bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of SEC61A1 mutant R236C in two patient-derived cellular platforms
Authors: Weiand Matthias , Sandfort Vanessa , Nadzemova Oksana , Schierwagen Robert , Trebicka Jonel , Schlevogt Bernhard , Kabar Iyad , Schmidt Hartmut , Zibert Andree 
Published: April 2024

AbstractSEC61A1 encodes a central protein of the mammalian translocon and dysfunction results in severe disease. Recently, mutation R236C was identified in patients having autosomal dominant polycystic liver disease (ADPLD). The molecular phenotype of R236C was assessed in two cellular platforms. Cells were immortalized by retroviral transduction of an oncogene (UCi) or reprogrammed to induced pluripotent stem cells (iPSC) that were differentiated to cholangiocyte progenitor-like cells (CPLC). UCi and CPLC were subjected to analyses of molecular pathways that were associated with development of disease. UCi displayed markers of epithelial cells, while CPLCs expressed typical markers of both cholangiocytes and hepatocytes. Cells encoding R236C showed a stable, continuous proliferation in both platforms, however growth rates were reduced as compared to wildtype control. Autophagy, cAMP synthesis, and secretion of important marker proteins were reduced in R236C-expressing cells. In addition, R236C induced increased calcium leakiness from the ER to the cytoplasm. Upon oxidative stress, R236C led to a high induction of apoptosis and necrosis. Although the grade of aberrant cellular functions differed between the two platforms, the molecular phenotype of R236C was shared suggesting that the mutation, regardless of the cell type, has a dominant impact on disease-associated pathways.
Gingival proteomics reveals the role of TGF beta and YAP/TAZ signaling in Raine syndrome fibrosis
Authors: Costa Cláudio Rodrigues Rezende , Chalgoumi Rym , Baker Amina , Guillou Clément , Yamaguti Paulo Marcio , Simancas Escorcia Victor , Abbad Lilia , Amorin Bruna Rabelo , de Lima Caroline Lourenço , Cannaya Vidjea , Benassarou Mourad , Berdal Ariane , Chatziantoniou Christos , Cases Olivier , Cosette Pascal , Kozyraki Renata , Acevedo Ana Carolina 
Published: April 2024

AbstractRaine syndrome (RNS) is a rare autosomal recessive osteosclerotic dysplasia. RNS is caused by loss-of-function disease-causative variants of the FAM20C gene that encodes a kinase that phosphorylates most of the secreted proteins found in the body fluids and extracellular matrix. The most common RNS clinical features are generalized osteosclerosis, facial dysmorphism, intracerebral calcifications and respiratory defects. In non-lethal RNS forms, oral traits include a well-studied hypoplastic amelogenesis imperfecta (AI) and a much less characterized gingival phenotype. We used immunomorphological, biochemical, and siRNA approaches to analyze gingival tissues and primary cultures of gingival fibroblasts of two unrelated, previously reported RNS patients. We showed that fibrosis, pathological gingival calcifications and increased expression of various profibrotic and pro-osteogenic proteins such as POSTN, SPARC and VIM were common findings. Proteomic analysis of differentially expressed proteins demonstrated that proteins involved in extracellular matrix (ECM) regulation and related to the TGFβ/SMAD signaling pathway were increased. Functional analyses confirmed the upregulation of TGFβ/SMAD signaling and subsequently uncovered the involvement of two closely related transcription cofactors important in fibrogenesis, Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). Knocking down of FAM20C confirmed the TGFβ-YAP/TAZ interplay indicating that a profibrotic loop enabled gingival fibrosis in RNS patients. In summary, our in vivo and in vitro data provide a detailed description of the RNS gingival phenotype. They show that gingival fibrosis and calcifications are associated with, and most likely caused by excessed ECM production and disorganization. They furthermore uncover the contribution of increased TGFβ–YAP/TAZ signaling in the pathogenesis of the gingival fibrosis.
The role of mood and arousal in the effect of background music on attentional state and performance during a sustained attention task
Authors: Kiss Luca , Linnell Karina J. 
Published: April 2024

AbstractAcross two online experiments, this study explored the effect of preferred background music on attentional state and performance, as well as on mood and arousal, during a vigilance task. It extended recent laboratory findings—showing an increase in task-focus and decrease in mind-wandering states with music—to environments with more distractions around participants. Participants—people who normally listen to background music during attention-demanding tasks—completed the vigilance task in their homes both with and without their chosen music and reported their attentional state, subjective arousal, and mood valence throughout the task. Experiment 1 compared music to relative silence and Experiment 2 compared music against the backdrop of continuous noise to continuous noise alone. In both experiments, music decreased mind-wandering and increased task-focus. Unlike in previous laboratory studies, in both experiments music also led to faster reaction times while increasing low-arousal external-distraction states. Importantly, mood and arousal increased with music and were shown to mediate its effects on reaction time and for the first time attentional state, both separately and together. Serial mediation effects were mostly confined to models where mood was entered first and arousal second and were consistent with the mood-arousal account of the impact of background music listening.
Development and validation of AI/ML derived splice-switching oligonucleotides
Authors: Fronk Alyssa D , Manzanares Miguel A , Zheng Paulina , Geier Adam , Anderson Kendall , Stanton Shaleigh , Zumrut Hasan , Gera Sakshi , Munch Robin , Frederick Vanessa , Dhingra Priyanka , Arun Gayatri , Akerman Martin 
Published: April 2024

AbstractSplice-switching oligonucleotides (SSOs) are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of functional, verifiable, and therapeutic SSOs. We trained XGboost tree models using splicing factor (SF) pre-mRNA binding profiles and spliceosome assembly information to identify modulatory SSO binding sites on pre-mRNA. Using Shapley and out-of-bag analyses we also predicted the identity of specific SFs whose binding to pre-mRNA is blocked by SSOs. This step adds considerable transparency to AI/ML-driven drug discovery and informs biological insights useful in further validation steps. We applied this approach to previously established functional SSOs to retrospectively identify the SFs likely to regulate those events. We then took a prospective validation approach using a novel target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13). Targeting NEDD4Le13 with an AI/ML-designed SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGFβ pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data.
Insights into a surface-modified Li(Ni0.80Co0.15Al0.05)O2 cathode by atomic layer fluorination for improved cycling behaviour
Authors: Charles-Blin Youn , Hatim Oumaima , Clarac Mélissa , Perbost Anne-Marie , Liminana Solveine , Lopez Laura , Gimello Olinda , Guérin Katia , Dubois Marc , Deschamps Michael , Flahaut Delphine , Martinez Hervé , Monconduit Laure , Louvain Nicolas 
Published: April 2024

Atomic layer fluorination of Li(Ni0.80Co0.15Al0.05)O2 leads to improved charge/discharge cyclability in Li-ion cells and limited electrolyte decomposition.
A short-term rodent model for non-alcoholic steatohepatitis induced by a high-fat diet and carbon tetrachloride
Authors: Araujo Layanne C.C. , Dias Carolina C.B. , Sucupira Felipe G. , Ramalho Leandra N.Z. , Camporez João Paulo 
Published: April 2024

Abstract
Several models of mice-fed high-fat diets have been used to trigger non-alcoholic steatohepatitis and some chemical substances, such as carbon tetrachloride. The present study aimed to evaluate the joint action of a high-fat diet and CCl4 in developing a short-term non-alcoholic steatohepatitis model. C57BL6/J mice were divided into two groups: standard diet-fed (SD), the high-fat diet-fed (HFD) and HFD + fructose-fed and carbon tetrachloride (HFD+CCl4). The animals fed with HFD+CCl4 presented increased lipid deposition compared with both SD and HFD mice. Plasma cholesterol was increased in animals from the HFD+CCl4 group compared with the SD and HFD groups, without significant differences between the SD and HFD groups. Plasma triglycerides showed no significant difference between the groups. The HFD+CCl4 animals had increased collagen deposition in the liver compared with both SD and HFD groups. Hydroxyproline was also increased in the HFD+CCl4 group. Liver enzymes, alanine aminotransferase and aspartate aminotransferase, were increased in the HFD+CCl4 group, compared with SD and HFD groups. Also, CCl4 was able to trigger an inflammatory process in the liver of HFD-fed animals by promoting an increase of ∼2 times in macrophage activity, ∼6 times in F4/80 gene expression, and pro-inflammatory cytokines (IL-1b and TNFa), in addition to an increase in inflammatory pathway protein phosphorylation (IKKbp). HFD e HFD+CCl4 animals increased glucose intolerance compared with SD mice, associated with reduced insulin-stimulated AKT activity in the liver. Therefore, our study has shown that short-term HFD feeding associated with fructose and CCl4 can trigger non-alcoholic steatohepatitis and cause damage to glucose metabolism.
Understanding and computational design of genetic circuits of metabolic networks
Authors: Berkvens Alicia , Salinas Luis , Remeijer Maaike , Planqué Robert , Teusink Bas , Bruggeman Frank J. 
Published: April 2024

AbstractThe expression of metabolic proteins is controlled by genetic circuits, matching metabolic demands and changing environmental conditions. Ideally, this regulation brings about a competitive level of metabolic fitness. Understanding how cells can achieve a robust (close-to-optimal) functioning of metabolism by appropriate control of gene expression aids synthetic biology by providing design criteria of synthetic circuits for biotechnological purposes. It also extends our understanding of the designs of genetic circuitry found in nature such as metabolite control of transcription factor activity, promoter architectures and transcription factor dependencies, and operon composition (in bacteria). Here, we review, explain and illustrate an approach that allows for the inference and design of genetic circuitry that steers metabolic networks to achieve a maximal flux per unit invested protein across dynamic conditions. We discuss how this approach and its understanding can be used to rationalize Escherichia coli’s strategy to regulate the expression of its ribosomes and infer the design of circuitry controlling gene expression of amino-acid biosynthesis enzymes. The inferred regulation indeed resembles E. coli’s circuits, suggesting that these have evolved to maximize amino-acid production fluxes per unit invested protein. We end by an outlook of the use of this approach in metabolic engineering applications.
Ultrasound-Guided Modified Thread Carpal Tunnel Release for Carpal Tunnel Syndrome: A Pilot Study
Authors: Kim Jaewon , Kim Jae Min , Park Hae-Yeon , Kim In Jong 
Published: April 2024

Abstract
Purpose This study aimed to investigate the effectiveness and safety of modified thread carpal tunnel release (mTCTR) using Smartwire-01 in patients with carpal tunnel syndrome (CTS).
Materials and Methods Patients with CTS who required CTR were enrolled. Symptom severity and functional status were assessed using the Boston Carpal Tunnel Syndrome Questionnaire-Symptom Severity Scale (BCTQ-SSS) and Functional Status Scale (BCTQ-FSS), and pain was assessed using a numerical rating scale (NRS) at 4, 8, and 12 weeks after mTCTR. The scores were compared with the pre-procedural scores. The electrophysiologic study and median nerve cross-sectional area (CSA) measurements at the wrist before and 12 weeks after mTCTR were compared.
Results A total of 11 patients were included. No adverse effects were reported throughout the study period. The NRS, BCTQ-SSS, and BCTQ-FSS scores significantly improved at 4 weeks after mTCTR, and this improvement persisted throughout the follow-up period (NRS and BCTQ-SSS, P < 0.001; BCTQ-FSS, P = 0.012). After 12 weeks, the latency and velocity of the median sensory nerve action potential significantly improved, compared with those before mTCTR (latency, 5.4 ± 1.3 to 4.7 ± 1.1 ms, P = 0.01; velocity 27.8 ± 6.8 to 31.8 ± 7.4 m/s, P = 0.019). No significant change was observed in the median nerve CSA before and after mTCTR.
Conclusion mTCTR using Smartwire-01 is a safe and effective procedure and a possible alternative to surgery.
Language model-based labeling of German thoracic radiology reports
Authors: Wollek Alessandro , Haitzer Philip , Sedlmeyr Thomas , Hyska Sardi , Rueckel Johannes , Sabel Bastian O. , Ingrisch Michael , Lasser Tobias 
Published: April 2024

AbstractThe aim of this study was to explore the potential of weak supervision in a deep learning-based label prediction model. The goal was to use this model to extract labels from German free-text thoracic radiology reports on chest X-ray images and for training chest X-ray classification models.The proposed label extraction model for German thoracic radiology reports uses a German BERT encoder as a backbone and classifies a report based on the CheXpert labels. For investigating the efficient use of manually annotated data, the model was trained using manual annotations, weak rule-based labels, and both. Rule-based labels were extracted from 66071 retrospectively collected radiology reports from 2017–2021 (DS 0), and 1091 reports from 2020–2021 (DS 1) were manually labeled according to the CheXpert classes. Label extraction performance was evaluated with respect to mention extraction, negation detection, and uncertainty detection by measuring F1 scores. The influence of the label extraction method on chest X-ray classification was evaluated on a pneumothorax data set (DS 2) containing 6434 chest radiographs with associated reports and expert diagnoses of pneumothorax. For this, DenseNet-121 models trained on manual annotations, rule-based and deep learning-based label predictions, and publicly available data were compared.The proposed deep learning-based labeler (DL) performed on average considerably stronger than the rule-based labeler (RB) for all three tasks on DS 1 with F1 scores of 0.938 vs. 0.844 for mention extraction, 0.891 vs. 0.821 for negation detection, and 0.624 vs. 0.518 for uncertainty detection. Pre-training on DS 0 and fine-tuning on DS 1 performed better than only training on either DS 0 or DS 1. Chest X-ray pneumothorax classification results (DS 2) were highest when trained with DL labels with an area under the receiver operating curve (AUC) of 0.939 compared to RB labels with an AUC of 0.858. Training with manual labels performed slightly worse than training with DL labels with an AUC of 0.934. In contrast, training with a public data set resulted in an AUC of 0.720.Our results show that leveraging a rule-based report labeler for weak supervision leads to improved labeling performance. The pneumothorax classification results demonstrate that our proposed deep learning-based labeler can serve as a substitute for manual labeling requiring only 1000 manually annotated reports for training.Wollek A, Haitzer P, Sedlmeyr T et al. Language modelbased labeling of German thoracic radiology reports. Fortschr Röntgenstr 2024; DOI 10.1055/a-2287-5054
Synthesis and Dynamic Behaviors of 5,7,8,10-Tetraphenyl-1,14-dianilinotripyrrins
Authors: Seki Shu , Tanaka Takayuki , Nishiyama Ayane , Matsuo Yusuke 
Published: April 2024

Abstract5,7,8,10-Tetraphenyl-1,14-di(arylamino)tripyrrins have been synthesized via 5,7,8,10-tetraphenyltripyrrane. The structures and dynamic equilibrium between single helical monomer and double helical dimer were analyzed by 1H NMR spectra and X-ray diffraction analysis. Their dimerization association constants in CDCl3 are larger than those of previously reported dianilinotripyrrin derivatives. In DMSO, they exhibited luminescence around 700 nm as a consequence of restricted rotational relaxation by the phenyl groups installed at the 7,8-positions.
Equilibrium structure and shape of Ag and Pt nanoparticles grown on silica surfaces: From experimental investigations to the determination of a metal–silica potential
Authors: Ait Hellal F. , Andreazza-Vignolle C. , Andreazza P. , Puibasset J. 
Published: April 2024

A combination of experimental and numerical investigations on metallic silver and platinum nanoparticles deposited on silica substrates is presented, with a focus on metal–substrate interactions. Experimentally, the nanoparticles, obtained by ultra-high vacuum atom deposition, are characterized by grazing-incidence small-angle x-ray scattering and high resolution transmission electronic microscopy to determine their structure and morphology and, in particular, their aspect ratio (height/diameter), which quantifies the metal–substrate interaction, from the as-grown to equilibrium state. Numerically, the interactions between the metal and the silica species are modeled with the Lennard-Jones (12, 6) potential, with two parameters for each metal and silica species. The geometric parameters were found in the literature, while the energetic parameters were determined from our experimental measurements of the aspect ratio. The parameters are as follows: σAg–O = 0.278 nm, σAg–Si = 0.329 nm, ɛAg–O = 75 meV, and ɛAg–Si = 13 meV for Ag–silica and σPt–O = 0.273 nm, σPt–Si = 0.324 nm, ɛPt–O = 110 meV, and ɛPt–Si = 18 meV for Pt–silica. The proposed Ag–silica potential reproduces quantitatively the unexpected experimental observation of the variation of the aspect ratio for Ag nanoparticles larger than 5 nm, which has been interpreted as a consequence of the silica roughness. The nanoparticle orientation, structure, and disorder are also considered. This metal–silica potential for Ag and Pt should be helpful for further studies on pure metals as well as their alloys.
The performance of OPC and OPC3 water models in predictions of 2D structures under nanoconfinement
Authors: Wei Laiyang , Li Xiaojiao , Bai Qi , Kang Jing , Song Jueying , Zhu Shuang , Shen Lin , Wang Huan , Zhu Chongqin , Fang Weihai 
Published: April 2024

Nanoconfined water plays an important role in broad fields of science and engineering. Classical molecular dynamics (MD) simulations have been widely used to investigate water phases under nanoconfinement. The key ingredient of MD is the force field. In this study, we systematically investigated the performance of a recently introduced family of globally optimal water models, OPC and OPC3, and TIP4P/2005 in describing nanoconfined two-dimensional (2D) water ice. Our studies show that the melting points of the monolayer square ice (MSI) of all three water models are higher than the melting points of the corresponding bulk ice Ih. Under the same conditions, the melting points of MSI of OPC and TIP4P/2005 are the same and are ∼90 K lower than that of the OPC3 water model. In addition, we show that OPC and TIP4P/2005 water models are able to form a bilayer AA-stacked structure and a trilayer AAA-stacked structure, which are not the cases for the OPC3 model. Considering the available experimental data and first-principles simulations, we consider the OPC water model as a potential water model for 2D water ice MD studies.
Formation of a two-dimensional helical square tube ice in hydrophobic nanoslit using the TIP5P water model
Authors: Li Jiaxian , Zhu Chongqin , Zhao Wenhui , Gao Yurui , Bai Jaeil , Jiang Jian , Zeng Xiao Cheng 
Published: April 2024

In extreme and nanoconfinement conditions, the tetrahedral arrangement of water molecules is challenged, resulting in a rich and new phase behavior unseen in bulk phases. The unique phase behavior of water confined in hydrophobic nanoslits has been previously observed, such as the formation of a variety of two-dimensional (2D) ices below the freezing temperature. The primary identified 2D ice phase, termed square tube ice (STI), represents a unique arrangement of water molecules in 2D ice, which can be viewed as an array of 1D ice nanotubes stacked in the direction parallel to the confinement plane. In this study, we report the molecular dynamics (MD) simulations evidence of a novel 2D ice phase, namely, helical square tube ice (H-STI). H-STI is characterized by the stacking of helical ice nanotubes in the direction parallel to the confinement plane. Its structural specificity is evident in the presence of helical square ice nanotubes, a configuration unseen in both STI and single-walled ice nanotubes. A detailed analysis of the hydrogen bonding strength showed that H-STI is a 2D ice phase diverging from the Bernal–Fowler–Pauling ice rules by forming only two strong hydrogen bonds between adjacent molecules along its helical ice chain. This arrangement of strong hydrogen bonds along ice nanotube and weak bonds between the ice nanotube shows a similarity to quasi-one-dimensional van der Waals materials. Ab initio molecular dynamics simulations (over a 30 ps) were employed to further verify H-STI’s stability at 1 GPa and temperature up to 200 K.
Linguistic similarities between Asho Chin and Burmese
Authors: Otsuka Kosei 
Published: April 2024

Abstract
Asho Chin (ISO 639-3: csh), also known as Plains Chin, is a Kuki-Chin language spoken mainly in the southwestern
areas of Myanmar, where Burmese is the dominant language. This paper presents a qualitative linguistic analysis to explore the
similarities between Asho Chin and Burmese. The analysis reveals a significant influence of Burmese on Asho Chin that goes beyond
vocabulary to include grammatical features. Additionally, the study highlights the importance of considering both the temporal and
geographical context of Burmese loanwords in Asho Chin. The findings suggest that Asho Chin is constantly evolving, largely due to
the continued influence of Burmese. This influence is evident in the range of loanwords and linguistic structures in Asho Chin
that appear to have resulted from interaction with Burmese.
Networking in online collaborative translation
Authors: Xu Minhui , Duan Tianze 
Published: April 2024

Abstract
Translation practice on the internet has produced a new mode of translation activity that has significantly
changed the traditional understanding of translation, especially the relationship between different agents. Drawing on Latour’s
Actor-Network Theory (ANT), this study attempts to explore the networking procedure of the translation activity on the website
Wuxia­world of the Chinese martial arts novel Horizon, Bright Moon, Sabre, examining the dynamics of the formation
and function of the network and the roles played by the actors involved. It focuses on the four aspects delineated by ANT: the
confirmation of the scenario, the problematization of content, the enrollment of actors, and the completion of the network. The
findings suggest that the translation practice on Wuxia­world establishes a well-constructed, not a random and unorganized,
network, which attracts loyal fan-readers, enrolls qualified translators, maintains a well-functioning network, and presents a
dynamic structure of immediate interactivity. All these lead to a new and reshaped translator-reader relationship of instant
interaction.