bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-scale assembly of the wild cereal relative Elymus sibiricus
Authors: Shen Wenjie , Liu Bo , Guo Jialei , Yang Ying , Li Xiaohui , Chen Jie , Dou Quanwen 
Published: July 2024

AbstractElymus species, belonging to Triticeae tribe, is a tertiary gene pool for improvement of major cereal crops. Elymus sibiricus, a tetraploid with StH genome, is a typical species in the genus Elymus, which is widely utilized as a high-quality perennial forage grass in template regions. In this study, we report the construction of a chromosome-scale reference assembly of E. sibiricus line Gaomu No. 1 based on PacBio HiFi reads and chromosome conformation capture. Subgenome St and H were well phased by assisting with kmer and subgenome-specific repetitive sequence. The total assembly size was 6.929 Gb with a contig N50 of 49.518 Mb. In total, 89,800 protein-coding genes were predicted. The repetitive sequences accounted for 82.49% of the genome in E. sibiricus. Comparative genome analysis confirmed a major species-specific 4H/6H reciprocal translocation in E. sibiricus. The E. sibiricus assembly will be much helpful to exploit genetic resource of StH species in genus Elymus, and provides an important tool for E. sibiricus domestication.
Geoid Undulation Model as Vertical Reference in Indonesia
Authors: Pahlevi Arisauna , Syafarianty Agustina , Susilo Susilo , Lumban-Gaol Yustisi , Putra Widy , Triarahmadhana Bagas , Bramanto Brian , Muntaha Raa , El Fadhila King , Ladivanov Febriananda , Amrossalma Harka , Islam Lukman , Novianto Dwi , Huda Safirotul , Wismadi Tunjung , Efendi Joni , Ramadhan Alkindi , Wijaya Dudy , Prijatna Kosasih , Pramono Gatot 
Published: July 2024

AbstractIndonesia released a new regional geoid model in 2020—the Indonesian Geoid 2020 (INAGEOID2020). It covers the Indonesian region with a spatial resolution of 0.01 × 0.01 degree with the unit in meters. The model was generated through a series of data and computations. Three components of gravity data, i.e., the observed free-air anomaly, the long-wave from the global geoid model, and the short-wave from the terrain model, were employed. The computation was performed using the Remove-Compute-Restore technique with the Fast Fourier Transformation approach. The output was then fitted to the geoid at tide stations by adding a fitting plane to the geoid model. The fitting plane was constructed based on the difference between the geoid model and each tide gauge benchmark. The final geoid model was evaluated by comparing the model with the reference data. Based on quality metrics, the accuracy of INAGEOID2020 varied between 6 cm to 29 cm. Any interested user can use this gridded geoid model to convert geodetic to orthometric heights and vice versa.
Generation of novel lipid metabolism-based signatures to predict prognosis and immunotherapy response for colorectal adenocarcinoma
Authors: Wang Yi , Yao Jun , Zhang Zhe , Wei Luxin , Wang Sheng 
Published: July 2024

AbstractLipid metabolism reprogramming involves in epithelial-mesenchymal transition (EMT), cancer stemness and immune checkpoints (ICs), which influence the metastasis of cancer. This study aimed to generate lipid metabolism-based signatures to predict prognosis, immunotherapy and chemotherapy response for colorectal adenocarcinoma (COAD). Transcriptome data and clinical information of COAD patients were collected from the cancer genome atlas (TCGA) database. The expression of EMT-, stem cell-, and IC-related genes were assessed between COAD and control samples. Modules and genes correlated EMT, ICs and stemness signatures were identified through weighted gene co-expression network analysis (WGCNA). Prognostic signatures were generated and then the distribution of risk genes was evaluated using single-cell RNA sequencing (scRNA-seq) data from GSE132465 dataset. COAD patients exhibited increased EMT score and stemness along with decreased ICs. Next, 12 hub genes (PIK3CG, ALOX5AP, PIK3R5, TNFAIP8L2, DPEP2, PIK3CD, PIK3R6, GGT5, ELOVL4, PTGIS, CYP7B1 and PRKD1) were found within green and yellow modules correlated with EMT, stemness and ICs. Lipid metabolism-based prognostic signatures were generated based on PIK3CG, GGT5 and PTGIS. Patients with high-risk group had poor prognosis, elevated ESTIMATEScore and StromalScore, 100% mutation rate and higher TIDE score. Samples in low-risk group had more immunogenicity on ICIs. Notably, PIK3CG was expressed in B cells, while GGT5 and PTGIS were expressed in stromal cells. This study generates lipid metabolism-based signatures correlated with EMT, stemness and ICs for predicting prognosis of COAD, and provides potential therapeutic targets for immunotherapy in COAD.
Forward head posture associated with reduced cardiorespiratory fitness in psychotic disorders compared to autism spectrum disorder and healthy controls
Authors: van de Meent Ilona , Koomen Lisanne , de Boer Renske , Le Clercq Lonneke , Janssen Dieuwertje , Boute Mikel , Maat Arija , van Dellen Edwin , Cahn Wiepke 
Published: July 2024

AbstractIndividuals with psychotic disorders often lead sedentary lives, heightening the risk of developing forward head posture. Forward head posture affects upper cervical vertebrae, raising the likelihood of daily discomforts like skeletal misalignment, neck pain, and reduced cardiorespiratory fitness. Improving cardiorespiratory fitness in psychotic disorders is relevant, given its proven benefits in enhancing physical and mental health. This study investigates forward head posture by measuring craniovertebral angles in psychotic disorders and the relationship with reduced cardiorespiratory fitness. To determine whether forward head posture is specific to psychotic disorders, we also included individuals with autism spectrum disorder and healthy controls. Among 85 participants (32 psychotic disorders, 26 autism spectrum disorder, 27 healthy controls), photogrammetric quantification revealed a significantly lower mean craniocervical angle in psychotic disorders compared to autism spectrum disorder (p =  < 0.02) and the healthy control group (p =  < 0.01). Reduced craniovertebral angle is related to diminished cardiorespiratory fitness in psychosis (R2 = 0.45, p =  < 0.01) but not in other control groups. This study found reduced craniovertebral angles, indicating forward head posture in psychotic disorders. Moreover, this relates to diminished cardiorespiratory fitness. Further research is needed to examine the underlying causes and to investigate whether this can be reversed through physical therapy.
Radiology and multi-scale data integration for precision oncology
Authors: Paverd Hania , Zormpas-Petridis Konstantinos , Clayton Hannah , Burge Sarah , Crispin-Ortuzar Mireia 
Published: July 2024

AbstractIn this Perspective paper we explore the potential of integrating radiological imaging with other data types, a critical yet underdeveloped area in comparison to the fusion of other multi-omic data. Radiological images provide a comprehensive, three-dimensional view of cancer, capturing features that would be missed by biopsies or other data modalities. This paper explores the complexities and challenges of incorporating medical imaging into data integration models, in the context of precision oncology. We present the different categories of imaging-omics integration and discuss recent progress, highlighting the opportunities that arise from bringing together spatial data on different scales.
Estimation of ventilatory thresholds during exercise using respiratory wearable sensors
Authors: Contreras-Briceño Felipe , Cancino Jorge , Espinosa-Ramírez Maximiliano , Fernández Gonzalo , Johnson Vader , Hurtado Daniel E. 
Published: July 2024

AbstractVentilatory thresholds (VTs) are key physiological parameters used to evaluate physical performance and determine aerobic and anaerobic transitions during exercise. Current assessment of these parameters requires ergospirometry, limiting evaluation to laboratory or clinical settings. In this work, we introduce a wearable respiratory system that continuously tracks breathing during exercise and estimates VTs during ramp tests. We validate the respiratory rate and VTs predictions in 17 healthy adults using ergospirometry analysis. In addition, we use the wearable system to evaluate VTs in 107 recreational athletes during ramp tests outside the laboratory and show that the mean population values agree with physiological variables traditionally used to exercise prescription. We envision that respiratory wearables can be useful in determining aerobic and anaerobic parameters with promising applications in health telemonitoring and human performance.
Mechanistic insight into benzylidene-directed glycosylation reactions using cryogenic infrared spectroscopy
Authors: Chang Chun-Wei , Greis Kim , Prabhu Gurpur Rakesh D. , Wehner Dana , Kirschbaum Carla , Ober Katja , Torres-Boy América Y. , Leichnitz Sabrina , Meijer Gerard , von Helden Gert , Seeberger Peter H. , Pagel Kevin 
Published: July 2024

AbstractThe stereoselective formation of 1,2-cis glycosidic linkages is challenging. The currently most widely used strategy for their installation uses 4,6-O-benzylidene-protected building blocks. The stereoselectivity of this reaction is thought to be driven by a covalent intermediate, which reacts via an SN2 mechanism. However, the role of cationic SN1-type intermediates in this reaction is unclear. Here we elucidate the structure of glycosyl cations carrying 4,6-O-benzylidene groups using cryogenic infrared ion spectroscopy and computational methods. The data reveal that the intermediates form anhydro cations, which correlates well with the stereoselective outcome of SN1-type glycosylations. The study highlights how cryogenic infrared spectroscopy can elucidate the role of intermediates in sugar chemistry and how these structural data can be linked to reactions in solution.
Oblique spin injection to graphene via geometry controlled magnetic nanowires
Authors: Toscano-Figueroa Jesus C. , Burrow Daniel , Guarochico-Moreira Victor H. , Xie Chengkun , Thomson Thomas , Grigorieva Irina V. , Vera-Marun Ivan J. 
Published: July 2024

AbstractWe exploit the geometry of magnetic nanowires, which define 1D contacts to an encapsulated graphene channel, to introduce an out-of-plane component in the polarisation of spin carriers. By design, the magnetic nanowires traverse the angled sides of the 2D material heterostructure. Consequently, the easy axis of the nanowires is inclined, and so the local magnetisation is oblique at the injection point. As a result, when performing non-local spin valve measurements we simultaneously observe both switching and spin precession phenomena, implying the spin population possesses both in-plane and out-of-plane polarisation components. By comparing the relative magnitudes of these components, we quantify the angle of the total spin polarisation vector. The extracted angle is consistent with the angle of the nanowire at the graphene interface, evidencing that the effect is a consequence of the device geometry. This simple method of spin-based vector magnetometry provides an alternative technique to define the spin polarisation in 2D spintronic devices.
Mucosal IFNλ1 mRNA-based immunomodulation effectively reduces SARS-CoV-2 induced mortality in mice
Authors: Macht Anna , Huang Yiqi , Reinert Line S , Grass Vincent , Lohmer Kristin , Aristizabal Prada Elke Tatjana , Babel Eveline , Semmler Alexandra , Zhang Wen , Wegner Andrea , Lichtenegger-Hartl Eva , Haas Sonja , Hasenpusch Günther , Meyer Steffen , Paludan Søren R , Pichlmair Andreas , Rudolph Carsten , Langenickel Thomas 
Published: July 2024

AbstractRNA vaccines elicit protective immunity against SARS-CoV-2, but the use of mRNA as an antiviral immunotherapeutic is unexplored. Here, we investigate the activity of lipidoid nanoparticle (LNP)-formulated mRNA encoding human IFNλ1 (ETH47), which is a critical driver of innate immunity at mucosal surfaces protecting from viral infections. IFNλ1 mRNA administration promotes dose-dependent protein translation, induction of interferon-stimulated genes without relevant signs of unspecific immune stimulation, and dose-dependent inhibition of SARS-CoV-2 replication in vitro. Pulmonary administration of IFNλ1 mRNA in mice results in a potent reduction of virus load, virus-induced body weight loss and significantly increased survival. These data support the development of inhaled administration of IFNλ1 mRNA as a potential prophylactic option for individuals exposed to SARS-CoV-2 or at risk suffering from COVID-19. Based on the broad antiviral activity of IFNλ1 regardless of virus or variant, this approach might also be utilized for other respiratory viral infections or pandemic preparedness.
Dantrolene corrects cellular disease features of Darier disease and may be a novel treatment
Authors: Hunt Matthew , Wang Nuoqi , Pupinyo Naricha , Curman Philip , Torres Monica , Jebril William , Chatzinikolaou Maria , Lorent Julie , Silberberg Gilad , Bansal Ritu , Burner Teresa , Zhou Jing , Kimeswenger Susanne , Hoetzenecker Wolfram , Choate Keith , Bachar-Wikstrom Etty , Wikstrom Jakob D 
Published: July 2024

AbstractDarier disease (DD) is a rare severe acantholytic skin disease caused by mutations in the ATP2A2 gene that encodes for the sarco/endoplasmic reticulum calcium ATPase isoform 2 (SERCA2). SERCA2 maintains endoplasmic reticulum calcium homeostasis by pumping calcium into the ER, critical for regulating cellular calcium dynamics and cellular function. To date, there is no treatment that specifically targets the disease mechanisms in DD. Dantrolene sodium (Dl) is a ryanodine receptor antagonist that inhibits calcium release from ER to increase ER calcium levels and is currently used for non-dermatological indications. In this study, we first identified dysregulated genes and molecular pathways in DD patient skin, demonstrating downregulation of cell adhesion and calcium homeostasis pathways, as well as upregulation of ER stress and apoptosis. We then show in various in vitro models of DD and SERCA2 inhibition that Dl aided in the retention of ER calcium and promoted cell adhesion. In addition, Dl treatment reduced ER stress and suppressed apoptosis. Our findings suggest that Dl specifically targets pathogenic mechanisms of DD and may be a potential treatment.
The Emergence of Verb Patterns in Arabic in Children With Developmental Language Disorder Compared to Children With Typical Development
Authors: Tallas-Mahajna Naila , Armon-Lotem Sharon , Saiegh-Haddad Elinor 
Published: July 2024

Purpose:

The Arabic verb system features a nonlinear root and pattern derivational morphology. Previous studies suggest that young Arabic and Hebrew speakers' early verb use is based on semantic complexity rather than derivational morphological structure. The present study examines the role of morphological and semantic complexity in the emergence of the verb
derivational
morphology in Arabic speaking children with developmental language disorder (DLD) compared to children with typical language development (TLD).

Method:
Natural language data were collected from native Arabic-speaking children (40 with DLD; aged 4–6 years and 133 with TLD aged 2;6–6;0 [years;months]) using picture-based elicitation tasks, and verbs were coded morphologically for derivational features and for features of semantic complexity.

Results:
The results showed that children with DLD demonstrated a more limited production of verb patterns, both in types and in tokens, than age-matched children with TLD. Also, children with DLD age 5;0–6;0 were similar in types and tokens of verb patterns to younger children with TLD at the age of 3;6–4 years. Moreover, while children with TLD at the age of 2;6–3 years used a smaller number of verb patterns than older 4;0–5;0 aged children with DLD, the two groups were not different in verb semantics. Finally, the morphological and semantic diversity demonstrated by the children with DLD was similar to the morphological and semantic diversity shown by children with TLD.

Conclusion:
Our findings support the conclusion that children with DLD and with TLD acquire the derivational verb system in the same pathway and the quantitative lexical differences between the two groups support a delay rather than a deviation from the typical developmental trajectory.
Two‐stage algorithm for traffic signal optimization and web‐service system development
Authors: Lee Seungyeop , Eom Myungeun , Kim Byung‐In 
Published: July 2024

AbstractEfficient control of traffic signals for vehicles and pedestrians at intersections is critical for relieving traffic congestion. Considering the unique characteristics of intersections, such as the number of roads, the presence or absence of crosswalks, road geometric shapes, and traffic demand patterns, an appropriate phase sequence and duration for traffic signals must be established at each intersection. This paper proposes a simulation‐based two‐stage algorithm comprising integer‐constrained Adam (ICA) and tabu search (TS) to optimize the phase sequence and duration for arbitrary intersections with arbitrary traffic‐demand patterns. The ICA promptly identifies a promising region in which a global optimal solution is likely to be obtained, whereas TS determines the best solution near the region. The performance of the proposed algorithm that optimizes phase durations with fixed phase sequence is evaluated against several baseline methods using 24 instances across six actual intersections. Experimental results show that the proposed algorithm reduces the average travel time by 20.2% compared with existing traffic signals within a computation time of 4 min, thus providing a near‐optimal solution eight times faster than commonly used population‐based metaheuristics. Furthermore, the algorithm demonstrates robust performance across heterogeneous vehicles and recommends the best phase sequence that effectively alleviates congestion in current traffic signal systems. The optimized phase sequence with best phase durations further reduces the average travel time by approximately 11.3% compared with the existing phase sequence with best phase durations at an actual intersection. To facilitate its widespread use, a free, open web‐service system named “Smart Intersection for Traffic Efficiency” is developed, which enables users to optimize traffic signal systems without requiring optimization background or simulation knowledge.
Asymmetries in asymptotic giant branch stars and their winds
Authors: Wiegert Joachim , Freytag Bernd , Höfner Susanne 
Published: July 2024

Context. Asymptotic giant branch (AGB) stars are significant contributors to the metal enrichment of the interstellar medium. They have strong dust-driven winds that have their origin in regions close to the AGB star’s surface, where dense dust clouds form.
Aims. In this methods paper, we adapted models from advanced radiation-hydrodynamical (RHD) simulations as input for radiative transfer software to create synthetic observables. A major goal is to describe an AGB star’s non-sphericity and to simulate its effects on the surrounding dusty envelope.
Methods. We developed tools in Python to translate models of an AGB star and its dust-driven wind from 3D RHD simulations with CO5BOLD into the format used for radiative transfer with RADMC-3D. We preserved the asymmetric shape of the AGB star by including the star as a ‘dust species’ and by using temperature data computed in CO5BOLD. The circumstellar silicate dust from the 3D RHD simulation is included using Mg2SiO4 opacity data in RADMC-3D with spatially dependent grain sizes. We compared images and spectral energy distributions (SEDs) created with RADMC-3D of a model snapshot with similar output made with a spherically symmetric stellar atmosphere from the 1D program DARWIN and with a point source star in RADMC-3D.
Results. Our CO5BOLD model features substantial and clumpy dust formation just above 3.4 au from the grid centre (∼1 R⋆ above the star), and large-scale structures due to giant convection cells are visible on the stellar surface. With the properties of VLTI as a basis, we have created simple synthetic observables where the dust clouds close to the star and features on the stellar surface are resolved. The flux density and the contrast to the star are high enough that optical interferometers, such as the VLTI, should be able to detect these dust clouds. We find that it is important to include asymmetric stellar models since their irregular shapes, radiation fields, and their dusty envelopes even put their marks on spatially unresolved observables and affect the flux levels and shapes of the SEDs. The effects on flux levels can mostly be linked to the clumpiness of the circumstellar dust. In contrast, the angle-dependent illumination resulting from temperature variations on the stellar surface causes shifts in the wavelengths of the flux maximum, as shown by replacing the asymmetric star with a spherical one.
Conclusions. The methods presented here are an important step towards producing realistic synthetic observables and testing predictions of advanced 3D RHD models. With the model used here, we find that optical interferometers should be able to resolve thermal emission from dense clouds in the dust-formation zone close to an AGB star. Taking the angle-dependence of SEDs as a proxy for temporal variations in unresolved data, we conclude that not all variability observed in AGB stars should be interpreted as global changes in the sense of spherical models.