bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis
Authors: Ohara Kentaro , Rendeiro André Figueiredo , Bhinder Bhavneet , Eng Kenneth Wha , Ravichandran Hiranmayi , Nguyen Duy , Pisapia David , Vosoughi Aram , Fernandez Evan , Shohdy Kyrillus S. , Manohar Jyothi , Beg Shaham , Wilkes David , Robinson Brian D. , Khani Francesca , Bareja Rohan , Tagawa Scott T. , Ouseph Madhu M. , Sboner Andrea , Elemento Olivier , Faltas Bishoy M. , Mosquera Juan Miguel
Published: March 2024

The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are not well understood, and there is a lack of knowledge regarding the genomic and transcriptomic differences between primary and metastatic UTUC. To address these gaps, we integrate whole-exome sequencing, RNA sequencing, and Imaging Mass Cytometry using lanthanide metal-conjugated antibodies of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. We perform a spatially-resolved single-cell analysis of cancer, immune, and stromal cells to understand the evolution of primary to metastatic UTUC. We discover that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature are stable across primary and matched metastatic UTUC. Molecular and immune subtypes are consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single cells. Molecular subtypes at the single-cell level are highly conserved between primary and metastatic UTUC tumors within the same patient.
Evolutionary origin of Hoxc13-dependent skin appendages in amphibians
Authors: Carron Marjolein , Sachslehner Attila Placido , Cicekdal Munevver Burcu , Bruggeman Inge , Demuynck Suzan , Golabi Bahar , De Baere Elfride , Declercq Wim , Tschachler Erwin , Vleminckx Kris , Eckhart Leopold
Published: March 2024

Cornified skin appendages, such as hair and nails, are major evolutionary innovations of terrestrial vertebrates. Human hair and nails consist largely of special intermediate filament proteins, known as hair keratins, which are expressed under the control of the transcription factor Hoxc13. Here, we show that the cornified claws of Xenopus frogs contain homologs of hair keratins and the genes encoding these keratins are flanked by promoters in which binding sites of Hoxc13 are conserved. Furthermore, these keratins and Hoxc13 are co-expressed in the claw-forming epithelium of frog toe tips. Upon deletion of hoxc13, the expression of hair keratin homologs is abolished and the development of cornified claws is abrogated in X. tropicalis. These results indicate that Hoxc13-dependent expression of hair keratin homologs evolved already in stem tetrapods, presumably as a mechanism for protecting toe tips, and that this ancestral genetic program was coopted to the growth of hair in mammals.
Optimizing quantum gates towards the scale of logical qubits
Authors: Klimov Paul V. , Bengtsson Andreas , Quintana Chris , Bourassa Alexandre , Hong Sabrina , Dunsworth Andrew , Satzinger Kevin J. , Livingston William P. , Sivak Volodymyr , Niu Murphy Yuezhen , Andersen Trond I. , Zhang Yaxing , Chik Desmond , Chen Zijun , Neill Charles , Erickson Catherine , Grajales Dau Alejandro , Megrant Anthony , Roushan Pedram , Korotkov Alexander N. , Kelly Julian , Smelyanskiy Vadim , Chen Yu , Neven Hartmut
Published: March 2024

A foundational assumption of quantum error correction theory is that quantum gates can be scaled to large processors without exceeding the error-threshold for fault tolerance. Two major challenges that could become fundamental roadblocks are manufacturing high-performance quantum hardware and engineering a control system that can reach its performance limits. The control challenge of scaling quantum gates from small to large processors without degrading performance often maps to non-convex, high-constraint, and time-dynamic control optimization over an exponentially expanding configuration space. Here we report on a control optimization strategy that can scalably overcome the complexity of such problems. We demonstrate it by choreographing the frequency trajectories of 68 frequency-tunable superconducting qubits to execute single- and two-qubit gates while mitigating computational errors. When combined with a comprehensive model of physical errors across our processor, the strategy suppresses physical error rates by ~3.7× compared with the case of no optimization. Furthermore, it is projected to achieve a similar performance advantage on a distance-23 surface code logical qubit with 1057 physical qubits. Our control optimization strategy solves a generic scaling challenge in a way that can be adapted to a variety of quantum operations, algorithms, and computing architectures.
Fast Human Motion reconstruction from sparse inertial measurement units considering the human shape
Authors: Xiao Xuan , Wang Jianjian , Feng Pingfa , Gong Ao , Zhang Xiangyu , Zhang Jianfu
Published: March 2024

Inertial Measurement Unit-based methods have great potential in capturing motion in large-scale and complex environments with many people. Sparse Inertial Measurement Unit-based methods have more research value due to their simplicity and flexibility. However, improving the computational efficiency and reducing latency in such methods are challenging. In this paper, we propose Fast Inertial Poser, which is a full body motion estimation deep neural network based on 6 inertial measurement units considering body parameters. We design a network architecture based on recurrent neural networks according to the kinematics tree. This method introduces human body shape information by the causality of observations and eliminates the dependence on future frames. During the estimation of joint positions, the upper body and lower body are estimated using separate network modules independently. Then the joint rotation is obtained through a well-designed single-frame kinematics inverse solver. Experiments show that the method can greatly improve the inference speed and reduce the latency while ensuring the reconstruction accuracy compared with previous methods. Fast Inertial Poser runs at 65 fps with 15 ms latency on an embedded computer, demonstrating the efficiency of the model.
Dynamics of extrachromosomal circular DNA in rice
Authors: Zhuang Jundong , Zhang Yaoxin , Zhou Congcong , Fan Danlin , Huang Tao , Feng Qi , Lu Yiqi , Zhao Yan , Zhao Qiang , Han Bin , Lu Tingting
Published: March 2024

The genome’s dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling the widespread presence of eccDNA across six rice tissues and revealing its formation as a universal and random process. Interestingly, we discover that direct repeats play a pivotal role in eccDNA formation, pointing to a unique origin mechanism. Despite eccDNA’s prevalence in coding sequences, its impact on gene expression is minimal, implying its roles beyond gene regulation. We also observe the association between eccDNA’s formation and minor chromosomal deletions, providing insights of its possible function in regulating genome stability. Further, we discover eccDNA specifically accumulated in rice leaves, which may be associated with DNA damage caused by environmental stressors like intense light. In summary, our research advances understanding of eccDNA’s role in the genomic architecture and offers valuable insights for rice cultivation and breeding.
Co-targeting the kappa opioid receptor and dopamine transporter reduces motivation to self-administer cocaine and partially reverses dopamine system dysregulation
Authors: Estave Paige M. , Albertson Steven E. , Karkhanis Anushree N. , Jones Sara R.
Published: March 2024

Cocaine disrupts dopamine (DA) and kappa opioid receptor (KOR) system activity, with long-term exposure reducing inhibiton of DA uptake by cocaine and increasing KOR system function. Single treatment therapies have not been successful for cocaine use disorder; therefore, this study focuses on a combination therapy targeting the dopamine transporter (DAT) and KOR. Sprague Dawley rats self-administered 5 days of cocaine (1.5 mg/kg/inf, max 40 inf/day, FR1), followed by 14 days on a progressive ratio (PR) schedule (0.19 mg/kg/infusion). Behavioral effects of individual and combined administration of phenmetrazine and nBNI were then examined using PR. Additionally, ex vivo fast scan cyclic voltammetry was then used to assess alterations in DA and KOR system activity in the nucleus accumbens before and after treatments. Chronic administration of phenmetrazine as well as the combination of phenmetrazine and nBNI—but not nBNI alone—significantly reduced PR breakpoints. In addition, the combination of phenmetrazine and nBNI partially reversed cocaine-induced neurodysregulations of the KOR and DA systems, indicating therapeutic benefits of targeting the DA and KOR systems in tandem. These data highlight the potential benefits of the DAT and KOR as dual-cellular targets to reduce motivation to administer cocaine and reverse cocaine-induced alterations of the DA system.
Ultra-compact and efficient photonic waveguide bends with different configurations designed by topology optimization
Authors: Irfan Sabaina , Kim Jae-Yong , Kurt Hamza
Published: March 2024

Transporting light signals over the corners and sharp bends imposes high optical loss and distortion on the mode profiles. Usually, bends with larger radii are used in circuits to minimize the loss over transmission, resulting in a severe limitation in integration density. In this paper, we propose novel topology-optimized optimized L-bend and U-bend structures designed for a 220 nm silicon-on-insulator (SOI) platform. Optimized L-bends with footprints of 2.5 µm × 2.5 µm, 1.5 µm × 1.5 µm, and 1 µm × 1 µm show maximum insertion losses of only 0.07 dB, 0.26 dB, and 0.78 dB, respectively. For optimized U-bends with footprints of 3 µm × 3.6 µm, 2.5 µm × 2.5 µm, and 1.5 µm × 1.5 µm, the maximum insertion losses are 0.07 dB, 0.21 dB, and 3.16 dB. These optimized bends reduce the maximum insertion loss by over 50% compared to un-optimized arc-type bends across a broad wavelength range of 1450–1650 nm. Experimental verification of a meander line with 16 optimized U-bends (3 µm × 3.6 µm) demonstrates an averaged insertion loss of 1.23 dB in the wavelength range of 1520–1580 nm, agreeing with simulated results and indicating a high potential of loss reduction with optimized bends.
Estimate the burden of malnutrition among children with cerebral palsy in Sub-Saharan Africa: a systematic review with meta-analysis
Authors: Chanie Ermias Sisay , Moges Natnael , Baye Fikadie Dagnew , Mekonnen Gebrehiwot Berie , Fekadie Mengistu Melak , Bazezew Lakachew Yismaw , Anley Denekew Tenaw , Zemene Melkamu Aderajew , Gebeyehu Natnael Atnafu , Adella Getachew Asmare , Kassie Gizachew Ambaw , Mengstie Misganaw Asmamaw , Seid Mohammed Abdu , Abebe Endeshaw Chekol , Gesese Molalegn Mesele , Tegegne Kirubel Dagnaw , Kebede Yenealem Solomon , Bantie Berihun , Feleke Sefineh Fenta , Dejenie Tadesse Asmamaw , Bayih Wubet Alebachew , Kassaw Amare , Dessie Anteneh Mengist , Azanaw Melkalem Mamuye , Chanie Sewunt Sisay
Published: March 2024

Malnutrition is more prevalent among children with cerebral palsy and a major factor for child morbidity and mortality in children with different co-morbidity, especially in Sub-Saharan Africa: The main aim of this systematic review and meta-analysis was to estimate the burden of malnutrition among children with cerebral palsy in Sub-Saharan Africa. We searched PubMed, Web of Science, Google Scholar, Research Gate, and institutional repositories for papers that reported the proportion of malnutrition among children with cerebral palsy that were published between December 2010 and September 2023. Data were retrieved using the standardized JBI data extraction checklist through Microsoft Excel, and then exported to STATA 17 for further analysis. DerSimonian and Laird’s estimator was used to calculate the pooled effect size in the random-effects model. Statistics such as the Cochran Q test and I2 test were employed to measure heterogeneity. Egger's test and the funnel plot were used to look for publication bias. This systematic review and meta-analysis used 16 studies from Sub-Saharan Africa to estimate the proportion of malnutrition among 2,120 children with cerebral palsy. The pooled proportion of malnutrition among children with cerebral palsy in Sub-Saharan Africa by using random-effects model analysis was found to be 59.7% (95% CI; 49.8–69.6). The proportion of malnutrition was also estimated by sample sizes categorized as ≤ 120 and > 120, and the proportion of malnutrition was found to be 54.0 (95% CI: 44.7–63.3) and 64.5 (95% CI: 50.5–78.5). Moreover, the proportion of malnutrition was estimated by accounting for the difference in the year of publication. In this regard, the study classified before ≤ 2017 and > 2017, and the proportion of malnutrition was found to be 53.7 (95% CI: 38.0–69.3) and 62.5 (95% CI: 49.7–75.3) in Sub-Saharan Africa respectively. Malnutrition among children with cerebral in Sub-Saharan Africa was found to be very high. Hence, enhancing and developing strategic guidelines for malnutrition screening, prevention, and nutritional support are crucial among children with cerebral palsy. Furthermore, systematic review, randomized control trials, and qualitative studies are recommended to understand the burden more among children with cerebral palsy in the continent.
The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients
Authors: Linowiecka Kinga , Guz Jolanta , Dziaman Tomasz , Urbanowska–Domańska Olga , Zarakowska Ewelina , Szpila Anna , Szpotan Justyna , Skalska-Bugała Aleksandra , Mijewski Paweł , Siomek-Górecka Agnieszka , Różalski Rafał , Gackowski Daniel , Oliński Ryszard , Foksiński Marek
Published: March 2024

The active DNA demethylation process, which involves TET proteins, can affect DNA methylation pattern. TET dependent demethylation results in DNA hypomethylation by oxidation 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and its derivatives. Moreover, TETs’ activity may be upregulated by ascorbate. Given that aberrant DNA methylation of genes implicated in breast carcinogenesis may be involved in tumor progression, we wanted to determine whether breast cancer patients exert changes in the active DNA demethylation process. The study included blood samples from breast cancer patients (n = 74) and healthy subjects (n = 71). We analyzed the expression of genes involved in the active demethylation process (qRT-PCR), and 5–mC and its derivatives level (2D-UPLC MS/MS). The ascorbate level was determined using UPLC-MS. Breast cancer patients had significantly higher TET3 expression level, lower 5-mC and 5-hmC DNA levels. TET3 was significantly increased in luminal B breast cancer patients with expression of hormone receptors. Moreover, the ascorbate level in the plasma of breast cancer patients was decreased with the accompanying increase of sodium-dependent vitamin C transporters (SLC23A1 and SLC23A2). The presented study indicates the role of TET3 in DNA demethylation in breast carcinogenesis.
Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration
Authors: Yamada Mamiko , Maeta Kazuhiro , Suzuki Hisato , Kurosawa Ryo , Takenouchi Toshiki , Awaya Tomonari , Ajiro Masahiko , Takeuchi Atsuko , Nishio Hisahide , Hagiwara Masatoshi , Miya Fuyuki , Matsuo Masafumi , Kosaki Kenjiro
Published: March 2024

Pathogenic variants in WDR45 on chromosome Xp11 cause neurodegenerative disorder beta-propeller protein-associated neurodegeneration (BPAN). Currently, there is no effective therapy for BPAN. Here we report a 17-year-old female patient with BPAN and show that antisense oligonucleotide (ASO) was effective in vitro. The patient had developmental delay and later showed extrapyramidal signs since the age of 15 years. MRI findings showed iron deposition in the globus pallidus and substantia nigra on T2 MRI. Whole genome sequencing and RNA sequencing revealed generation of pseudoexon due to inclusion of intronic sequences triggered by an intronic variant that is remote from the exon–intron junction: WDR45 (OMIM #300526) chrX(GRCh37):g.48935143G > C, (NM_007075.4:c.235 + 159C > G). We recapitulated the exonization of intron sequences by a mini-gene assay and further sought antisense oligonucleotide that induce pseudoexon skipping using our recently developed, a dual fluorescent splicing reporter system that encodes two fluorescent proteins, mCherry, a transfection marker designed to facilitate evaluation of exon skipping and split eGFP, a splicing reaction marker. The results showed that the 24-base ASO was the strongest inducer of pseudoexon skipping. Our data presented here have provided supportive evidence for in vivo preclinical studies.
Prediction model and assessment of malnutrition in patients with stable chronic obstructive pulmonary disease
Authors: Shen Xurui , Qian Ruiqi , Wei Yuan , Tang Zhichao , Zhong Huafei , Huang Jianan , Zhang Xiuqin
Published: March 2024

Chronic obstructive pulmonary disease (COPD) combined with malnutrition results in decreased exercise capacity and a worse quality of life. We aimed to develop an observational case–control study to explore the effective and convenient method to identify potential individuals is lacking. This study included data from 251 patients with COPD and 85 participants in the control group. Parameters and body composition were compared between groups, and among patients with varied severity. The LASSO approach was employed to select the features for fitting a logistic model to predict the risk of malnutrition in patients with stable COPD. Patients with COPD exhibited significantly lower 6-min walk distance (6MWD), handgrip strength, fat-free mass index (FFMI), skeletal muscle mass (SMM) and protein. The significant predictors identified following LASSO selection included 6MWD, waist-to-hip ratio (WHR), GOLD grades, the COPD Assessment Test (CAT) score, and the prevalence of acute exacerbations. The risk score model yielded good accuracy (C-index, 0.866 [95% CI 0.824–0.909]) and calibration (Brier score = 0.150). After internal validation, the adjusted C-index and Brier score were 0.849, and 0.165, respectively. This model may provide primary physicians with a simple scoring system to identify malnourished patients with COPD and develop appropriate rehabilitation interventions.
Effects of releasing ankle joint during electrically evoked cycling in persons with motor complete spinal cord injury
Authors: Hamdan Puteri Nur Farhana , Hamzaid Nur Azah , Hasnan Nazirah , Abd Razak Nasrul Anuar , Razman Rizal , Usman Juliana
Published: March 2024

Literature has shown that simulated power production during conventional functional electrical stimulation (FES) cycling was improved by 14% by releasing the ankle joint from a fixed ankle setup and with the stimulation of the tibialis anterior and triceps surae. This study aims to investigate the effect of releasing the ankle joint on the pedal power production during FES cycling in persons with spinal cord injury (SCI). Seven persons with motor complete SCI participated in this study. All participants performed 1 min of fixed-ankle and 1 min of free-ankle FES cycling with two stimulation modes. In mode 1 participants performed FES-evoked cycling with the stimulation of quadriceps and hamstring muscles only (QH stimulation), while Mode 2 had stimulation of quadriceps, hamstring, tibialis anterior, and triceps surae muscles (QHT stimulation). The order of each trial was randomized in each participant. Free-ankle FES cycling offered greater ankle plantar- and dorsiflexion movement at specific slices of 20° crank angle intervals compared to fixed-ankle. There were significant differences in the mean and peak normalized pedal power outputs (POs) [F(1,500) = 14.03, p < 0.01 and F(1,500) = 7.111, p = 0.008, respectively] between fixed- and free-ankle QH stimulation, and fixed- and free-ankle QHT stimulation. Fixed-ankle QHT stimulation elevated the peak normalized pedal PO by 14.5% more than free-ankle QH stimulation. Releasing the ankle joint while providing no stimulation to the triceps surae and tibialis anterior reduces power output. The findings of this study suggest that QHT stimulation is necessary during free-ankle FES cycling to maintain power production as fixed-ankle.
A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems
Authors: Stuart Jacqui , Ryan Ken G. , Pearman John K. , Thomson-Laing Jacob , Hampton Hannah G. , Smith Kirsty F.
Published: March 2024

Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and ‘other microalgae’. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.
Clustering analysis for the evolutionary relationships of SARS-CoV-2 strains
Authors: Chen Xiangzhong , Wang Mingzhao , Liu Xinglin , Zhang Wenjie , Yan Huan , Lan Xiang , Xu Yandi , Tang Sanyi , Xie Juanying
Published: March 2024

To explore the differences and relationships between the available SARS-CoV-2 strains and predict the potential evolutionary direction of these strains, we employ the hierarchical clustering analysis to investigate the evolutionary relationships between the SARS-CoV-2 strains utilizing the genomic sequences collected in China till January 7, 2023. We encode the sequences of the existing SARS-CoV-2 strains into numerical data through k-mer algorithm, then propose four methods to select the representative sample from each type of strains to comprise the dataset for clustering analysis. Three hierarchical clustering algorithms named Ward-Euclidean, Ward-Jaccard, and Average-Euclidean are introduced through combing the Euclidean and Jaccard distance with the Ward and Average linkage clustering algorithms embedded in the OriginPro software. Experimental results reveal that BF.28, BE.1.1.1, BA.5.3, and BA.5.6.4 strains exhibit distinct characteristics which are not observed in other types of SARS-CoV-2 strains, suggesting their being the majority potential sources which the future SARS-CoV-2 strains’ evolution from. Moreover, BA.2.75, CH.1.1, BA.2, BA.5.1.3, BF.7, and B.1.1.214 strains demonstrate enhanced abilities in terms of immune evasion, transmissibility, and pathogenicity. Hence, closely monitoring the evolutionary trends of these strains is crucial to mitigate their impact on public health and society as far as possible.
Non-fluorescent transient states of tyrosine as a basis for label-free protein conformation and interaction studies
Authors: Bagheri Niusha , Chen Hongjian , Rabasovic Mihailo , Widengren Jerker
Published: March 2024

The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Similar to most fluorescent organic molecules, these amino acids can undergo transitions into dark meta-stable states, such as triplet and photo-radical states. On the one hand, these transitions limit the fluorescence signal, but they are also highly environment-sensitive and can offer an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, by analyzing the average intensity of tyrosine emission under different excitation modulations with the transient state monitoring (TRAST) technique, we explored the photo physics of tyrosine as a basis for such environment-sensitive readouts. From how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we first established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), and how its conformation is changed upon calcium binding. From these TRAST experiments, performed with 280 nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.
Study on the material source and enrichment mechanism of REE-rich phosphorite in Zhijin, Guizhou
Authors: Wang Jingya , Qiao Zhongkun
Published: March 2024

Rare earth element (REE)-rich phosphorite in the Guizhou region mainly exists in the Doushantuo Formation and Gezhongwu Formation in early Cambrian strata, which are some of the important strata containing phosphorite resources in China. The early Cambrian Zhijin phosphorite in Guizhou Province, China, has high rare earth element and yttrium (REY) contents of up to 2500 ppm, with heavy REY (HREY) contents accounting for ~ 30% of the total REY contents. However, the specific controlling source and environment of phosphorite (especially the REEs in Zhijin phosphorite) are still unsolved. Through field geological investigations; mineralogical, geochemical, Sr–Nd isotope analyses; and tectonic characteristics, the material source, sedimentary environment and seawater dynamics of REEs in phosphorite are studied. It is considered that the REEs enriched in the Zhijin phosphorite are mainly affected by precipitation from hydrothermal fluid. Moreover, from the late Ediacaran to the early Cambrian, the depositional environment from the bottom to the top of the water tended to be hypoxic, and the activity of hot water fluid tended to be strong. The change in redox conditions is closely related to the rise and fall of sea level. Combined with the tectonic background, these results show that the weakly oxidized environment may be an important factor controlling the enrichment of REEs. The enrichment of REEs may be closely related to volcanic hydrothermal activity, later diagenesis and seawater dynamics.
Association between circadian physical activity trajectories and incident type 2 diabetes in the UK Biobank
Authors: Bai Pufei , Shao Xian , Chen Lianqin , Zhou Saijun , Lin Yao , Liu Hongyan , Yu Pei
Published: March 2024

Physical activity (PA) is linked to a decreased risk of type 2 diabetes mellitus (T2DM). However, the influence of circadian PA trajectories remains uncertain. This study aims to explore the optimal circadian PA trajectory pattern for reducing the risk of T2DM. Methods: A total of 502,400 participants were recruited from the UK Biobank between 2006 and 2010, and 102,323 participants provided valid accelerometer-captured acceleration data. After excluding individuals with prior T2DM, 99,532 participants were included in the final analysis. We initially investigated the association between PA intensity at 24 hourly time points and T2DM. Subsequently, PA trajectories were identified using K-means cluster analysis. Cox proportional hazard models were employed to estimate hazard ratios (HR). Four distinct PA trajectories were identified: consistently low, single peak, double peak, and intense trajectories. Compared to consistently low, single peak, double peak and intense PA trajectory reduced the risk of T2DM progressively. Sensitivity analyses, further excluding individuals with glycated hemoglobin (HbA1c) ≥ 6.5% or random glucose ≥ 11.1 mmol/L and adjusted for daily average acceleration, yielded consistent results. This confirms that the ideal circadian PA trajectory serves as a protective factor, independently of PA intensity. Subgroup analyses indicated that these effects were more pronounced in men and individuals with eGFR < 60 mL/(min*1.73 m2). In conclusion, ideal circadian PA trajectory patterns (especially intense and then double peak) reduced risk of T2DM.
Distribution and protection of Thesium chinense Turcz. under climate and land use change
Authors: Zhang Boyan , Chen Bingrui , Zhou Xinyu , Zou Hui , Duan Detai , Zhang Xiyuan , Zhang Xinxin
Published: March 2024

Wild medicinal plants are prominent in the field of Traditional Chinese Medicine (TCM), but their availability is being impacted by human activities and ecological degradation in China. To ensure sustainable use of these resources, it is crucial to scientifically plan areas for wild plant cultivation. Thesium chinense, a known plant antibiotic, has been overharvested in recent years, resulting in a sharp reduction in its wild resources. In this study, we employed three atmospheric circulation models and four socio-economic approaches (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5) to investigate the primary environmental factors influencing the distribution of T. chinense. We also examined changes in its suitable area using the Biomod2 package. Additionally, we utilized the PLUS model to project and analyze future land use changes in climate-stable regions for T. chinense. Our planning for wild tending areas of T. chinense was facilitated by the ZONATION software. Over the next century, the climate-stable regions for T. chinense in China is approximately 383.05 × 104 km2, while the natural habitat in this region will progressively decline. Under the current climate conditions, about 65.06% of the habitats in the high suitable areas of T. chinense are not affected by future land use changes in China. Through hotspot analysis, we identified 17 hotspot cities as ideal areas for the wild tending of T. chinense, including 6 core hotspot cities, 6 sub-hotspot cities, and 5 fringe hotspot cities. These findings contribute to a comprehensive research framework for the cultivation planning of T. chinense and other medicinal plants.
Differential scanning fluorimetry to assess PFAS binding to bovine serum albumin protein
Authors: Alesio Jessica , Bothun Geoffrey D.
Published: March 2024

The rapid screening of protein binding affinity for poly- and perfluoroalkyl substances (PFAS) benefits risk assessment and fate and transport modelling. PFAS are known to bioaccumulate in livestock through contaminated food and water. One excretion pathway is through milk, which may be facilitated by binding to milk proteins such as bovine serum albumin (BSA). We report a label-free differential scanning fluorimetry approach to determine PFAS–BSA binding over a broad temperature range. This method utilizes the tryptophan residue within the protein binding pocket as an intrinsic fluorophore, eliminating the need for fluorophore labels that may influence binding. BSA association constants were determined by (a) an equilibrium-based model at the melting temperature of BSA and (b) the Hill adsorption model to account for temperature dependent binding and binding cooperativity. Differences in binding between PFAS and fatty acid analogs revealed that a combination of size and hydrophobicity drives PFAS binding.
Using surface-enhanced Raman spectroscopy to probe artificial dye degradation on hair buried in multiple soils for up to eight weeks
Authors: Holman Aidan P. , Peterson Mackenzi , Linhart Emily , Kurouski Dmitry
Published: March 2024

The discovery of clandestine burials poses unique challenges for forensic specialists, requiring diverse expertise to analyze remains in various states. Bones, teeth, and hair often endure the test of time, with hair particularly exposed to the external environment. While existing studies focus on the degradation of virgin hair influenced by soil pH and decomposition fluids, the interaction between artificial dyes on hair and soil remains underexplored. This paper introduces a novel approach to forensic hair analysis that is based on high-throughput, nondestructive, and non-invasive surface-enhanced Raman spectroscopy (SERS) and machine learning. Using this approach, we investigated the reliability of the detection and identification of artificial dyes on hair buried in three distinct soil types for up to eight weeks. Our results demonstrated that SERS enabled the correct prediction of 97.9% of spectra for five out of the eight dyes used within the 8 weeks of exposure. We also investigated the extent to which SERS and machine learning can be used to predict the number of weeks since burial, as this information may provide valuable insights into post-mortem intervals. We found that SERS enabled highly accurate exposure intervals to soils for specific dyes. The study underscores the high achievability of SERS in extrapolating colorant information from dyed hairs buried in diverse soils, with the suggestion that further model refinement could enhance its reliability in forensic applications.
Effects of γ-polyglutamic acid supplementation on alfalfa growth and rhizosphere soil microorganisms in sandy soil
Authors: Guo Zhen , Wang Jian , Chen Tianqing , Zhang Haiou , Hou Xiandong , Li Juan
Published: March 2024

This study aimed at exploring the effects of γ-polyglutamic acid on the growth of desert alfalfa and the soil microorganisms in the rhizosphere. The study examined the effects of varying concentrations of γ-polyglutamic acid (0%-CK, 2%-G1, 4%-G2, 6%-G3) on sandy soil, the research investigated its impact on the growth characteristics of alfalfa, nutrient content in the rhizosphere soil, and the composition of bacterial communities. The results indicated that there were no significant differences in soil organic matter, total nitrogen, total phosphorus, total potassium, and available phosphorus content among the G1, G2, and G3 treatments. Compared to CK, the soil nutrient content in the G2 treatment increased by 14.81–186.67%, showing the highest enhancement. In terms of alfalfa growth, the G2 treatment demonstrated the best performance, significantly increasing plant height, chlorophyll content, above-ground biomass, and underground biomass by 54.91–154.84%. Compared to the CK treatment, the number of OTUs (operational taxonomic units) in the G1, G2, and G3 treatments increased by 14.54%, 8.27%, and 6.84%, respectively. The application of γ-polyglutamic acid altered the composition and structure of the bacterial community, with Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota accounting for 84.14–87.89% of the total bacterial community. The G2 treatment significantly enhanced the diversity and evenness of soil bacteria in the rhizosphere. Redundancy analysis revealed that organic matter, total nitrogen, total potassium, moisture content, and pH were the primary factors influencing the structure of bacterial phyla. At the genus level, moisture content emerged as the most influential factor on the bacterial community. Notably, moisture content exhibited a strong positive correlation with Acidobacteriota, which in turn was positively associated with indicators of alfalfa growth. In summary, the application of γ-polyglutamic acid at a 4% ratio has the potential for improving sandy soil quality, promoting plant growth, and regulating the rhizosphere microbial community.
Impact on urban river water quality and pollution control of water environmental management projects based on SMS-Mike21 coupled simulation
Authors: Wei Huaibin , Rao Yiding , Liu Jing , Wang Yao , Cao Yongxiao
Published: March 2024

To explore the impact of expanding Nanyang Sewage Purification Center (NSPC) on the main sewage discharge area of Bai River, we constructed a 2D hydrodynamic-water quality model based on surface water modeling system (SMS) and Mike21. Simulating three sewage discharge conditions in wet, normal, and dry season, we evaluated three indicators (COD, NH3-N, and BOD5) by the single-factor pollution index and provided recommendations for water environment management. The results showed that, maximum absolute error of water level was 0.08 m, percentage bias coefficient of COD, NH3-N and BOD5were 19.3%, 16.2% and 23.1%, indicating the SMS and Mike21 coupling model was applicable; water quality of the assessment section were upgraded from the original class IV, V, V (Condition 1) to class IV, III, II (Condition 2) and class IV, III, III (Condition 3) in the wet, normal and dry season, indicating that NSPC's expansion had improved the water quality of the assessment section; as the primary pollutant, BOD5concentration in the downstream was lower than the upstream, which was due to the dilution effect of river. Therefore, on the basis of expanding NSPC, we recommend to remediation of BOD5by physical, chemical, and biological methods. This study broadens new ideas for the application of Mike21, and provide a reference for the prevention and improvement of river water pollution in urban areas.
Prognosis significance and potential association between ALDOA and AKT expression in colorectal cancer
Authors: Xu Menglin , Xi Shihang , Li Haoran , Xia Yong , Mei Guangliang , Cheng Zhengwu
Published: March 2024

Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive tract and a leading cause of cancer-related death worldwide. Since many CRC patients are diagnosed already in the advanced stage, and traditional chemoradiotherapy is prone to drug resistance, it is important to find new therapeutic targets. In this study, the expression levels of ALDOA and p-AKT were detected in cancer tissues and paired normal tissues, and it was found that they were significantly increased in CRC tissues, and their high expression indicated poor prognosis. Moreover, a positive correlation between the expression of ALDOA and p-AKT was found in CRC tissues and paired normal tissues. In addition, the Kaplan–Meier analysis revealed that the group with both negative of ALDOA/p-AKT expression had longer five-year survival rates compared with the other group. Besides, the group with both high expression of ALDOA/p-AKT had a worse prognosis compared with the other group. Based on the expression of ALDOA and p-AKT in tumor tissues, we can effectively distinguish tumor tissues from normal tissues through cluster analysis. Furthermore, we constructed nomograms to predict 3-year and 5-year overall survival, showing that the expression of ALDOA/p-AKT plays a crucial role in predicting the prognosis of CRC patients. Therefore, ALDOA/p-AKT may act as a crucial role in CRC, which may provide new horizons for targeted therapies for CRC.
Association of resistance training and moderate-to-vigorous physical activity with clinical outcomes in men with airflow limitation: a nationwide population-based study
Authors: Kim Taeyun , Hyun Seok Min , Shin Sun Hye , Im Yunjoo , Na Yoonju , Do Jong Geol , Park Hye Yun , Kong Sunga
Published: March 2024

Aerobic moderate-to-vigorous physical activity (MVPA) is recommended for individuals with chronic diseases. However, the association between resistance training (RT) in addition to moderate to vigorous physical activity (MVPA) and sleep duration, as well as respiratory symptoms, in patients with chronic obstructive pulmonary disease has not been thoroughly investigated. This population-based cross-sectional study used data from the Korea National Health and Nutrition Examination Survey between 2014 and 2019. A total of 61,754 individuals were identified and men with airflow limitation (FEV1/FVC < 0.7) who engaged in aerobic MVPA were selected (n = 794). Weighted percentages and odds ratio (OR) of sleep problems (≤ 5 or ≥ 9 h), chronic cough, and chronic sputum were estimated. A multivariate-adjusted complex sample logistic regression model was used to calculate ORs and 95% confidence intervals (CI). Subgroup analyses were conducted using the forced expiratory volume (FEV1) % of the predicted value (%pred) ≥ 80 vs. < 80. The percentages of sleep problems, chronic cough, and chronic sputum production were lower in men who underwent aerobic MVPA + RT than in those who underwent aerobic MVPA alone. The multivariable-adjusted OR of sleep problems was 0.44 (95% CI 0.25–0.77) in individuals undergoing aerobic MVPA + RT compared to aerobic MVPA alone. The ORs of chronic cough and sputum were 0.35 (95% CI 0.13–0.94) and 0.51 (95% CI 0.30–0.87), respectively. These associations were only significant in individuals with FEV1 < 80% pred. Compared with aerobic MVPA alone, aerobic MVPA + RT was associated with appropriate sleep duration and a decrease in chronic cough and sputum in male with airflow limitation. This was more pronounced in individuals with a FEV1 < 80% pred.
Neural architecture search via progressive partial connection with attention mechanism
Authors: Jin Cong , Huang Jinjie , Chen Yuanjian
Published: March 2024

Differentiable architecture search requires a larger computational consumption during architecture search, and there exists the depth gap problem under deeper network architecture. In this paper, we propose an attention-based progressive partially connected neural architecture search method (PPCAtt-NAS) to address these two issues. First, we introduce a progressive search strategy in the architecture search phase, build up the sophistication of the architecture gradually and perform path-level pruning in stages to bridge the depth gap. Second, we adopt a partial search scheme that performs channel-level partial sampling of the network architecture to further reduce the computational complexity of the architecture search. In addition, an attention mechanism is devised to improve the architecture search capability by enhancing the relevance between the feature channels. Finally, we conduct extensive comparison experiments with state-of-the-art methods on several public datasets, and our method is able to present higher architecture performance.
Association between systemic sclerosis and risk of cerebrovascular and cardiovascular disease: a meta-analysis
Authors: Chen I-Wen , Wang Wei-Ting , Lai Yi-Chen , Lin Chien-Ming , Liu Ping-Hsin , Wu Su-Zhen , Hung Kuo-Chuan
Published: March 2024

We aimed to evaluate the association between systemic sclerosis (SSc) and major cerebrovascular/cardiovascular risks through a systematic approach. Databases were systematically searched from their inception to October 10, 2023 for studies comparing cerebrovascular/cardiovascular event rates between patients with SSc and controls. The primary outcome was the stroke risk in patients with SSc. Secondary outcomes included risk of myocardial infarction (MI), cardiovascular disease (CVD), peripheral vascular disease (PVD), and venous thromboembolism (VTE). Seventeen studies with 6,642,297 participants were included. SSc was associated with a significantly increased risk of stroke (HR, 1.64; 95% confidence interval [CI], 1.35–2.01), CVD (HR, 2.12; 95% CI, 1.36–3.3), MI (HR, 2.15; 95% CI, 1.23–3.77), VTE (HR, 2.75; 95% CI, 1.77–4.28), and PVD (HR, 5.23; 95% CI, 4.25–6.45). Subgroup analysis revealed a significantly increased stroke risk in the non-Asian group (HR, 1.55; 95% CI, 1.26–1.9), while the Asian group displayed a higher but not statistically significant risk (HR, 1.86; 95% CI, 0.97–3.55). The study found that SSc is associated with a significantly increased risk of cerebrovascular/cardiovascular events. These findings highlight the importance of vasculopathy in SSc and suggest the need for enhanced clinical monitoring and preventive measures in this high-risk population.
Comprehensive enhancement in electrocatalytic oxygen evolution performance of nickel and cobalt complexes derived from π-conjugated N-heterocyclic carbene ligands through carbon composite strategy
Authors: Vijayakumar Monica , Yhobu Zhoveta , Małecki Jan Grzegorz , Nagaraju Dodahhali H. , Keri Rangappa S. , Budagumpi Srinivasa
Published: March 2024

Tailored NHC ligands featuring π-conjugated appendants along with the establishment of durable π–π stacking interactions between the NHC complexes (Ni/Co) and graphitic carbon substrates to boost the oxygen evolution performance are studied.
Novel photocatalytic carbon dots: efficiently inhibiting amyloid aggregation and quickly disaggregating amyloid aggregates
Authors: Shao Xu , Wang Chao , Wang Chaoli , Bai Mengyao , Hou Tongtong , Wang Xin , Yan Chaoren , Guan Ping , Hu Xiaoling
Published: March 2024

Novel photocatalytic carbon dots: efficiently inhibiting amyloid aggregation, quickly disaggregating amyloid aggregates and alleviating Aβ42-induced cytotoxicity.
Effect of organoclay on the physical properties of colorless and transparent copoly(amide imide) nanocomposites
Authors: Na Changyub , Kwac Lee Ku , Kim Hong Gun , Chang Jin-Hae
Published: March 2024

Copoly(amic acid) was prepared using the diamine monomer TFAB and the anhydride monomers 6FDA and BPA.
An efficient mRNA display protocol yields potent bicyclic peptide inhibitors for FGFR3c: outperforming linear and monocyclic formats in affinity and stability
Authors: Villequey Camille , Zurmühl Silvana S. , Cramer Christian N. , Bhusan Bhaskar , Andersen Birgitte , Ren Qianshen , Liu Haimo , Qu Xinping , Yang Yang , Pan Jia , Chen Qiujia , Münzel Martin
Published: March 2024

This work presents an efficient mRNA display protocol for making large libraries of bicyclic peptides and evaluating their performance vs. linear and monocyclic formats for affinity, specificity & plasma stability in a selection against FGFR3c.
Non-invasive diagnosis of bacterial and non-bacterial inflammations using a dual-enzyme-responsive fluorescent indicator
Authors: He Yue , Yang Majun , Cui Jingyi , Zhao Can , Jiang Bin , Guan Jiayun , Zhou Xiaobo , He Miao , Zhen Yaya , Zhang Yuxue , Jing Rongrong , Wang Qi , Qin Yuling , Wu Li
Published: March 2024

A dual-enzyme-responsive indicator for the non-invasive diagnosis of bacterial and non-bacterial inflammations has been developed. This indicator responds to NAD(P)H and NTR in inflammations, emitting two distinct turn-on fluorescence signals.
Fasting mimicking diet extends lifespan and improves intestinal and cognitive health
Authors: Wang Qingyi , Xu Jilei , Luo Man , Jiang Yao , Gu Yanrou , Wang Qiwen , He Jiamin , Sun Yong , Lin Yifeng , Feng Lijun , Chen Shujie , Hou Tongyao
Published: March 2024

FMD prolongs life, improves cognition and slows the ageing of the intestines. Microbiota and gut immunity may play a role.
Microfluidic-assisted formulation of cell membrane-camouflaged anisotropic nanostructures
Authors: Kenry
Published: March 2024

This work reports the development of a high-throughput microfluidic-based platform for the formulation of cell membrane-camouflaged anisotropic gold nanostructures with minimized phagocytic uptake and enhanced cancer cell targeting.
Effects of the surface energy and surface stress on the phase stability of spin crossover nano-objects: a thermodynamic approach
Authors: Mi Shiteng , Ridier Karl , Molnár Gábor , Nicolazzi William , Bousseksou Azzedine
Published: March 2024

Calculated temperature dependence of the high spin fraction for spin crossover thin films. All input parameters are measurable physical quantities.
Temperature modulated sustainable on/off photosynthesis switching of microalgae towards hydrogen evolution
Authors: Li Shangsong , Xu Zhijun , Lin Song , Li Luxuan , Huang Yan , Qiao Xin , Huang Xin
Published: March 2024

Copolymer PNIPAM–BA is used to co-assemble with algae into sol–gel reversibly switchable living material, which can be regulated by changing the temperature to trigger functionality switching between oxygen and hydrogen evolution on demand.