bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robotic, transanal, and laparoscopic total mesorectal excision for locally advanced mid/low rectal cancer: European multicentre, propensity score-matched study
Authors: de’Angelis Nicola , Marchegiani Francesco , Martínez-Pérez Aleix , Biondi Alberto , Pucciarelli Salvatore , Schena Carlo Alberto , Pellino Gianluca , Kraft Miquel , van Lieshout Annabel S , Morelli Luca , Valverde Alain , Lupinacci Renato Micelli , Gómez-Abril Segundo A , Persiani Roberto , Tuynman Jurriaan B , Espin-Basany Eloy , Ris Frederic ,   European MRI and Rectal Cancer Surgery (EuMaRCS) Study Group, Bianchi Giorgio , Martí-Martínez Eva , Torres-Sánchez Teresa , Sebastián-Tomás Juan Carlos , Maretto Isacco , Spolverato Gaya , Guadagni Simone , Solis Alejandro 
Published: May 2024

Abstract

Background
Total mesorectal excision (TME) is the standard surgery for low/mid locally advanced rectal cancer. The aim of this study was to compare three minimally invasive surgical approaches for TME with primary anastomosis (laparoscopic TME, robotic TME, and transanal TME).

Methods
Records of patients undergoing laparoscopic TME, robotic TME, or transanal TME between 2013 and 2022 according to standardized techniques in expert centres contributing to the European MRI and Rectal Cancer Surgery III (EuMaRCS-III) database were analysed. Propensity score matching was applied to compare the three groups with respect to the complication rate (primary outcome), conversion rate, postoperative recovery, and survival.

Results
A total of 468 patients (mean(s.d.) age of 64.1(11) years) were included; 190 (40.6%) patients underwent laparoscopic TME, 141 (30.1%) patients underwent robotic TME, and 137 (29.3%) patients underwent transanal TME. Comparative analyses after propensity score matching demonstrated a higher rate of postoperative complications for laparoscopic TME compared with both robotic TME (OR 1.80, 95% c.i. 1.11–2.91) and transanal TME (OR 2.87, 95% c.i. 1.72–4.80). Robotic TME was associated with a lower rate of grade A anastomotic leakage (2%) compared with both laparoscopic TME (8.8%) and transanal TME (8.1%) (P = 0.031). Robotic TME (1.4%) and transanal TME (0.7%) were both associated with a lower conversion rate to open surgery compared with laparoscopic TME (8.8%) (P &lt; 0.001). Time to flatus and duration of hospital stay were shorter for patients treated with transanal TME (P = 0.003 and 0.001 respectively). There were no differences in operating time, intraoperative complications, blood loss, mortality, readmission, R0 resection, or survival.

Conclusion
In this multicentre, retrospective, propensity score-matched, cohort study of patients with locally advanced rectal cancer, newer minimally invasive approaches (robotic TME and transanal TME) demonstrated improved outcomes compared with laparoscopic TME.
Assessing the cortical microstructure in contralesional sensorimotor areas after stroke
Authors: Wróbel Paweł P , Guder Stephanie , Feldheim Jan F , Graterol Pérez Jose A , Frey Benedikt M , Choe Chi-un , Bönstrup Marlene , Cheng Bastian , Rathi Yogesh , Pasternak Ofer , Thomalla Götz , Gerloff Christian , Shenton Martha E , Schulz Robert 
Published: May 2024

Abstract
Cortical thickness analyses have provided valuable insights into changes in cortical brain structure after stroke and their association with recovery. Across studies though, relationships between cortical structure and function show inconsistent results. Recent developments in diffusion-weighted imaging of the cortex have paved the way to uncover hidden aspects of stroke-related alterations in cortical microstructure, going beyond cortical thickness as a surrogate for cortical macrostructure. Animal data obtained in rats and monkeys have evidenced that contralesional motor areas undergo degenerative alterations in their microstructure which are accompanied by compensatory changes as well. We hypothesized that cortical diffusion imaging can detect similar changes in human stroke survivors. We re-analysed clinical and imaging data of 42 well-recovered chronic stroke patients from two independent cohorts (mean age 64 years, 4 left-handed, 71% male, 16 right-sided strokes) and 33 healthy controls of similar age and gender. Cortical fractional anisotropy, axial diffusivity, radial diffusivity and cortical thickness values were obtained for six key sensorimotor areas of the contralesional hemisphere. The regions included the primary motor cortex, dorsal and ventral premotor cortex, supplementary and pre-supplementary motor areas and primary somatosensory cortex. Linear models were estimated for group comparisons between patients and controls and for correlations between cortical fractional anisotropy, axial diffusivity, radial diffusivity and cortical thickness and clinical scores. Against our hypothesis, we did not find any significant alterations in contralesional cortical microstructure after stroke. Likewise, we did not detect any correlations between cortical microstructure and behavioural scores. Future analyses are warranted to investigate whether such alterations might occur in different populations, e.g. in later stages of recovery, in more severely impaired patients, or only in the ipsilesional hemisphere in patients with specific lesion patterns.
Interactions between physical exercise, associative memory, and genetic risk for Alzheimer’s disease
Authors: Igloi Kinga , Marin Bosch Blanca , Kuenzi Noémie , Thomas Aurélien , Lauer Estelle , Bringard Aurélien , Schwartz Sophie 
Published: May 2024

Abstract
The ε4 allele of the APOE gene heightens the risk of late onset Alzheimer’s disease. ε4 carriers, may exhibit cognitive and neural changes early on. Given the known memory-enhancing effects of physical exercise, particularly through hippocampal plasticity via endocannabinoid signaling, here we aimed to test whether a single session of physical exercise may benefit memory and underlying neurophysiological processes in young ε3 carriers (ε3/ε4 heterozygotes, risk group) compared with a matched control group (homozygotes for ε3). Participants underwent fMRI while learning picture sequences, followed by cycling or rest before a memory test. Blood samples measured endocannabinoid levels. At the behavioral level, the risk group exhibited poorer associative memory performance, regardless of the exercising condition. At the brain level, the risk group showed increased medial temporal lobe activity during memory retrieval irrespective of exercise (suggesting neural compensatory effects even at baseline), whereas, in the control group, such increase was only detectable after physical exercise. Critically, an exercise-related endocannabinoid increase correlated with task-related hippocampal activation in the control group only. In conclusion, healthy young individuals carrying the ε4 allele may present suboptimal associative memory performance (when compared with homozygote ε3 carriers), together with reduced plasticity (and functional over-compensation) within medial temporal structures.
The Impact of Firm Heterogeneity on International Risk-Sharing
Authors: Chang Ming-Jen , Chen Shikuan , Wu Yen-Chen 
Published: May 2024

Abstract
This study is significant as it explores whether firm heterogeneity with non-tradable goods and financial integration contributes to better international risk-sharing. We construct a dynamic stochastic general equilibrium framework to examine the impact of wealth effects on international risk-sharing. Our findings reveal that the wealth effect is another crucial factor for the limited risk-sharing observed in response to a positive idiosyncratic shock affecting heterogeneous firms, despite the non-tradable goods sector and incomplete financial market being the primary reasons for limited risk-sharing between the two countries. We further investigate the implication of wealth effects for international risk-sharing and demonstrate that financial frictions across borders impede the spillover of wealth effects from the home country to the foreign country, resulting in decreased risk-sharing (the consumption co-movement across countries is low). The impact of wealth effects will be weakened if domestic households prefer to consume more non-tradable or home-produced goods, leading to lower risk-sharing.
Control of sulfur number in sulfur-containing compounds: the effect of base type, equivalent of the base, and reaction solvent in synthesizing linear sulfur
Authors: Nishimura Ryuto , Kobayashi Yuichiro , Kamioka Ryunosuke , Hashimoto Shun , Yamaguchi Hiroyasu 
Published: May 2024

Abstract
Since the properties of sulfur-containing compounds depend on the number of sulfur atoms (sulfur number) contained in the compounds, it is desirable to develop a method to control the sulfur number. A common method for synthesizing sulfur-containing compounds is to mix sulfur with a base to form linear sulfur, which is then reacted with an organic compound to obtain a sulfur-containing compound. In this study, we systematically investigated the relationships between the type of base, equivalent amount of base, the reaction solvent, and the sulfur number in the resulting sulfur-containing compound. The sulfur numbers of sulfur-containing compounds prepared in water were controlled by the equivalent ratio of elemental sulfur (S8) and base. Sulfur-containing compounds with high sulfur values were obtained using solvents with low dielectric constants and with lower base equivalents compared to S8.
Bakry–Émery–Ricci curvature: an alternative network geometry measure in the expanding toolbox of graph Ricci curvatures
Authors: Mondal Madhumita , Samal Areejit , Münch Florentin , Jost Jürgen 
Published: May 2024

Abstract
The characterization of complex networks with tools originating in geometry, for instance through the statistics of so-called Ricci curvatures, is a well established tool of network science. Various types of such Ricci curvatures capture different aspects of network geometry. In the present work, we investigate Bakry–Émery–Ricci curvature, a notion of discrete Ricci curvature that has been studied much in geometry, but so far has not been applied to networks. We explore on standard classes of artificial networks as well as on selected empirical ones to what the statistics of that curvature are similar to or different from that of other curvatures, how it is correlated to other important network measures, and what it tells us about the underlying network. We observe that most vertices typically have negative curvature. Furthermore, the curvature distributions are different for different types of model networks. We observe a high positive correlation between Bakry–Émery–Ricci and both Forman–Ricci and Ollivier–Ricci curvature, and in particular with the augmented version of Forman–Ricci curvature while comparing them for both model and real-world networks. We investigate the correlation of Bakry–Émery–Ricci curvature with degree, clustering coefficient and vertex centrality measures. Also, we investigate the importance of vertices with highly negative curvature values to maintain communication in the network. Additionally, for Forman–Ricci, Augmented Forman–Ricci and Ollivier–Ricci curvature, we compare the robustness of the networks by comparing the sum of the incident edges and the minimum of the incident edges as vertex measures and find that the sum identifies vertices that are important for maintaining the connectivity of the network. The computational time for Bakry–Émery–Ricci curvature is shorter than that required for Ollivier–Ricci curvature but higher than for Augmented Forman–Ricci curvature. We therefore conclude that for empirical network analysis, the latter is the tool of choice.
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish
Authors: Wang Yuanyuan , Yang Yexin , Liu Yi , Liu Chao , Xu Meng , Fang Miao , Mu Xidong 
Published: May 2024

Abstract
Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution.
Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
Authors: Choudhary Preeti , Feng Zukang , Berrisford John , Chao Henry , Ikegawa Yasuyo , Peisach Ezra , Piehl Dennis W , Smith James , Tanweer Ahsan , Varadi Mihaly , Westbrook John D , Young Jasmine Y , Patwardhan Ardan , Morris Kyle L , Hoch Jeffrey C , Kurisu Genji , Velankar Sameer , Burley Stephen K 
Published: May 2024

Abstract
The Protein Data Bank (PDB) is the global repository for public-domain experimentally determined 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from trusted external biodata resources. While each Worldwide PDB (wwPDB) partner has made best efforts to provide up-to-date external annotations, accessing and integrating information from disparate wwPDB data centers can be an involved process. To address this issue, the wwPDB has established the PDB Next Generation (or NextGen) Archive, developed to centralize and streamline access to enriched structural annotations from wwPDB partners and trusted external sources. At present, the NextGen Archive provides mappings between experimentally determined 3D structures of proteins and UniProt amino acid sequences, domain annotations from Pfam, SCOP2 and CATH databases and intra-molecular connectivity information. Since launch, the PDB NextGen Archive has seen substantial user engagement with over 3.5 million data file downloads, ensuring researchers have access to accurate, up-to-date and easily accessible structural annotations.
Database URL: http://www.wwpdb.org/ftp/pdb-nextgen-archive-site
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity
Authors: Bettacchioli Eléonore , Chiche Laurent , Chaussabel Damien , Cornec Divi , Jourde-Chiche Noémie , Rinchai Darawan 
Published: May 2024

Abstract
In the field of complex autoimmune diseases such as systemic lupus erythematosus (SLE), systems immunology approaches have proven invaluable in translational research settings. Large-scale datasets of transcriptome profiling have been collected and made available to the research community in public repositories, but remain poorly accessible and usable by mainstream researchers. Enabling tools and technologies facilitating investigators’ interaction with large-scale datasets such as user-friendly web applications could promote data reuse and foster knowledge discovery. Microarray blood transcriptomic data from the LUPUCE cohort (publicly available on Gene Expression Omnibus, GSE49454), which comprised 157 samples from 62 adult SLE patients, were analyzed with the third-generation (BloodGen3) module repertoire framework, which comprises modules and module aggregates. These well-characterized samples corresponded to different levels of disease activity, different types of flares (including biopsy-proven lupus nephritis), different auto-antibody profiles and different levels of interferon signatures. A web application was deployed to present the aggregate-level, module-level and gene-level analysis results from LUPUCE dataset. Users can explore the similarities and heterogeneity of SLE samples, navigate through different levels of analysis, test hypotheses and generate custom fingerprint grids and heatmaps, which may be used in reports or manuscripts. This resource is available via this link: https://immunology-research.shinyapps.io/LUPUCE/. This web application can be employed as a stand-alone resource to explore changes in blood transcript profiles in SLE, and their relation to clinical and immunological parameters, to generate new research hypotheses.
Validation of the CREST model and comparison with SCAI shock classification for the prediction of circulatory death in resuscitated out-of-hospital cardiac arrest
Authors: Watson Samuel A , Mohanan Shamika , Abdrazak Muhamad , Roy Roman , Parczewska Alexandra , Kanyal Ritesh , McGarvey Michael , Dworakowski Rafal , Webb Ian , O’Gallagher Kevin , Melikian Narbeh , Auzinger Georg , Patel Sameer , Jaguszewski Miłosz J , Stahl Daniel , Shah Ajay , MacCarthy Philip , Byrne Jonathan , Pareek Nilesh 
Published: May 2024

Abstract

Aims
We validated the CREST model, a 5 variable score for stratifying the risk of circulatory aetiology death (CED) following out-of-hospital cardiac arrest (OHCA) and compared its discrimination with the SCAI shock classification. Circulatory aetiology death occurs in approximately a third of patients admitted after resuscitated OHCA. There is an urgent need for improved stratification of the patient with OHCA on arrival to a cardiac arrest centre to improve patient selection for invasive interventions.

Methods and results
The CREST model and SCAI shock classification were applied to a dual-centre registry of 723 patients with cardiac aetiology OHCA, both with and without ST-elevation myocardial infarction (STEMI), between May 2012 and December 2020. The primary endpoint was a 30-day CED. Of 509 patients included (62.3 years, 75.4% male), 125 patients had CREST = 0 (24.5%), 162 had CREST = 1 (31.8%), 140 had CREST = 2 (27.5%), 75 had CREST = 3 (14.7%), 7 had a CREST of 4 (1.4%), and no patients had CREST = 5. Circulatory aetiology death was observed in 91 (17.9%) patients at 30 days [STEMI: 51/289 (17.6%); non-STEMI (NSTEMI): 40/220 (18.2%)]. For the total population, and both NSTEMI and STEMI subpopulations, an increasing CREST score was associated with increasing CED (all P &lt; 0.001). The CREST score and SCAI classification had similar discrimination for the total population [area under the receiver operating curve (AUC) = 0.72/calibration slope = 0.95], NSTEMI cohort (AUC = 0.75/calibration slope = 0.940), and STEMI cohort (AUC = 0.69 and calibration slope = 0.925). Area under the receiver operating curve meta-analyses demonstrated no significant differences between the two classifications.

Conclusion
The CREST model and SCAI shock classification show similar prediction results for the development of CED after OHCA.
Selection leads to false inferences of introgression using popular methods
Authors: Smith Megan L , Hahn Matthew W 
Published: May 2024

Abstract
Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g. of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum. Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium-divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed.
Spearmint targets microtubules by (−)-carvone
Authors: Hering Nathalie , Schmit Anne-Catherine , Herzog Etienne , Corbin Louis-Thibault , Schmidt-Speicher Leona , Ahrens Ralf , Fauconnier Marie-Laure , Nick Peter 
Published: May 2024

Abstract
Allelopathy can provide sustainable alternatives to herbicides because it is based on specific signals rather than generic toxicity. We show that the allelopathic activity of Spearmint and Watermint is linked with their main compounds, (−)-carvone and (+)-menthofuran, both deriving from (−)-limonene. Germination of Poppy and Cress, and root growth of Arabidopsis thaliana are inhibited by very low concentrations of (−)-carvone, acting even through the gas phase. (+)-Menthofuran is active as well, but at lower efficacy. Using fluorescently tagged marker lines in tobacco BY-2 cells and Arabidopsis roots, we demonstrate a rapid degradation of microtubules and a remodeling of actin filaments in response to (−)-carvone and, to a milder extent, to (+)-menthofuran. This cytoskeletal response is followed by cell death. By means of a Root Chip system, we can follow the tissue dependent response of the cytoskeleton and show a cell-type dependent gradient of sensitivity between meristem and distal elongation zone, accompanied by programmed cell death.
A Culture of Commodification? Labour Rights in the Charter of Fundamental Rights of the European Union
Authors: Alexandris Polomarkakis Konstantinos 
Published: May 2024

Abstract
This article examines the deficiencies of the labour rights enshrined in the Charter of Fundamental Rights of the European Union (EU). It draws on the notion of labour as a fictive commodity in order to showcase how labour rights in the Charter can also be framed as being part of a commodification process, owing to a culture of commodification that is prevalent across the various institutions of the EU, and which has influenced the drafting, application and interpretation of those rights. As a result, labour rights may exist, but are only allocated a perfunctory role of maintaining the status of labour as a commodity. Their justiciability is questionable and there are limitations on their scope and direct effect. Finally, labour rights in the Charter are often conceived as subordinate to economic freedoms, exhibiting strong path-dependence and leading to a series of missed opportunities for their decommodifying potential to materialise.