with bone marrow stromal cells
Authors: Saadallah Khansa , Vianay Benoît , Bonnemay Louise , Pasquer Hélène , Kelly Lois , Culeux Cécile , Marie Raphael , Fodil Sofiane , Chaintreuil Paul , Kerreneur Emeline , Jacquel Arnaud , Raffoux Emmanuel , Nizard Rémy , Blanchoin Laurent , Benajiba Lina , Théry Manuel 
Published: June 2024

AbstractHematopoietic stem and progenitor cells (HSPCs) establish specific interactions with bone marrow stromal cells, leading to their polarization. Given the role of cell polarity in protection against tumorigenesis and the importance of the niche in hematological disorders such as acute myeloid leukemias (AMLs), we investigated the polarization capacities of leukemic blasts from patients. Using engineered micro-niches and centrosome position with respect to the contact site with stromal cells as a proxy for cell polarization, we showed that AML cell lines and primary cells from AML patient blasts were unable to polarize in contact with healthy stromal cells. In return, exposure to AML patient-derived stromal cells compromised the polarization of healthy adult HSPCs and AML blasts from patients. Using live cell imaging in engineered “bone-marrow-on-a-chip”, we further revealed that stromal cells from a leukemic niche increased the migration speed and distance of healthy HSPCs and AML blast as compared to their behavior in contact with healthy stromal cells. The results collectively demonstrated the respective influences of intrinsic AML blast transformation and extrinsic contact with AML stromal cells on the defective polarization of AML blast. They suggested that leukemic progression is associated with cell polarization defects and proposed new methodological approaches to investigate this relationship in AML progression.
Pronouns reactivate conceptual representations in human hippocampal neurons
Authors: Dijksterhuis D. E. , Self M. W. , Possel J. K. , Peters J. C. , van Straaten E.C.W. , Idema S. , Baaijen J. C. , van der Salm S. M. A. , Aarnoutse E.J. , van Klink N. C. E. , van Eijsden P. , Hanslmayr S. , Chelvarajah R. , Roux F. , Kolibius L. D. , Sawlani V. , Rollings D. T. , Dehaene S. , Roelfsema P. R. 
Published: June 2024

AbstractDuring discourse comprehension, every new word adds to an evolving representation of meaning that accumulates over consecutive sentences and constrains the next words. To minimize repetition and utterance length, languages use pronouns, like the word ‘she’, to refer to nouns and phrases that were previously introduced. It has been suggested that language comprehension requires that pronouns activate the same neuronal representations as the nouns themselves. Here, we test this hypothesis by recording from individual neurons in the human hippocampus during a reading task. We found that cells that are selective to a particular noun are later reactivated by pronouns that refer to the cells’ preferred noun. These results imply that concept cells contribute to a rapid and dynamic semantic memory network which is recruited during language comprehension. This study uniquely demonstrates, at the single-cell level, how memory and language are linked.
Adiponectin pathway activation dampens inflammation and enhances alveolar macrophage fungal killing via LC3-associated phagocytosis
Authors: Goli Sri Harshini , Lim Joo-Yeon , Basaran-Akgul Nese , Templeton Steven P. 
Published: June 2024

AbstractAlthough innate immunity is critical for antifungal host defense against the human opportunistic fungal pathogenAspergillus fumigatus, potentially damaging inflammation must be controlled. Adiponectin (APN) is an adipokine produced mainly in adipose tissue that exerts anti-inflammatory effects in adipose-distal tissues such as the lung. We observed 100% mortality and increased fungal burden and inflammation in neutropenic mice with invasive aspergillosis (IA) that lack APN or the APN receptors AdipoR1 or AdipoR2. Alveolar macrophages (AMs), early immune sentinels that detect and respond to lung infection, express both receptors, and APN-/- AMs exhibited an inflammatory/M1 phenotype that was associated with decreased fungal killing. Pharmacological stimulation of AMs with AdipoR agonist AdipoRon partially rescued deficient killing in APN-/- AMs that was dependent on both receptors. Finally, APN-enhanced fungal killing was associated with increased activation of the non-canonical LC3 pathway of autophagy. Thus, our study identifies a novel role for APN in LC3-mediated killing ofA.fumigatus.Author SummaryAspergillus fumigatusis a human fungal pathogen that causes an often-fatal invasive infection of the lung in immune compromised individuals, a population that is increasing. Since current antifungal drugs have limited efficacy, it is important to identify pathways that may be pharmaceutically targeted to complement existing therapies. Adiponectin (APN) is an anti-inflammatory intercellular cytokine messenger produced mainly in adipose tissue that protects against invasive aspergillosis. Alveolar macrophages are early immune sentinel cells in the lung, and we report that AMs from mice lacking APN exhibit an inflammatory phenotype and reduced killing ofA. fumigatusspores that is improved when AMs are treated with a drug (AdipoRon) that simulates APN binding to its receptors AdipoR1 and AdipoR2. Furthermore, APN was associated with activation of LC3-associated phagocytosis, a mechanism of fungal killing important for host defense againstA. fumigatusinfection. Thus, we identify therapeutic potential of the APN pathway in stimulation of immune-mediated fungal killing and treatment of fungal infection.
Automated high-throughput selection of DNA aptamers using a common optical next-generation sequencer
Authors: Drees Alissa , Ahlers Christian , Kehrer Timothy , Ehmke Natascha , Grün Alice Frederike Rosa , Uetrecht Charlotte , Ignatova Zoya , Schumacher Udo , Fischer Markus 
Published: June 2024

AbstractAptamers are conventionally selected via ‘Systematic Evolution of Ligands by Exponential Enrichment’ (SELEX). This process is, however, laborious, time-consuming, and has a relatively low efficacy. Here, we developed an automated high-throughput screening platform for the selection of DNA aptamers which consists of an optical next-generation sequencer with a modified software and hardware to automatically perform fluorescence-based binding assays on the displayed DNA sequences subsequent to sequencing. Using this platform, after only three to five SELEX rounds we selected highly affine DNA aptamers for the lectins LecA and LecB ofPseudomonas aeruginosaas well as for thePseudomonasExotoxin A. In comparison, twelve rounds of conventional SELEX resulted in three-fold less affine aptamers for LecA and PEA and none for LecB. Our high throughput-approach bears great potential to augment SELEX as it significantly increases time efficiency, enabling the selection of aptamers within only one week.
The DNA damage response relies on the characteristics of ionizing particles in myogenic cells
Authors: Sutcu Haser Hasan , Thomas--Joyeux Arthur , Cardot-Martin Mikaël , Vianna François , Benadjaoud Mohamed Amine , Benderitter Marc , Baldeyron Céline 
Published: June 2024

AbstractDNA integrity and stability are vital for proper cellular activity. Nevertheless, to treat cancer patients, DNA is the main target for inducing tumoral cell death. Nowadays, cancer treatment is improving by the development of new technologies, protocols and strategies. Amongst them, the introduction of charged particles as a form of radiotherapy is underway. However, tumor-neighboring healthy tissues are still exposed to ionizing radiations (IR) and subject to late side effects. Skeletal muscle is one of those tissues most likely to be affected. To decipher the DNA damage response (DDR) of skeletal muscle cells, myogenic cells, we irradiated them with microbeams of protons or α-particles and followed the accumulation of DDR proteins at irradiation sites. Thereby, we showed that myoblasts, proliferating myogenic cells, repair IR-induced DNA damage through both non-homologous end-joining and homologous recombination with different recruitment dynamics depending on the characteristics of ionizing particles (type, energy deposition and time after irradiation), whereas myotubes, post-mitotic myogenic cells, display reduced DNA damage response.SummaryMouse skeletal muscle cells and their precursor cells irradiated by ion microbeam show DNA damage response and DNA repair dynamics that vary according to the characteristics of ionizing particles delivered.Graphical Abstract
Thalamocortical contributions to hierarchical cognitive control
Authors: Chen Xitong , Leach Stephanie C. , Hollis Juniper , Cellier Dillan , Hwang Kai 
Published: June 2024

AbstractCognitive flexibility relies on hierarchically structured task representations that organize task contexts, relevant environmental features, and subordinate decisions. Despite ongoing interest in the human thalamus, its role in cognitive control has been understudied. This study explored thalamic representation and thalamocortical interactions that contribute to hierarchical cognitive control in humans. We found that several thalamic nuclei, including the anterior, mediodorsal, ventrolateral, and pulvinar nuclei, exhibited stronger evoked responses when subjects switch between task contexts. Decoding analysis revealed that thalamic activity encodes task contexts within the hierarchical task representations. To determine how thalamocortical interactions contribute to task representations, we developed a thalamocortical functional interaction model to predict task-related cortical representation. This data-driven model outperformed comparison models, particularly in predicting activity patterns in cortical regions that encode context representations. Collectively, our findings highlight the significant contribution of thalamic activity and thalamocortical interactions for contextually guided hierarchical cognitive control.