bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel immune-related gene signature for diagnosis and potential immunotherapy of microsatellite stable endometrial carcinoma
Authors: Xiao Yunyun , Yu XiaoChuan , Wang Yaping , Song Guangyao , Liu Ming , Wang Daqing , Wang Huali 
Published: February 2024

AbstractAn immune-related gene signature (IRGS) was established to better understand the molecular and immunologic characteristics of microsatellite instable (MSI) and microsatellite stable (MSS) endometrial carcinoma (EC), and provide potential immunotherapy directions for MSS patients. Top 20 immune-related hub genes were screened by weight gene coexpression network analysis (WGCNA), and an IRGS was further established through Cox regression analysis. The molecular and immune characteristics were clarified in IRGS high and low risk groups. Expression and MS status validation of the IRGS were conducted through quantitative real-time Polymerase Chain Reaction (rt-qPCR) and immunohistochemistry (IHC) analysis. The IRGS includes 2 oncogenes (AGTR1 and HTR3C) and 2 tumor suppressor genes (CD3E and SERPIND1). Patients in IRGS high-risk group were more with MSS status, higher tumor grade, later FIGO stage, serous histology and elder ages compared with IRGS low-risk group (P < 0.05). Besides, patients in MSS group were more FIGO stages II–IV (42.7% vs. 26%), serous histology (35.7% vs. 5.3%) and with higher IRGS risk score (1.51 ± 3.11 vs. 1.02 ± 0.67) (P < 0.05) than patients in MSI group. Furthermore, patients in IRGS high-risk group had higher tumor purity, more Macrophages M1 and Macrophages M2 infiltrating, higher proportion of Macrophages M2 and Dendritic cells activated, lower proportion of T cells regulatory (Tregs), lower tumor mutation burden (TMB). Correspondingly, subjects in IRGS low-risk group had higher immunphenoscores than IRGS high-risk group. The relative mRNA level of AGTR1 and HTR3C were gradually increase, while CD3E and SERPIND1 were reversed in rt-qPCR. Through IHC experiments, AGTR1(69.2% vs 30%, P = 0.074) and HTR3C (76.9% vs 30%, P = 0.024) had higher positive staining rates in ECs than non-ECs. While SERPIND1 (84.6% vs 20%, P = 0.003) and CD3E (61.5% vs 40%, P = 0.000) had higher positive staining rates in non-ECs. IRGS is a potential diagnostic and prognostic biomarker for EC. IRGS low risk group might benefit from immune checkpoint inhibitors, while IRGS high risk group deserve other potential immunotherapy.
Child–Pugh grade deterioration stratified by the etiology after transcatheter arterial chemoembolization as initial treatment for hepatocellular carcinoma
Authors: Yoshitomi Kengo , Hayashi Tsuguru , Oe Shinji , Shibata Michihiko , Honma Yuichi , Harada Masaru , Kooka Yohei 
Published: February 2024

AbstractTranscatheter arterial chemoembolization (TACE) is a standard treatment for intermediate-stage hepatocellular carcinoma (HCC). However, TACE can cause deterioration of liver functions. We aimed to identify the factors that influence deterioration of liver function after TACE. We retrospectively analyzed 262 patients who underwent TACE as initial treatment for HCC with Child–Pugh grade A. We divided them into three groups stratified by the etiology of underlying liver disease. Patients were classified into hepatitis B virus (HBV) group, hepatitis C virus (HCV) group, and non-HBV / non-HCV (NBNC) group. Liver functions at one month after TACE and time to Child–Pugh grade B or C were compared between the three groups. The HBV, HCV and NBNC groups contained 23, 123 and 116 patients, respectively. The decline in albumin level after TACE was significantly higher in NBNC group than other groups (p = 0.02). NBNC group showed a shorter time to Child–Pugh grade deterioration compared with HBV group and HCV group (p < 0.001). Multivariate Cox regression analysis showed that NBNC group was a significant factor for Child–Pugh grade deterioration (Hazard ratio 3.74, 95% confidence interval 1.89–7.40, p < 0.001). These results revealed that liver functions worsened most remarkably in NBNC group after TACE.
Dietary acid load and cirrhosis-related mortality: a prospective cohort study
Authors: Pashayee-Khamene Fereshteh , Heidari Zeinab , Fotros Danial , Hekmatdoost Azita , Karimi Sara , Ahmadzadeh Saleheh , Saberifiroozi Mehdi , Hatami Behzad , Yari Zahra 
Published: February 2024

AbstractAs a global health concern, cirrhosis contributes significantly to morbidity and mortality. This prospective cohort study aimed to investigate the association between dietary acid load (DAL) and cirrhosis-related mortality. Present study was conducted on 121 patients with newly diagnosed cirrhosis who were followed up for 48 months. Anthropometric measures, nutritional status and dietary intakes were assessed and DAL was estimated based on potential renal acid load (PRAL) and net endogenous acid production (NEAP) scores. Crude and multivariable-adjusted hazard ratios (HR) with 95% confidence intervals (CI) were estimated using Cox proportional hazard analyses. Participants in the high PRAL and NEAP scores had significantly higher intakes of grains and lower intakes of fruits and vegetables. Also, the intake of dairy products and legumes, nuts and seeds decreased significantly with increasing NEAP score. After adjustment of all the confounders, the risk of mortality in the second and third tertiles of PRAL was 5.9 times and 10.97 higher than those in the first tertile, respectively (P trend: 0.006). Similarly, comparing the risk of mortality in the second and third tertiles with the first tertile of NEAP showed a 4.46-fold and 12.3-fold increased risk, respectively (P trend: 0.010). Our findings suggested that DAL was significantly associated with cirrhosis-related mortality and highlight the need for further research to understand the underlying mechanisms and establish optimal DAL levels in cirrhotic patients.
Neutrophil-to-lymphocyte ratio is associated with sarcopenia risk in overweight maintenance hemodialysis patients
Authors: Nie Huibin , Liu Yan , Zeng Xiaoyan , Chen Min 
Published: February 2024

AbstractNeutrophil-to-lymphocyte ratio (NLR), a novel inflammatory marker, is strongly associated with the risk of sarcopenia. Notably, being overweight has been found to accelerate the loss of skeletal muscle mass and function in chronic kidney disease (CKD) patients. However, the effect of overweight status on the relationship between NLR and sarcopenia risk has been poorly studied. We conducted a cross-sectional study at a hemodialysis center in Chengdu, China, from September to December 2022. The prevalence of sarcopenia was determined according to the Asian Working Group for Sarcopenia (AWGS). Participants were stratified based on body mass index (BMI) categories for the Asian population (non-overweight < 23 kg/m2 and overweight ≥ 23 kg/m2). 272 participants aged 18–85 years were included, with 144 being male. The overall prevalence of sarcopenia was 32.72% (89/272). After adjusting for covariates, NLR was significantly associated with sarcopenia risk in overweight participants (OR 1.60, 95% CI 1.15–2.24, p = 0.006), whereas it was not significant in the non-overweight group (OR 0.88, 95% CI 0.70–1.10, p = 0.254). Moreover, subgroup analysis showed a significant interactive association between NLR and overweight status with respect to sarcopenia. These findings emphasize the potential significance of regular screening of NLR for the early detection of sarcopenia in overweight patients undergoing maintenance hemodialysis.
Pathway for a martensitic quartz–coesite transition
Authors: Schaffrinna Tim , Milman Victor , Winkler Björn 
Published: February 2024

AbstractAn atomistic pathway for a strain-induced subsolidus martensitic transition between quartz and coesite was found by computing the set of the smallest atomic displacements required to transform a quartz structure into a coesite structure. A minimal transformation cell with 24 $${\hbox {SiO}_{2}}$$

SiO
2

formula units is sufficient to describe the diffusionless martensitic transition from quartz to coesite. We identified two families of invariant shear planes during the martensitic transition, near the {10$${\bar{1}}$$

1

¯

1} and {12$${\bar{3}}$$

3

¯

2} set of planes, in agreement with the orientation of planar defect structures observed in quartz samples which experienced hypervelocity impacts. We calculated the reaction barrier using density functional theory and found that the barrier of 150 meV/atom is pressure invariant from ambient pressure up to 5 GPa, while the mean principal stress limiting the stability of strained quartz is $$\approx$$
≈
2 GPa. The model calculations quantitatively confirm that coesite can be formed in strained quartz at pressures significantly below the hydrostatic equilibrium transition pressure.
Protracted molecular dynamics and secondary structure introspection to identify dual-target inhibitors of Nipah virus exerting approved small molecules repurposing
Authors: Yang Siyun , Kar Supratik 
Published: February 2024

AbstractNipah virus (NiV), with its significantly higher mortality rate compared to COVID-19, presents a looming threat as a potential next pandemic, particularly if constant mutations of NiV increase its transmissibility and transmission. Considering the importance of preventing the facilitation of the virus entry into host cells averting the process of assembly forming the viral envelope, and encapsulating the nucleocapsid, it is crucial to take the Nipah attachment glycoprotein-human ephrin-B2 and matrix protein as dual targets. Repurposing approved small molecules in drug development is a strategic choice, as it leverages molecules with known safety profiles, accelerating the path to finding effective treatments against NiV. The approved small molecules from DrugBank were used for repurposing and were subjected to extra precision docking followed by absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling. The 4 best molecules were selected for 500 ns molecular dynamics (MD) simulation followed by Molecular mechanics with generalized Born and surface area solvation (MM-GBSA). Further, the free energy landscape, the principal component analysis followed by the defined secondary structure of proteins analysis were introspected. The inclusive analysis proposed that Iotrolan (DB09487) and Iodixanol (DB01249) are effective dual inhibitors, while Rutin (DB01698) and Lactitol (DB12942) were found to actively target the matrix protein only.
Spatial and economic quantification of provisioning service by eelgrass beds in Lake Notoro, Hokkaido, Japan
Authors: Ito Keizo , Sonoki Shiori , Minami Kenji , Chiba Susumu , Shirakawa Hokuto , Kawajiri Toshifumi , Zhu Yanhui , Miyashita Kazushi 
Published: February 2024

AbstractEelgrass beds provide a habitat for many high-value fishery resources, and provisioning services, one of the ecosystem services, need to be quantified. However, few examples have been evaluated spatially. We determined the distribution of eelgrass beds in Lake Notoro, a marine lagoon in Hokkaido, Japan, and quantified the provisioning services by the eelgrass beds in relation to Pandalus latirostris, a fishery resource. Acoustic measurement surveys of the eelgrass beds and catch surveys of the shrimp were conducted in July and August 2015. The relationship between catch per unit effort (CPUE) of shrimp and the distribution of eelgrass beds was shown. The estimated distribution area of eelgrass beds was 7.07 km2. Shrimp was frequently caught at water depths of 3–5 m, approximately 200 m from the edge of the eelgrass beds. The expected catch of shrimp in the fishing area of Lake Notoro in 2015 was 25.37 tons and US$ 463.6 thousand. Eelgrass beds were found to affect the fisheries production not only on the inside but also at the edge and outside. The entire coastal space should be evaluated, while considering the effect of the distribution of eelgrass beds, to quantify the provisioning services.
Protein function prediction as approximate semantic entailment
Authors: Kulmanov Maxat , Guzmán-Vega Francisco J. , Duek Roggli Paula , Lane Lydie , Arold Stefan T. , Hoehndorf Robert 
Published: February 2024

AbstractThe Gene Ontology (GO) is a formal, axiomatic theory with over 100,000 axioms that describe the molecular functions, biological processes and cellular locations of proteins in three subontologies. Predicting the functions of proteins using the GO requires both learning and reasoning capabilities in order to maintain consistency and exploit the background knowledge in the GO. Many methods have been developed to automatically predict protein functions, but effectively exploiting all the axioms in the GO for knowledge-enhanced learning has remained a challenge. We have developed DeepGO-SE, a method that predicts GO functions from protein sequences using a pretrained large language model. DeepGO-SE generates multiple approximate models of GO, and a neural network predicts the truth values of statements about protein functions in these approximate models. We aggregate the truth values over multiple models so that DeepGO-SE approximates semantic entailment when predicting protein functions. We show, using several benchmarks, that the approach effectively exploits background knowledge in the GO and improves protein function prediction compared to state-of-the-art methods.
Automatic design of stigmergy-based behaviours for robot swarms
Authors: Salman Muhammad , Garzón Ramos David , Birattari Mauro 
Published: February 2024

AbstractStigmergy is a form of indirect communication and coordination in which individuals influence their peers by modifying the environment in various ways, including rearranging objects in space and releasing chemicals. For example, some ant species lay pheromone trails to efficiently navigate between food sources and nests. Besides being used by social animals, stigmergy has also inspired the development of algorithms for combinatorial optimisation and multi-robot systems. In swarm robotics, collective behaviours based on stigmergy have always been designed manually, which is time consuming, costly, hardly repeatable, and depends on the expertise of the designer. Here, we show that stigmergy-based behaviours can be produced via automatic design: an optimisation process based on simulations generates collective behaviours for a group of robots that can lay and sense artificial pheromones. The results of our experiments indicate that the collective behaviours designed automatically are as good as—and in some cases better than—those produced manually. By taking advantage of pheromone-based stigmergy, the automatic design process generated collective behaviours that exhibit spatial organisation, memory, and communication.
Magnonic combinatorial memory
Authors: Balinskyy Mykhaylo , Khitun Alexander 
Published: February 2024

AbstractIn this work, we consider a type of magnetic memory where information is encoded into the mutual arrangement of magnets. The device is an active ring circuit comprising magnetic and electric parts connected in series. The electric part includes a broadband amplifier, phase shifters, and attenuators. The magnetic part is a mesh of magnonic waveguides with magnets placed on the waveguide junctions. There are amplitude and phase conditions for auto-oscillations to occur in the active ring circuit. The frequency(s) of the auto-oscillation and spin wave propagation path(s) in the magnetic part depends on the mutual arrangement of magnets in the mesh. The propagation path is detected with a set of power sensors. The correlation between circuit parameters and spin wave path is the basis of memory operation. The combination of input/output switches connecting electric and magnetic parts and electric phase shifters constitute the memory address. The output of the power sensors is the memory state. We present experimental data on the proof-of-the-concept experiments on the prototype with three magnets placed on top of a single-crystal yttrium iron garnet Y3Fe2(FeO4)3 (YIG) film. There are three selected places for the magnets to be placed. There is a variety of spin wave propagation paths for each configuration of magnets. The results demonstrate a robust operation with an On/Off ratio for path detection exceeding 35 dB at room temperature. The number of possible magnet arrangements scales factorially with the size of the magnetic part. The number of possible paths per one configuration scales factorial as well. It makes it possible to drastically increase the data storage density compared to conventional memory devices. Magnonic combinatorial memory with an array of 100 × 100 magnets can store all information generated by humankind. Physical limits and constraints are also discussed.
Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
Authors: Tsouris Andreas , Brach Gauthier , Friedrich Anne , Hou Jing , Schacherer Joseph 
Published: February 2024

AbstractUnraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level.
Autoregressive modelling for Sub‐THz spatio‐temporal wideband scattered reflection coefficient measurement of complex structures
Authors: Serghiou Demos , Khalily Mohsen , Ali Ali , Brown Tim , Tafazolli Rahim 
Published: February 2024

AbstractThe authors present spatio‐temporally resolved wideband measurements of Sub‐Terahertz (Sub‐THz) reflection coefficients in the frequency range of 92–110 GHz. A stochastic model for single reflection fixed links that is capable of modelling random scattering from small‐scale discontinuities such as those encountered in complex structures in walls and partitions of buildings is presented. The model auto‐regressively produces filter coefficients that are fed into an Infinite‐Impulse‐Response (IIR) filter which convolves them with the spatio‐temporal series in order to generate the next output sample based on previous observations. The IIR filter allows for flexible stochastic generation of samples, and its parameters can be adjusted as needed to suit different channel conditions. A total of 20 suitable start‐up filter coefficients are generated from 21.7 % of the sample size for each complex delay tap distribution, which corresponds to 50 complex instances of the channel. These coefficients are then utilised to validate the remaining measured sample set. The model is in quantitative agreement with measurement statistics and can be used to construct relatively simple modified reflection coefficients that can be used in micro‐cellular ray‐optical network planning tools.
FAUST
Authors: Vastel C. , Sakai T. , Ceccarelli C. , Jiménez-Serra I. , Alves F. , Balucani N. , Bianchi E. , Bouvier M. , Caselli P. , Chandler C. J. , Charnley S. , Codella C. , De Simone M. , Dulieu F. , Evans L. , Fontani F. , Lefloch B. , Loinard L. , Menard F. , Podio L. , Sabatini G. , Sakai N. , Yamamoto S. 
Published: February 2024

Aims. Interstellar complex organic molecules (iCOMs) are species commonly found in the interstellar medium. They are believed to be crucial seed species for the build-up of chemical complexity in star forming regions as well as our own Solar System. Thus, understanding how their abundances evolve during the star formation process and whether it enriches the emerging planetary system is of paramount importance.
Methods. We use data from the ALMA Large Program FAUST (Fifty AU STudy of the chemistry in the disk and envelope system of solar protostars) to study the compact line emission towards the [BHB2007] 11 proto-binary system (sources A and B), where a complex structure of filaments connecting the two sources with a larger circumbinary disk has previously been detected. More than 45 methyl formate (CH3OCHO) lines are clearly detected with upper energies in the [123, 366] K range, as well as 8 dimethyl ether transitions (CH3OCH3) in the [93, 191] K range, 1 ketene transition (H2CCO) and 4 formic acid transitions (t-HCOOH). We compute the abundance ratios with respect to CH3OH for CH3OCHO, CH3OCH3, H2CCO, t-HCOOH (as well as an upper limit for CH3CHO) through a radiative transfer analysis. We also report the upper limits on the column densities of nitrogen bearing iCOMs, N(C2H5CN) and N(C2H3CN).
Results. The emission from the detected iCOMs and their precursors is compact and encompasses both protostars, which are separated by only 0.2″ (~28 au). The integrated intensities tend to align with the Southern filament, revealed by the high spatial resolution observations of the dust emission at 1.3 mm. A Position-Velocity and 2D analysis are performed on the strongest and uncontaminated CH3OCH3 transition and show three different spatial and velocity regions, two of them being close to 11B (Southern filament) and the third one near 11A.
Conclusions. All our observations suggest that the detected methanol, as well as the other iCOMs, are generated by the shocked gas from the incoming filaments streaming towards [BHB2007] 11A and 11B, respectively, making this source one of the few where chemical enrichment of the gas caused by the streaming material is observed.
Erstdiagose einer Ostitis cystica fibrosa bei tumoröser Raumforderung der Brustwirbelsäule
Authors: Riehle Marion , Schmidt René 
Published: February 2024

ZusammenfassungDer primäre Hyperparathyreoidismus (PHPT) tritt überwiegend bei Frauen um das 50. Lebensjahr mit einer Prävalenz von 25–30/100.000 auf. Aufgrund einer erhöhten Osteoklastenaktivität treten bei langfristig unbehandeltem PHPT katabole Knochenumbauprozesse auf, die im Vollbild zu einer Ostitis cystica fibrosa (von-Recklinghausen-Krankheit des Knochens) führen können. Diese Erkrankung ist sehr selten und betrifft lediglich 3% der Patienten.Wir beschreiben den Fall einer 61-jährigen Patientin, die mit einer Paraparese infolge spinaler Kompression bei tumoröser Raumforderung auf Höhe des 9. Brustwirbelkörpers (BWK) vorgestellt wurde. Nach notfallmäßiger dorsaler Stabilisierung und Dekompression kam es zu einer raschen restitutio ad integrum. Histologische, immunhistochemische und laborchemische Ergebnisse ergaben die Diagnose einer Ostitis cystica fibrosa bei PHPT.Da der PHPT als Differenzialdiagnose zu Osteoporose und zystischen Knochentumoren kurativ therapiert werden kann, ist das rechtzeitige Erkennen zur Vermeidung von sekundären Organschädigungen und pathologischen Frakturen essenziell.