bluuebunny/crossref_metadata_2025 huggingface dataset:
L’égalité des peuples en contexte fédéral ?
Authors: Boileau Xavier
Published: January 2024

Les pays ayant une structure politique fédérale sont souvent confrontés aux revendications de leurs États membres pour obtenir plus d'autonomie politique. Pour répondre à ces revendications, les théoriciens du fédéralisme multinational ont proposé de reconnaître un droit à l'autodétermination interne qu'ils ont pris soin d'encadrer de diverses manières. Bien qu'intéressante, cette proposition pourrait toutefois s'avérer insuffisante pour répondre aux inégalités entre les peuples au sein d'une même fédération. C'est la thèse que nous défendrons dans le présent article. Nous montrerons que le concept d'autodétermination interne défendu par Kymlicka reste indéterminé et ouvre la porte à des interprétations plus exigeantes.
A cross-cultural archery analogy in Matteo Ricci's Tianzhu shiyi
Authors: Hosle Paul K.
Published: January 2024

In the sixth chapter of his Tianzhu shiyi (天主實義, “The True Meaning of the Lord of Heaven”), Matteo Ricci offers a critique of the anti-intentionalistic thread that he detects in the Chinese philosophical tradition. In this brief essay, I offer an analysis of a noteworthy archery analogy that Ricci employs to describe the nature of ethical action as an intentional process with a conscious aim. I trace how Ricci skilfully combines Western and Chinese images and categories to craft this simile. Before that, I set the stage by offering some preliminary comments that contextualize Ricci's interest in the question of intentional vs. non-intentional conduct.
Childhood abuse and neglect and profiles of adult emotion dynamics
Authors: Myroniuk S. , Reitsema A. M. , de Jonge P. , Jeronimus B. F.
Published: January 2024

Childhood maltreatment (CM) is experienced by ∼40% of all children at major personal and societal costs. The divergent associations between emotional, physical, and sexual abuse or neglect in childhood and differences in adult emotional functioning and regulation were examined in terms of daily emotion intensity, variability, instability, inertia, and diversity, reported over 30 days by 290 Dutch aged 19-73. Participants described their abuse/neglect experiences retrospectively using the Childhood Trauma Questionnaire (CTQ). Dissecting CM effects on adult emotion dynamics may inform theories on the ontogenesis and functioning of emotions, on effects of abuse and neglect, to better understand (dys)functional emotional development, and to prevent their adverse sequelae. Structural equation models (SEM) showed that most types of CM were associated with specific patterns of emotion dynamics, and only emotional abuse had no unique effects on the emotional dynamic indices. Emotional neglect was associated with most measures of emotion dynamics (i.e., less intense, variable, unstable, and diverse emotions). Sexual abuse associated with increases and physical neglect decreases in negative affect variability and instability. Physical abuse was associated with inertia but with a small effect size. Social contact frequency did not mediate much of the relationship between CM types and emotion dynamics.
A construction of free dcpo-cones
Authors: Chen Yuxu , Kou Hui , Lyu Zhenchao , Xie Xiaolin
Published: January 2024

We give a construction of the free dcpo-cone over any dcpo. There are two steps for getting this result. Firstly, we extend the notion of power domain to directed spaces which are equivalent to$T_0$monotone-determined spaces introduced by Erné, and we construct the probabilistic powerspace of the monotone determined space, which is defined as a free monotone determined cone. Secondly, we take D-completion of the free monotone determined cone over the dcpo with its Scott topology. In addition, we show that generally the valuation power domain of any dcpo is not the free dcpo-cone.
Decision support tools for sustainable water management: Lessons learned from two decades of using MULINO-DSS
Authors: Giupponi Carlo , Balabanis Panagiotis , Cojocaru George , F. Vázquez Jacobo , Mysiak Jaroslav
Published: January 2024

In late 2000, the European Union adopted the Water Framework Directive (WFD) and funded a series of research and innovation projects to support its implementation. One of these was the MULINO project (MULti-sectoral, INtegrated and Operational Decision Support System for Sustainable Use of Water Resources at the Catchment Scale). Its main product was a decision support system (mDSS) tool designed to help water managers make choices related to WFD implementation in a participatory manner. After the end of MULINO, a long sequence of research projects allowed for the maintenance and continuous development of its tool, which has been applied for more than 20 years in various contexts related to environmental and integrated management. This experience and an analysis of the literature allow us to draw some general conclusions regarding DSS tools for water management and their role in our societies. Lessons learned are proposed, from the need to frame tools within sound methodological frameworks for the management of decision processes, supporting instead of substituting decision-makers in their roles, to the trade-offs that appear between ease of use and specificity on one side and flexibility and reusability on the other. The specific strengths attributed to mDSS include the provision of an interface based on a simplified and understandable conceptual framework that facilitates communication with interested parties, the flexibility and ability to approach a wide variety of decisional issues, the relatively simple and understandable decision rules provided by the tool, and the simplified connections with other software environments. This paper presents the current version of the software and reports on the experience of its development and use over more than two decades; it also identifies the way forward.
Geräusche auf Intensivstationen: Perspektiven von Patient_innen und Eltern
Authors: Schön Isabel , Witek Sandra , Merz Nicola , Ziegler Sven , Feuchtinger Johanna
Published: January 2024

Zusammenfassung: Hintergrund: Schallpegel auf Intensivstationen übersteigen international empfohlene Grenzwerte. Das kann negative Auswirkungen bei Patient_innen, Angehörigen und Mitarbeiter_innen haben. Es mangelt aber an Evidenz zu lärmreduzierenden Maßnahmen. Fragestellung/Ziel: Ziele der Studie waren die Implementierung und Evaluation von stationsbezogenem Lärmmanagement auf Intensivstationen. Im vorliegenden Artikel wird der Fragestellung nach dem Geräusch- und Belastungserleben von Intensivpatient_innen bzw. der Eltern der neonatologischen Intensivpatient_innen nachgegangen. Methoden: Zu drei Erhebungszeitpunkten wurden insgesamt 33 semi-strukturierte Interviews mit Intensivpatient_innen und Eltern von neonatologischen Intensivpatient_innen auf drei Intensivstationen durchgeführt und inhaltsanalytisch ausgewertet. Ergebnisse: Geräusche auf Intensivstationen können belastend wirken (vor allem Alarme), aber auch als sinnhaft gedeutet werden. Das hängt nicht nur mit dem Kontext der Intensivstation, sondern auch mit persönlichen Erfahrungen und den sozialen Aspekten der Geräusche zusammen. Um Belastungen zu vermeiden bzw. zu reduzieren, wenden Teilnehmende individuelles Lärm(stress)management an. Das stationsbezogene Lärmmanagement dagegen hatte keine spezifische Wirkung auf die Teilnehmenden. Schlussfolgerungen: Die Erkenntnisse bieten Hinweise für geeignete Maßnahmen zur Reduktion der Lärmbelastung von Intensivpatient_innen und Eltern der neonatologischen Intensivpatient_innen. Es könnten Konzepte zur Unterstützung der Einordnung und Differenzierung von Geräuschen als Maßnahmen untersucht werden.
Outcomes of patients with multiple myeloma and 1q gain/amplification receiving autologous hematopoietic stem cell transplant: the MD Anderson cancer center experience
Authors: Pasvolsky Oren , Ghanem Sassine , Milton Denái R. , Rauf Mikael , Tanner Mark R. , Bashir Qaiser , Srour Samer , Saini Neeraj , Lin Paul , Ramdial Jeremy , Nieto Yago , Tang Guilin , Aljawai Yosra , Khan Hina N. , Kebriaei Partow , Lee Hans C. , Patel Krina K. , Thomas Sheeba K. , Weber Donna M. , Orlowski Robert Z. , Shpall Elizabeth J. , Champlin Richard E. , Qazilbash Muzaffar H.
Published: January 2024

The prognostic impact of additional copies of chromosome 1q (1q + ) on outcomes of newly-diagnosed multiple myeloma (NDMM) patients undergoing autologous transplantation (autoSCT) is unclear. We conducted a retrospective single-center analysis of NDMM patients with 1q21 gain/amplification (3 or ≥4 copies of 1q, respectively) that received autoSCT between 2008–2018. 213 patients were included (79% 1q gain; 21% 1q amplification). The most commonly used induction regimen was bortezomib, lenalidomide, and dexamethasone (41%). At day100 post-autoSCT and at best post-transplant response, 78% and 87% of patients achieved ≥VGPR, and 38% and 50% achieved MRD-negative ≥VGPR, respectively. Median PFS and OS for the entire cohort were 35.5 months and 81.4 months, respectively. On multivariable assessment for PFS, MRD negative ≥VGPR before autoSCT (HR 0.52, p = 0.013) was associated with superior PFS, whereas 1q amplification was associated with inferior PFS (2.03, p = 0.003). On multivariate analysis for OS, achieving MRD negative ≥VGPR at best post-transplant response was associated with superior survival (0.29, p < 0.001), whereas R-ISS III and concomitant del17p or t(4:14) were associated with inferior survival (6.95, p = 0.030, 2.33, p = 0.023 and 3.00, p = 0.047, respectively). In conclusion, patients with 1q+ NDMM, especially 1q amplification, have inferior survival outcomes compared to standard-risk disease after upfront autoSCT, though outcomes are better than other high-risk cytogenetic abnormalities.
Intratumoral presence of the genotoxic gut bacteria pks+ E. coli, Enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum and their association with clinicopathological and molecular features of colorectal cancer
Authors: Joo Jihoon E. , Chu Yen Lin , Georgeson Peter , Walker Romy , Mahmood Khalid , Clendenning Mark , Meyers Aaron L. , Como Julia , Joseland Sharelle , Preston Susan G. , Diepenhorst Natalie , Toner Julie , Ingle Danielle J. , Sherry Norelle L. , Metz Andrew , Lynch Brigid M. , Milne Roger L. , Southey Melissa C. , Hopper John L. , Win Aung Ko , Macrae Finlay A. , Winship Ingrid M. , Rosty Christophe , Jenkins Mark A. , Buchanan Daniel D.
Published: January 2024

Background

This study aimed to investigate clinicopathological and molecular tumour features associated with intratumoral pks+Escherichia coli (pks+E.coli+), pks+E.coli- (non-E.coli bacteria harbouring the pks island), Enterotoxigenic Bacteroides fragilis (ETBF) and Fusobacterium nucleatum (F. nucleatum).

Methods

We screened 1697 tumour-derived DNA samples from the Australasian Colorectal Cancer Family Registry, Melbourne Collaborative Cohort Study and the ANGELS study using targeted PCR.

Results

Pks+E.coli+ was associated with male sex (P < 0.01) and APC:c.835-8 A > G somatic mutation (P = 0.03). The association between pks+E.coli+ and APC:c.835-8 A > G was specific to early-onset CRCs (diagnosed<45years, P = 0.02). The APC:c.835-A > G was not associated with pks+E.coli- (P = 0.36). F. nucleatum was associated with DNA mismatch repair deficiency (MMRd), BRAF:c.1799T>A p.V600E mutation, CpG island methylator phenotype, proximal tumour location, and high levels of tumour infiltrating lymphocytes (Ps < 0.01). In the stratified analysis by MMRd subgroups, F. nucleatum was associated with Lynch syndrome, MLH1 methylated and double MMR somatic mutated MMRd subgroups (Ps < 0.01).

Conclusion

Intratumoral pks+E.coli+ but not pks+E.coli- are associated with CRCs harbouring the APC:c.835-8 A > G somatic mutation, suggesting that this mutation is specifically related to DNA damage from colibactin-producing E.coli exposures. F. nucleatum was associated with both hereditary and sporadic MMRd subtypes, suggesting the MMRd tumour microenvironment is important for F. nucleatum colonisation irrespective of its cause.
LanDis: the disease landscape explorer
Authors: Caniza Horacio , Cáceres Juan J. , Torres Mateo , Paccanaro Alberto
Published: January 2024

From a network medicine perspective, a disease is the consequence of perturbations on the interactome. These perturbations tend to appear in a specific neighbourhood on the interactome, the disease module, and modules related to phenotypically similar diseases tend to be located in close-by regions. We present LanDis, a freely available web-based interactive tool (https://paccanarolab.org/landis) that allows domain experts, medical doctors and the larger scientific community to graphically navigate the interactome distances between the modules of over 44 million pairs of heritable diseases. The map-like interface provides detailed comparisons between pairs of diseases together with supporting evidence. Every disease in LanDis is linked to relevant entries in OMIM and UniProt, providing a starting point for in-depth analysis and an opportunity for novel insight into the aetiology of diseases as well as differential diagnosis.
Field-induced bound-state condensation and spin-nematic phase in SrCu2(BO3)2 revealed by neutron scattering up to 25.9 T
Authors: Fogh Ellen , Nayak Mithilesh , Prokhnenko Oleksandr , Bartkowiak Maciej , Munakata Koji , Soh Jian-Rui , Turrini Alexandra A. , Zayed Mohamed E. , Pomjakushina Ekaterina , Kageyama Hiroshi , Nojiri Hiroyuki , Kakurai Kazuhisa , Normand Bruce , Mila Frédéric , Rønnow Henrik M.
Published: January 2024

In quantum magnetic materials, ordered phases induced by an applied magnetic field can be described as the Bose-Einstein condensation (BEC) of magnon excitations. In the strongly frustrated system SrCu2(BO3)2, no clear magnon BEC could be observed, pointing to an alternative mechanism, but the high fields required to probe this physics have remained a barrier to detailed investigation. Here we exploit the first purpose-built high-field neutron scattering facility to measure the spin excitations of SrCu2(BO3)2 up to 25.9 T and use cylinder matrix-product-states (MPS) calculations to reproduce the experimental spectra with high accuracy. Multiple unconventional features point to a condensation of S = 2 bound states into a spin-nematic phase, including the gradients of the one-magnon branches and the persistence of a one-magnon spin gap. This gap reflects a direct analogy with superconductivity, suggesting that the spin-nematic phase in SrCu2(BO3)2 is best understood as a condensate of bosonic Cooper pairs.
Scalable integrated two-dimensional Fourier-transform spectrometry
Authors: Xu Hongnan , Qin Yue , Hu Gaolei , Tsang Hon Ki
Published: January 2024

Integrated spectrometers offer the advantages of small sizes and high portability, enabling new applications in industrial development and scientific research. Integrated Fourier-transform spectrometers (FTS) have the potential to realize a high signal-to-noise ratio but typically have a trade-off between the resolution and bandwidth. Here, we propose and demonstrate the concept of the two-dimensional FTS (2D-FTS) to circumvent the trade-off and improve scalability. The core idea is to utilize 2D Fourier transform instead of 1D Fourier transform to rebuild spectra. By combining a tunable FTS and a spatial heterodyne spectrometer, the interferogram becomes a 2D pattern with variations of heating power and arm lengths. All wavelengths are mapped to a cluster of spots in the 2D Fourier map beyond the free-spectral-range limit. At the Rayleigh criterion, the demonstrated resolution is 250 pm over a 200-nm bandwidth. The resolution can be enhanced to 125 pm using the computational method.
Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson’s disease model
Authors: Morrone Parfitt Gustavo , Coccia Elena , Goldman Camille , Whitney Kristen , Reyes Ricardo , Sarrafha Lily , Nam Ki Hong , Sohail Soha , Jones Drew R. , Crary John F. , Ordureau Alban , Blanchard Joel , Ahfeldt Tim
Published: January 2024

Accumulation of advanced glycation end products (AGEs) on biopolymers accompanies cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early onset Parkinson’s Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. We demonstrated these processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes’ capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in a DJ1 loss-of-function PD model.
Elucidating protonation pathways in CO2 photoreduction using the kinetic isotope effect
Authors: Yin Shikang , Zhou Yiying , Liu Zhonghuan , Wang Huijie , Zhao Xiaoxue , Zhu Zhi , Yan Yan , Huo Pengwei
Published: January 2024

The surge in anthropogenic CO2 emissions from fossil fuel dependence demands innovative solutions, such as artificial photosynthesis, to convert CO2 into value-added products. Unraveling the CO2 photoreduction mechanism at the molecular level is vital for developing high-performance photocatalysts. Here we show kinetic isotope effect evidence for the contested protonation pathway for CO2 photoreduction on TiO2 nanoparticles, which challenges the long-held assumption of electron-initiated activation. Employing isotopically labeled H2O/D2O and in-situ diffuse reflectance infrared Fourier transform spectroscopy, we observe H+/D+-protonated intermediates on TiO2 nanoparticles and capture their inverse decay kinetic isotope effect. Our findings significantly broaden our understanding of the CO2 uptake mechanism in semiconductor photocatalysts.
Extrapolative prediction of small-data molecular property using quantum mechanics-assisted machine learning
Authors: Shimakawa Hajime , Kumada Akiko , Sato Masahiro
Published: January 2024

Data-driven materials science has realized a new paradigm by integrating materials domain knowledge and machine-learning (ML) techniques. However, ML-based research has often overlooked the inherent limitation in predicting unknown data: extrapolative performance, especially when dealing with small-scale experimental datasets. Here, we present a comprehensive benchmark for assessing extrapolative performance across 12 organic molecular properties. Our large-scale benchmark reveals that conventional ML models exhibit remarkable performance degradation beyond the training distribution of property range and molecular structures, particularly for small-data properties. To address this challenge, we introduce a quantum-mechanical (QM) descriptor dataset, called QMex, and an interactive linear regression (ILR), which incorporates interaction terms between QM descriptors and categorical information pertaining to molecular structures. The QMex-based ILR achieved state-of-the-art extrapolative performance while preserving its interpretability. Our benchmark results, QMex dataset, and proposed model serve as valuable assets for improving extrapolative predictions with small experimental datasets and for the discovery of novel materials/molecules that surpass existing candidates.
Action prediction in psychosis
Authors: Montobbio Noemi , Zingarelli Enrico , Folesani Federica , Memeo Mariacarla , Croce Enrico , Cavallo Andrea , Grassi Luigi , Fadiga Luciano , Panzeri Stefano , Belvederi Murri Martino , Becchio Cristina
Published: January 2024

Aberrant motor-sensory predictive functions have been linked to symptoms of psychosis, particularly reduced attenuation of self-generated sensations and misattribution of self-generated actions. Building on the parallels between prediction of self- and other-generated actions, this study aims to investigate whether individuals with psychosis also demonstrate abnormal perceptions and predictions of others’ actions. Patients with psychosis and matched controls completed a two-alternative object size discrimination task. In each trial, they observed reaching actions towards a small and a large object, with varying levels of temporal occlusion ranging from 10% to 80% of movement duration. Their task was to predict the size of the object that would be grasped. We employed a novel analytic approach to examine how object size information was encoded and read out across progressive levels of occlusion with single-trial resolution. Patients with psychosis exhibited an overall pattern of reduced and discontinuous evidence integration relative to controls, characterized by a period of null integration up to 20% of movement duration, during which they did not read any size information. Surprisingly, this drop in accuracy in the initial integration period was not accompanied by a reduction in confidence. Difficulties in action prediction were correlated with the severity of negative symptoms and impaired functioning in social relationships.
In vivo neuroprotective capacity of a Dunaliella salina extract - comprehensive transcriptomics and metabolomics study
Authors: Valdés Alberto , Sánchez-Martínez José David , Gallego Rocío , Ibáñez Elena , Herrero Miguel , Cifuentes Alejandro
Published: January 2024

In this study, an exhaustive chemical characterization of a Dunaliella salina (DS) microalga extract obtained using supercritical fluids has been performed, and its neuroprotective capacity has been evaluated in vivo using an Alzheimer’s disease (AD) transgenic model of Caenorhabditis elegans (strain CL4176). More than 350 compounds were annotated in the studied DS extract, with triacylglycerols, free fatty acids (FAs), carotenoids, apocarotenoids and glycerol being the most abundant. DS extract significantly protects C. elegans in a dose-dependent manner against Aβ-peptide paralysis toxicity, after 32 h, 53% of treated worms at 50 µg/mL were not paralyzed. This concentration was selected to further evaluate the transcriptomics and metabolomics changes after 26 h by using advanced analytical methodologies. The RNA-Seq data showed an alteration of 150 genes, mainly related to the stress and detoxification responses, and the retinol and lipid metabolism. The comprehensive metabolomics and lipidomics analyses allowed the identification of 793 intracellular metabolites, of which 69 were significantly altered compared to non-treated control animals. Among them, different unsaturated FAs, lysophosphatidylethanolamines, nucleosides, dipeptides and modified amino acids that have been previously reported as beneficial during AD progression, were assigned. These compounds could explain the neuroprotective capacity observed, thus, providing with new evidences of the protection mechanisms of this promising extract.
Catalytic asymmetric cationic shifts of aliphatic hydrocarbons
Authors: Wakchaure Vijay N. , DeSnoo William , Laconsay Croix J. , Leutzsch Markus , Tsuji Nobuya , Tantillo Dean J. , List Benjamin
Published: January 2024

Asymmetric catalysis is an advanced area of chemical synthesis, but the handling of abundantly available, purely aliphatic hydrocarbons has proven to be challenging. Typically, heteroatoms or aromatic substructures are required in the substrates and reagents to facilitate an efficient interaction with the chiral catalyst. Confined acids have recently been introduced as tools for homogenous asymmetric catalysis, specifically to enable the processing of small unbiased substrates1. However, asymmetric reactions in which both substrate and product are purely aliphatic hydrocarbons have not previously been catalysed by such super strong and confined acids. We describe here an imidodiphosphorimidate-catalysed asymmetric Wagner–Meerwein shift of aliphatic alkenyl cycloalkanes to cycloalkenes with excellent regio- and enantioselectivity. Despite their long history and high relevance for chemical synthesis and biosynthesis, Wagner–Meerwein reactions utilizing purely aliphatic hydrocarbons, such as those originally reported by Wagner and Meerwein, had previously eluded asymmetric catalysis.
Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism
Authors: Dunkelmann Daniel L. , Piedrafita Carlos , Dickson Alexandre , Liu Kim C. , Elliott Thomas S. , Fiedler Marc , Bellini Dom , Zhou Andrew , Cervettini Daniele , Chin Jason W.
Published: January 2024

The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1–3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4–6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs—this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-l-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs inEscherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.
Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
Authors: Xiao Yu , Chen Yan-Ming , Zou Zhongyu , Ye Chang , Dou Xiaoyang , Wu Jinjun , Liu Chang , Liu Shun , Yan Hao , Wang Pingluan , Zeng Tie-Bo , Liu Qinzhe , Fei Jingyi , Tang Weixin , He Chuan
Published: January 2024

RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA targets are still lacking, especially when the interaction is dynamic or samples are limited. Here we present an assay of reverse transcription-based RBP binding site sequencing (ARTR-seq), which relies on in situ reverse transcription of RBP-bound RNAs guided by antibodies to identify RBP binding sites. ARTR-seq avoids ultraviolet crosslinking and immunoprecipitation, allowing for efficient and specific identification of RBP binding sites from as few as 20 cells or a tissue section. Taking advantage of rapid formaldehyde fixation, ARTR-seq enables capturing the dynamic RNA binding by RBPs over a short period of time, as demonstrated by the profiling of dynamic RNA binding of G3BP1 during stress granule assembly on a timescale as short as 10 minutes.
A tablet-based multi-dimensional drawing system can effectively distinguish patients with amnestic MCI from healthy individuals
Authors: Zhang Xiaonan , Lv Liangliang , Shen Jiani , Chen Jinyu , Zhang Hui , Li Yang
Published: January 2024

The population with dementia is expected to rise to 152 million in 2050 due to the aging population worldwide. Therefore, it is significant to identify and intervene in the early stage of dementia. The Rey-Osterreth complex figure (ROCF) test is a visuospatial test scale. Its scoring methods are numerous, time-consuming, and inconsistent, which is unsuitable for wide application as required by the high number of people at risk. Therefore, there is an urgent need for a rapid, objective, and sensitive digital scoring method to detect cognitive dysfunction in the early stage accurately. This study aims to clarify the organizational strategy of aMCI patients to draw complex figures through a multi-dimensional digital evaluation system. At the same time, a rapid, objective, and sensitive digital scoring method is established to replace traditional scoring. The data of 64 subjects (38 aMCI patients and 26 NC individuals) were analyzed in this study. All subjects completed the tablet's Geriatric Complex Figure (GCF) test, including copying, 3-min recall, and 20-min delayed recall, and also underwent a standardized neuropsychological test battery and classic ROCF test. Digital GCF (dGCF) variables and conventional GCF (cGCF) scores were input into the forward stepwise logistic regression model to construct classification models. Finally, ROC curves were made to visualize the difference in the diagnostic value of dGCF variables vs. cGCF scores in categorizing the diagnostic groups. In 20-min delayed recall, aMCI patients' time in air and pause time were longer than NC individuals. Patients with aMCI had more short strokes and poorer ability of detail integration (all p < 0.05). The diagnostic sensitivity of dGCF variables for aMCI patients was 89.47%, slightly higher than cGCF scores (sensitivity: 84.21%). The diagnostic accuracy of both was comparable (dGCF: 70.3%; cGCF: 73.4%). Moreover, combining dGCF variables and cGCF scores could significantly improve the diagnostic accuracy and specificity (accuracy: 78.1%, specificity: 84.62%). At the same time, we construct the regression equations of the two models. Our study shows that dGCF equipment can quantitatively evaluate drawing performance, and its performance is comparable to the time-consuming cGCF score. The regression equation of the model we constructed can well identify patients with aMCI in clinical application. We believe this new technique can be a highly effective screening tool for patients with MCI.
The impact of the size and angle of the cochlear basal turn on translocation of a pre-curved mid-scala cochlear implant electrode
Authors: Pai Irumee , Connor Steve , Komninos Charalampos , Ourselin Sebastien , Bergeles Christos
Published: January 2024

Scalar translocation is a severe form of intra-cochlear trauma during cochlear implant (CI) electrode insertion. This study explored the hypothesis that the dimensions of the cochlear basal turn and orientation of its inferior segment relative to surgically relevant anatomical structures influence the scalar translocation rates of a pre-curved CI electrode. In a cohort of 40 patients implanted with the Advanced Bionics Mid-Scala electrode array, the scalar translocation group (40%) had a significantly smaller mean distance A of the cochlear basal turn (p < 0.001) and wider horizontal angle between the inferior segment of the cochlear basal turn and the mastoid facial nerve (p = 0.040). A logistic regression model incorporating distance A (p = 0.003) and horizontal facial nerve angle (p = 0.017) explained 44.0–59.9% of the variance in scalar translocation and correctly classified 82.5% of cases. Every 1mm decrease in distance A was associated with a 99.2% increase in odds of translocation [95% confidence interval 80.3%, 100%], whilst every 1-degree increase in the horizontal facial nerve angle was associated with an 18.1% increase in odds of translocation [95% CI 3.0%, 35.5%]. The study findings provide an evidence-based argument for the development of a navigation system for optimal angulation of electrode insertion during CI surgery to reduce intra-cochlear trauma.
On the complexity of quantum link prediction in complex networks
Authors: Moutinho João P. , Magano Duarte , Coutinho Bruno
Published: January 2024

Link prediction methods use patterns in known network data to infer which connections may be missing. Previous work has shown that continuous-time quantum walks can be used to represent path-based link prediction, which we further study here to develop a more optimized quantum algorithm. Using a sampling framework for link prediction, we analyze the query access to the input network required to produce a certain number of prediction samples. Considering both well-known classical path-based algorithms using powers of the adjacency matrix as well as our proposed quantum algorithm for path-based link prediction, we argue that there is a polynomial quantum advantage on the dependence on N, the number of nodes in the network. We further argue that the complexity of our algorithm, although sub-linear in N, is limited by the complexity of performing a quantum simulation of the network’s adjacency matrix, which may prove to be an important problem in the development of quantum algorithms for network science in general.
Sensing of heavy metal Pb2+ ions in water utilizing the photonic structure of highly controlled hexagonal TiON/TiO2 nanotubes
Authors: Elsayed Asmaa M. , Ahmed Ashour M. , Tammam M. T. , Eissa M. F. , Aly Arafa H.
Published: January 2024

The detection of heavy metals in water, especially Pb2+ ions, is important due to their severe hazardous effects. To address this issue, a highly controlled hexagonal TiON/TiO2 heterostructure has been synthesized in this study. The fabrication process involved the utilization of atomic layer deposition and direct current sputtering techniques to deposit TiO2 and TiON layers onto a porous Al2O3 membrane used as a template. The resulting heterostructure exhibits a well-ordered hollow tube structure with a diameter of 345 nm and a length of 1.2 µm. The electrochemical sensing of Pb2+ ions in water is carried out using a cyclic voltammetry technique under both light and dark conditions. The concentration range for the Pb2+ ions ranges from 10–5 to 10–1 M. The sensitivity values obtained for the sensor are 1.0 × 10–6 in dark conditions and 1.0 × 10–4 in light conditions. The remarkable enhancement in sensitivity under light illumination can be attributed to the increased activity and electron transfer facilitated by the presence of light. The sensor demonstrates excellent reproducibility, highlighting its reliability and consistency. These findings suggest that the proposed sensor holds great promise for the detection of Pb2+ ions in water, thereby facilitating environmental monitoring, water quality assessment, and safety regulation across various industries. Furthermore, the eco-friendly and straightforward preparation techniques employed in its fabrication provide a significant advantage for practical and scalable implementation.
Network-based pharmacology-based research on the effect and mechanism of the Hedyotis diffusa–Scutellaria Barbata pair in the treatment of hepatocellular carcinoma
Authors: Hou Changmiao , Wen Xiao , Yan Shifan , Gu Xiaoxiao , Jiang Yu , Chen Fang , Liu Yanjuan , Zhu Yimin , Liu Xiehong
Published: January 2024

The Hedyotis diffusa–Scutellaria officinalis pair (HD–SB) has therapeutic effects on a variety of cancers. Our study was to explore the mechanism of HD–SB in the treatment of hepatocellular carcinoma (HCC). A total of 217 active ingredients of HD–SB and 1196 HCC-related targets were reserved from the TCMSP and the SwissTarget Prediction database, and we got 63 intersection targets from GeneCards. We used a Venn diagram, and Cytoscape found that the three core ingredients were quercetin, luteolin, and baicalein. The PPI analysis showed that the core targets were TP53, CDK2, XPO1, and APP. Molecular docking results showed that these core ingredients had good binding potential with the core targets. HD–SB acts simultaneously on various HCC-related signaling pathways, including proteoglycans in cancer and the P53 signaling pathway. In vitro experiments confirmed that HD–SB can inhibit HepG2 cell proliferation by increasing TP53 and APP levels and decreasing XPO1 and CDK2 levels. This study analyzed active ingredients, core targets, and central mechanisms of HD–SB in the treatment of HCC. It reveals the role of HD–SB in targeting the P53 signaling pathway in the treatment of HCC. We hope that our research could provide a new perspective to the therapy of HCC and find new anticancer drugs.
Optical coupling control of isolated mechanical resonators
Authors: Onah F. E. , Jaramillo-Ávila B. R. , Maldonado-Villamizar F. H. , Rodríguez-Lara B. M.
Published: January 2024

We present a Hamiltonian model describing two pairs of mechanical and optical modes under standard optomechanical interaction. The vibrational modes are mechanically isolated from each other and the optical modes couple evanescently. We recover the ranges for variables of interest, such as mechanical and optical resonant frequencies and naked coupling strengths, using a finite element model for a standard experimental realization. We show that the quantum model, under this parameter range and external optical driving, may be approximated into parametric interaction models for all involved modes. As an example, we study the effect of detuning in the optical resonant frequencies modes and optical driving resolved to mechanical sidebands and show an optical beam splitter with interaction strength dressed by the mechanical excitation number, a mechanical bidirectional coupler, and a two-mode mechanical squeezer where the optical state mediates the interaction strength between the mechanical modes.
Machine learning assisted rational design of antimicrobial peptides based on human endogenous proteins and their applications for cosmetic preservative system optimization
Authors: Yue Lizhi , Song Liya , Zhu Siyu , Fu Xiaolei , Li Xuhui , He Congfen , Li Junxiang
Published: January 2024

Preservatives are essential components in cosmetic products, but their safety issues have attracted widespread attention. There is an urgent need for safe and effective alternatives. Antimicrobial peptides (AMPs) are part of the innate immune system and have potent antimicrobial properties. Using machine learning-assisted rational design, we obtained a novel antibacterial peptide, IK-16-1, with significant antibacterial activity and maintaining safety based on β-defensins. IK-16-1 has broad-spectrum antimicrobial properties against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans, and has no haemolytic activity. The use of IK-16-1 holds promise in the cosmetics industry, since it can serve as a preservative synergist to reduce the amount of other preservatives in cosmetics. This study verified the feasibility of combining computational design with artificial intelligence prediction to design AMPs, achieving rapid screening and reducing development costs.
Effect of diet supplemented with functional amino acids and polyphenols on gut health in broilers subjected to a corticosterone-induced stress
Authors: Yvon Sophie , Beaumont Martin , Dayonnet Alix , Eutamène Hélène , Lambert William , Tondereau Valérie , Chalvon-Demersay Tristan , Belloir Pauline , Paës Charlotte
Published: January 2024

To address the overuse of antimicrobials in poultry production, new functional feed ingredients, i.e. ingredients with benefits beyond meeting basic nutritional requirements, can play a crucial role thanks to their prophylactic effects. This study evaluated the effects of the supplementation of arginine, threonine and glutamine together with grape polyphenols on the gut integrity and functionality of broilers facing a stress condition. 108 straight-run newly hatched Ross PM3 chicks were kept until 35 days and were allocated to 3 treatments. Broilers in the control group were raised in standard conditions. In experimental groups, birds were administered with corticosterone in drinking water (CORT groups) to impair the global health of the animal and were fed a well-balanced diet supplemented or not with a mix of functional amino acids together with grape extracts (1 g/kg of diet—CORT + MIX group). Gut permeability was significantly increased by corticosterone in non-supplemented birds. This corticosterone-induced stress effect was alleviated in the CORT + MIX group. MIX supplementation attenuated the reduction of crypt depth induced by corticosterone. Mucin 2 and TNF-α gene expression was up-regulated in the CORT + MIX group compared to the CORT group. Caecal microbiota remained similar between the groups. These findings indicate that a balanced diet supplemented with functional AA and polyphenols can help to restore broiler intestinal barrier after a stress exposure.
Isotherms, kinetics and thermodynamic mechanism of methylene blue dye adsorption on synthesized activated carbon
Authors: El Jery Atef , Alawamleh Heba Saed Kariem , Sami Mustafa Humam , Abbas Hussein Abdullah , Sammen Saad Sh. , Ahsan Amimul , Imteaz M. A. , Shanableh Abdallah , Shafiquzzaman Md. , Osman Haitham , Al-Ansari Nadhir
Published: January 2024

The treatment of methylene blue (MB) dye wastewater through the adsorption process has been a subject of extensive research. However, a comprehensive understanding of the thermodynamic aspects of dye solution adsorption is lacking. Previous studies have primarily focused on enhancing the adsorption capacity of methylene blue dye. This study aimed to develop an environmentally friendly and cost-effective method for treating methylene blue dye wastewater and to gain insights into the thermodynamics and kinetics of the adsorption process for optimization. An adsorbent with selective methylene blue dye adsorption capabilities was synthesized using rice straw as the precursor. Experimental studies were conducted to investigate the adsorption isotherms and models under various process conditions, aiming to bridge gaps in previous research and enhance the understanding of adsorption mechanisms. Several adsorption isotherm models, including Langmuir, Temkin, Freundlich, and Langmuir–Freundlich, were applied to theoretically describe the adsorption mechanism. Equilibrium thermodynamic results demonstrated that the calculated equilibrium adsorption capacity (qe) aligned well with the experimentally obtained data. These findings of the study provide valuable insights into the thermodynamics and kinetics of methylene blue dye adsorption, with potential applications beyond this specific dye type. The utilization of rice straw as an adsorbent material presents a novel and cost-effective approach for MB dye removal from wastewater.
Quantifying changes in individual-specific template-based representations of center-of-mass dynamics during walking with ankle exoskeletons using Hybrid-SINDy
Authors: Rosenberg Michael C. , Proctor Joshua L. , Steele Katherine M.
Published: January 2024

Ankle exoskeletons alter whole-body walking mechanics, energetics, and stability by altering center-of-mass (CoM) motion. Controlling the dynamics governing CoM motion is, therefore, critical for maintaining efficient and stable gait. However, how CoM dynamics change with ankle exoskeletons is unknown, and how to optimally model individual-specific CoM dynamics, especially in individuals with neurological injuries, remains a challenge. Here, we evaluated individual-specific changes in CoM dynamics in unimpaired adults and one individual with post-stroke hemiparesis while walking in shoes-only and with zero-stiffness and high-stiffness passive ankle exoskeletons. To identify optimal sets of physically interpretable mechanisms describing CoM dynamics, termedtemplate signatures, we leveraged hybrid sparse identification of nonlinear dynamics (Hybrid-SINDy), an equation-free data-driven method for inferring sparse hybrid dynamics from a library of candidate functional forms. In unimpaired adults, Hybrid-SINDy automatically identified spring-loaded inverted pendulum-like template signatures, which did not change with exoskeletons (p > 0.16), except for small changes in leg resting length (p < 0.001). Conversely, post-stroke paretic-leg rotary stiffness mechanisms increased by 37–50% with zero-stiffness exoskeletons. While unimpaired CoM dynamics appear robust to passive ankle exoskeletons, how neurological injuries alter exoskeleton impacts on CoM dynamics merits further investigation. Our findings support Hybrid-SINDy’s potential to discover mechanisms describing individual-specific CoM dynamics with assistive devices.
Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption
Authors: Verstraeten Sophie , Layec Séverine , Auger Sandrine , Juste Catherine , Henry Céline , Charif Sawiya , Jaszczyszyn Yan , Sokol Harry , Beney Laurent , Langella Philippe , Thomas Muriel , Huillet Eugénie
Published: January 2024

The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium’s gene expression strategies. Here, we investigated the effect of acetate on temporal changes in the transcriptome of F. duncaniae A2-165 cultures using RNA sequencing. We compared gene expression patterns between two growth phases (early stationary vs. late exponential) and two acetate levels (low: 3 mM vs. high: 23 mM). Only in low-acetate conditions, a general stress response was activated. In high-acetate conditions, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. Specifically, expression was strongly activated in the case of the feoAABC operon, which encodes a FeoB ferrous iron transporter, but not in the case of the feoAB gene, which encodes a second putative FeoAB transporter. Moreover, excess ferrous iron repressed feoB expression but not feoAB. Lastly, FeoB but not FeoAB peptides from strain A2-165 were found in abundance in a healthy human fecal metaproteome. In conclusion, we characterized two early-stationary transcriptomes based on acetate consumption and this work highlights the regulation of feoB expression in F. duncaniae A2-165.
Targeting the dermis for melasma maintenance treatment
Authors: Han Hee Jeong , Kim Jin Cheol , Park Young Joon , Kang Hee Young
Published: January 2024

Melasma relapse is almost common after discontinuation of conventional treatment. Recent studies suggesting that photoaging dermis is the main pathomechanism of melasma, emphasize the dermal targeting therapy. We investigated maintenance effect of microneedling radiofrequency (RF) for melasma treatment. Subjects with melasma were administered oral tranexamic acid and triple combination cream for 2 months and a randomly assigned half face was treated with RF. After discontinuation of conventional therapy, the half face RF continued monthly over 6 months. Modified melasma area severity index (mMASI) score and L* value by a chromameter were collected monthly. Fifteen subjects were enrolled and eleven completed the 8-month study. At 2nd month of conventional therapy, all subjects showed improvement with a 64% reduction in mMASI score. With continuous RF treatment, the improvement was well maintained; whereas in untreated side, the Δ L* gradually decreased, returning to the baseline after the conventional therapy ended. The continuous microneedling RF therapy is beneficial in maintaining the conventional therapy of melasma suggesting the protective effect of dermal targeting therapy in melasma development.

(Clinical Trial registration number: NCT05710068, date of first registration: 02/02/2023).