bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting cell types with supervised contrastive learning on cells and their types
Authors: Heryanto Yusri Dwi , Zhang Yao-zhong , Imoto Seiya
Published: January 2024

Single-cell RNA-sequencing (scRNA-seq) is a powerful technique that provides high-resolution expression profiling of individual cells. It significantly advances our understanding of cellular diversity and function. Despite its potential, the analysis of scRNA-seq data poses considerable challenges related to multicollinearity, data imbalance, and batch effect. One of the pivotal tasks in single-cell data analysis is cell type annotation, which classifies cells into discrete types based on their gene expression profiles. In this work, we propose a novel modeling formalism for cell type annotation with a supervised contrastive learning method, named SCLSC (Supervised Contrastive Learning for Single Cell). Different from the previous usage of contrastive learning in single cell data analysis, we employed the contrastive learning for instance-type pairs instead of instance-instance pairs. More specifically, in the cell type annotation task, the contrastive learning is applied to learn cell and cell type representation that render cells of the same type to be clustered in the new embedding space. Through this approach, the knowledge derived from annotated cells is transferred to the feature representation for scRNA-seq data. The whole training process becomes more efficient when conducting contrastive learning for cell and their types. Our experiment results demonstrate that the proposed SCLSC method consistently achieves superior accuracy in predicting cell types compared to five state-of-the-art methods. SCLSC also performs well in identifying cell types in different batch groups. The simplicity of our method allows for scalability, making it suitable for analyzing datasets with a large number of cells. In a real-world application of SCLSC to monitor the dynamics of immune cell subpopulations over time, SCLSC demonstrates a capability to discriminate cell subtypes of CD19+ B cells that were not present in the training dataset.
Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney fibrosis
Authors: Rudman-Melnick Valeria , Adam Mike , Stowers Kaitlynn , Potter Andrew , Ma Qing , Chokshi Saagar M. , Vanhoutte Davy , Valiente-Alandi Iñigo , Lindquist Diana M. , Nieman Michelle L. , Kofron J. Matthew , Chung Eunah , Park Joo-Seop , Potter S. Steven , Devarajan Prasad
Published: January 2024

Examining kidney fibrosis is crucial for mechanistic understanding and developing targeted strategies against chronic kidney disease (CKD). Persistent fibroblast activation and tubular epithelial cell (TEC) injury are key CKD contributors. However, cellular and transcriptional landscapes of CKD and specific activated kidney fibroblast clusters remain elusive. Here, we analyzed single cell transcriptomic profiles of two clinically relevant kidney fibrosis models which induced robust kidney parenchymal remodeling. We dissected the molecular and cellular landscapes of kidney stroma and newly identified three distinctive fibroblast clusters with “secretory”, “contractile” and “vascular” transcriptional enrichments. Also, both injuries generated failed repair TECs (frTECs) characterized by decline of mature epithelial markers and elevation of stromal and injury markers. Notably, frTECs shared transcriptional identity with distal nephron segments of the embryonic kidney. Moreover, we identified that both models exhibited robust and previously unrecognized distal spatial pattern of TEC injury, outlined by persistent elevation of renal TEC injury markers including Krt8 and Vcam1, while the surviving proximal tubules (PTs) showed restored transcriptional signature. We also found that long-term kidney injuries activated a prominent nephrogenic signature, including Sox4 and Hox gene elevation, which prevailed in the distal tubular segments. Our findings might advance understanding of and targeted intervention in fibrotic kidney disease.
Molecular detection of Citrus exocortis viroid (CEVd), Citrus viroid-III (CVd-III), and Citrus viroid-IV (CVd-IV) in Palestine
Authors: Abualrob Aswar , Alabdallah Osama , Kubaa Raied Abou , Naser Sabri M. , Alkowni Raed
Published: January 2024

Citrus hosts various phytopathogens that have impacted productivity, including viroids. Missing data on the status of viroids in citrus in Palestine were not reported. This study was aimed to detect any of Citrus exocortis viroid (CEVd), Citrus viroid-III (CVd-III), and Citrus viroid-IV (CVd-IV) in the Palestinian National Agricultural Research Center (NARC) germplasm collection Field inspections found symptoms such as leaf epinasty; vein discoloration, and bark cracking on various citrus varieties. RT-PCR revealed a significant prevalence of CVd-IV; CEVd and CVd-III (47%, 31%, and 22%; respectively). CVd-III variants with 91.3% nucleic acid sequence homology have been reported. The sequence of each viroid were deposited in GenBank as (OP925746 for CEVd, OP902248 and OP902249 for CVd-III-PS-1 and -PS-2 isolates, and OP902247 for CVd-IV). This was the first to report three of citrus viroids in Palestine, appealing to apply of phytosanitary measures to disseminate healthy propagating materials free from viroids.
Deficiency of the lipid flippase ATP10A causes diet-induced dyslipidemia in female mice
Authors: Norris Adriana C. , Yazlovitskaya Eugenia M. , Zhu Lin , Rose Bailey S. , May Jody C. , Gibson-Corley Katherine N. , McLean John A. , Stafford John M. , Graham Todd R.
Published: January 2024

Genetic association studies have linked ATP10A and closely related type IV P-type ATPases (P4-ATPases) to insulin resistance and vascular complications, such as atherosclerosis. ATP10A translocates phosphatidylcholine and glucosylceramide across cell membranes, and these lipids or their metabolites play important roles in signal transduction pathways regulating metabolism. However, the influence of ATP10A on lipid metabolism in mice has not been explored. Here, we generated gene-specific Atp10A knockout mice and show that Atp10A−/− mice fed a high-fat diet did not gain excess weight relative to wild-type littermates. However, Atp10A−/− mice displayed female-specific dyslipidemia characterized by elevated plasma triglycerides, free fatty acids and cholesterol, as well as altered VLDL and HDL properties. We also observed increased circulating levels of several sphingolipid species along with reduced levels of eicosanoids and bile acids. The Atp10A−/− mice also displayed hepatic insulin resistance without perturbations to whole-body glucose homeostasis. Thus, ATP10A has a sex-specific role in regulating plasma lipid composition and maintaining hepatic liver insulin sensitivity in mice.
Role of the mechanical microenvironment on CD-44 expression of breast adenocarcinoma in response to radiotherapy
Authors: Frascogna Crescenzo , Mottareale Rocco , La Verde Giuseppe , Arrichiello Cecilia , Muto Paolo , Netti Paolo A. , Pugliese Mariagabriella , Panzetta Valeria
Published: January 2024

The biological effects of ionizing radiation are exploited in the clinical practice of radiotherapy to destroy tumour cells while sparing the surrounding normal tissue. While most of the radiotherapy research focused on DNA damage and repair, recently a great attention is going to cells' interactions with the mechanical microenvironment of both malignant and healthy tissues after exposure. In fact, the stiffness of the extracellular matrix can modify cells' motility and spreading through the modulation of transmembrane proteins and surface receptors' expression, such as CD-44. CD-44 receptor has held much interest also in targeted-therapy due to its affinity with hyaluronic acid, which can be used to functionalize biodegradable nanoparticles loaded with chemotherapy drugs for targeted therapy. We evaluated changes in CD-44 expression in two mammary carcinoma cell lines (MCF10A and MDA-MB-231) after exposure to X-ray (2 or 10 Gy). To explore the role of the mechanical microenvironment, we mimicked tissues' stiffness with polyacrylamide's substrates producing two different elastic modulus values (0.5 and 15 kPa). We measured a dose dependent increase in CD-44 relative expression in tumour cells cultured in a stiffer microenvironment. These findings highlight a crucial connection between the mechanical properties of the cell's surroundings and the post-radiotherapy expression of surface receptors.
Development and external validation of a clinical prediction model for predicting quality of recovery up to 1 week after surgery
Authors: van Beek Stefan , Nieboer Daan , Klimek Markus , Stolker Robert Jan , Mijderwijk Hendrik-Jan
Published: January 2024

The Quality of Recovery Score-40 (QoR-40) has been increasingly used for assessing recovery after patients undergoing surgery. However, a prediction model estimating quality of recovery is lacking. The aim of the present study was to develop and externally validate a clinical prediction model that predicts quality of recovery up to one week after surgery. The modelling procedure consisted of two models of increasing complexity (basic and full model). To assess the internal validity of the developed model, bootstrapping (1000 times) was applied. At external validation, the model performance was evaluated according to measures for overall model performance (explained variance (R2)) and calibration (calibration plot and slope). The full model consisted of age, sex, previous surgery, BMI, ASA classification, duration of surgery, HADS and preoperative QoR-40 score. At model development, the R2 of the full model was 0.24. At external validation the R2 dropped as expected. The calibration analysis showed that the QoR-40 predictions provided by the developed prediction models are reliable. The presented models can be used as a starting point for future updating in prediction studies. When the predictive performance is improved it could be implemented clinically in the future.
Electron-donating functional groups strengthen ligand-induced chiral imprinting on CsPbBr3 quantum dots
Authors: Dunlap-Shohl Wiley A. , Tabassum Nazifa , Zhang Peng , Shiby Elizabeth , Beratan David N. , Waldeck David H.
Published: January 2024

Chiral perovskite nanoparticles and films are promising for integration in emerging spintronic and optoelectronic technologies, yet few design rules exist to guide the development of chiral material properties. The chemical space of potential building blocks for these nanostructures is vast, and the mechanisms through which organic ligands can impart chirality to the inorganic perovskite lattice are not well understood. In this work, we investigate how the properties of chiral ammonium ligands, the most common organic ligand type used with perovskites, affect the circular dichroism of strongly quantum confined CsPbBr3 nanocrystals. We show that aromatic ammonium ligands with stronger electron-donating groups lead to higher-intensity circular dichroism associated with the lowest-energy excitonic transition of the perovskite nanocrystal. We argue that this behavior is best explained by a modulation of the exciton wavefunction overlap between the nanocrystal and the organic ligand, as the functional groups on the ligand can shift electron density toward the organic species-perovskite lattice interface to increase the imprinting.
EEG epilepsy seizure prediction: the post-processing stage as a chronology
Authors: Batista Joana , Pinto Mauro F. , Tavares Mariana , Lopes Fábio , Oliveira Ana , Teixeira César
Published: January 2024

Almost one-third of epileptic patients fail to achieve seizure control through anti-epileptic drug administration. In the scarcity of completely controlling a patient’s epilepsy, seizure prediction plays a significant role in clinical management and providing new therapeutic options such as warning or intervention devices. Seizure prediction algorithms aim to identify the preictal period that Electroencephalogram (EEG) signals can capture. However, this period is associated with substantial heterogeneity, varying among patients or even between seizures from the same patient. The present work proposes a patient-specific seizure prediction algorithm using post-processing techniques to explore the existence of a set of chronological events of brain activity that precedes epileptic seizures. The study was conducted with 37 patients with Temporal Lobe Epilepsy (TLE) from the EPILEPSIAE database. The designed methodology combines univariate linear features with a classifier based on Support Vector Machines (SVM) and two post-processing techniques to handle pre-seizure temporality in an easily explainable way, employing knowledge from network theory. In the Chronological Firing Power approach, we considered the preictal as a sequence of three brain activity events separated in time. In the Cumulative Firing Power approach, we assumed the preictal period as a sequence of three overlapping events. These methodologies were compared with a control approach based on the typical machine learning pipeline. We considered a Seizure Prediction horizon (SPH) of 5 mins and analyzed several values for the Seizure Occurrence Period (SOP) duration, between 10 and 55 mins. Our results showed that the Cumulative Firing Power approach may improve the seizure prediction performance. This new strategy performed above chance for 62% of patients, whereas the control approach only validated 49% of its models.
Arabic gum/chitosan/Zn–NPs composite film maintains the quality of Hass avocado fruit by delaying ripening and activating enzymatic defense mechanisms
Authors: Rashedy Ahmed A. , Abd El-Aziz Mahmoud E. , Abd-Allah Ahmed S. E. , Hamed Hamed H. , Emam Hala E. , Abd El-Moniem Eman A. A.
Published: January 2024

Avocado fruit is a climacteric fruit that has a short life after harvest. Chitosan (Ch) and Arabic gum (AG) have a pronounced effect on the storability of fruits. This investigation aimed to determine the effect of individual or combined use of Ch and AG as well as Ch/AG enriched with 2, 4, 8% Zn–NPs on physio-biochemical attributes and antioxidant capacity of Hass avocado fruit during cold storage (7 °C). The result showed that Ch or AG alone succeeded in maintaining fruit quality of Hass fruit during cold storage. Also, combined application of Ch/AG was more effective than individual application of Ch or AG in reducing fruit weight and polyphenol oxidase activity (PPO) as well as increasing total antioxidant capacity (TAC) and malondialdehyde (MDA). Moreover, Ch/AG coating enriched with 8% Zn–NPs recorded the lowest fruit weight loss, fruit decay %, TSS fruit content, fruit firmness and improved fruit skin and pulp color significantly compared to Ch/AG and control. Coating with Ch/AG/2%Zn NPs recorded the highest peroxidase (POD) activity, while Ch/AG/8% Zn–NPs recorded the highest TAC and the lowest PPO activity. Moreover, enriched Ch/GA with Zn–NPs recorded the highest CAT and POD activity compared to the control. This study shows the efficiency of Ch/AG enriched with Zn–NPs on preserving Hass avocado fruit quality during cold storage by delaying ripening process and activating enzymatic defense mechanisms.
Evolutionary patterns and microscopic mechanisms of strength in mine tailings backfilled with waste glass
Authors: Deng Daiqiang , Gao Yu , Chen Zimin , Wang Ye
Published: January 2024

In order to promote the sustainable use of resources and reduce the waste of waste glass and tailings resources. The present study focuses on a fluorite mine as the research subject, utilizing coarse tailings, fine tailings, cement substitute-curing agent, and recycled waste glass as the primary raw materials. It investigates the changes in compressive strength of coarse tailing with varying sand- binder ratios and glass content at 3-day, 7-day, and 28-day intervals when the filling slurry concentration is set at 77% and the ratio of coarse tailings to fine tailings is maintained at 2:1. The findings indicate that there is minimal impact on the compressive strength of test blocks when using a sand binder ratio of 4:1 and a glass sand content below 10%. However, once the glass sand content exceeds 10%, a significant decline in compressive strength occurs. Scanning electron microscope (SEM) images reveal ettringite crystal formation in test blocks with both 0% and 25% glass sand content due to high levels of Na2O in the glass sand. This leads to internal expansion within test blocks resulting in reduced strength. Notably, when using a sand-binder ratio of 8:1 along with a glass sand content of 25%, early strength characteristics are observed for test blocks. Furthermore, incorporating glass sand has little influence on late-stage strength for backfill when employing either an 8:1 or 12:1 sand-binder ratio. Based on this experiment conducted under conditions including mass concentration of 77%, the optimal waste-glass-to-mine-tailings-filling-sand-binder-ratio is determined as 8:1with a corresponding glass content of 25%.
Spatial inequalities and non-linear association of continuous variables with mortality risk of liver transplantation in Iran: a retrospective cohort study
Authors: Kazemimajd Somayeh , Roshanaei Ghodratollah , Tapak Leili
Published: January 2024

Liver transplantation is the second most common solid organ transplant and the best option for liver failure. Of course, patient survival after transplantation depends on many risk factors. The aim of this study was to investigate the spatial and non-linear effects of continuous risk factors on patient survival after liver transplantation. This retrospective cohort study (n = 3148) used data on liver transplantation in Iran (2004–2019). A generalized additive model with spatial effects and non-linear effects of age and Model for End-Stage Liver Disease (MELD) score variables by penalized spline was used. The majority of patients were male (63.3%), with a mean (SD) age of 42.65 (13.31) and a mean (SD) MELD score of 24.43 (6.72). The 1, 5, and 10-year survival rates were 88.2%, 84.6%, and 82.5% respectively. The non-linear effect showed a steeper slope of the age effect on the hazard of death after the age of 50 (p < 0.05), and the MELD score had a direct but non-linear relationship with the hazard of death (p < 0.05). In the spatial pattern, the provinces with a greater distance from the transplant center had significantly fewer old patients than other provinces. Also, more distant provinces with an older transplant age had higher post-transplant mortality rates. Our study showed that it is better to take age and MELD score into account in postoperative care. The spatial pattern of mortality risk reflects inequalities in access to transplantation and public health services after transplantation.
The spatial distribution of potentially toxic elements in the mountain forest topsoils (the Silesian Beskids, southern Poland)
Authors: Rahmonov Oimahmad , Sobala Michał , Środek Dorota , Karkosz Dominik , Pytel Sławomir , Rahmonov Małgorzata
Published: January 2024

Progressive industrialisation and urbanisation in recent decades have dramatically affected the soil cover and led to significant changes in its properties, which inevitably affect the functioning of other components of the forest ecosystems. The total content of Pb, Cd, Zn, Fe, Cr, Cu, Ni, As, and Hg was studied in twenty-five plots at different heights in the topsoil (organic and humus horizons) formed from the Carpathian flysch in the area of the Silesian Beskids (Western Carpathians). The aim of this article is to analyse the spatial distribution of potentially toxic elements in the mountain forest topsoil in different types of plant communities and to determine the relationship between altitude and potentially toxic elements contamination. The soils studied are acidic or very acidic, with an average range of 3.8 (H2O) and 2.9 (KCl). Concentrations of the metals Cd, Zn, Fe, Cr, Cu, Ni, and Hg on the plots that were analysed are within the range of permissible standards for forest ecosystems in Poland, while Pb and As exceed the permissible standards for this type of ecosystem. Spearman’s rank correlation coefficient showed a high correlation between Fe–Cr (r(32) = 0.879, Pb-Hg r(32) = 0.772, Ni–Cr r(32) = 0.738, Zn-Cd r(32) = 0.734, and Cu-Hg r(32) = 0.743, and a moderate statistically significant positive correlation between Cu-Pb r(32) = 0.667 and As-Pb r(32) = 0.557. No correlation was found between altitude and the occurrence of potentially toxic elements. The geo-accumulation index (Igeo) index, on the other hand, indicates that Pb, As, and Cd have the highest impact on soil contamination in all study plots: it classifies soils from moderately to strongly polluted. The enrichment factor (EF) obtained for As and Hg indicates significant-to-very high enrichment in all areas studied. The potential ecological risk index (PLI) calculated for the sites indicates the existence of pollution in all areas examined. The highest risk categories (considerable to very high) are associated with cadmium and mercury.
Enhancing citrus fruit yield investigations through flight height optimization with UAV imaging
Authors: Kwon Soon-Hwa , Ku Ki Bon , Le Anh Tuan , Han Gyung Deok , Park Yosup , Kim Jaehong , Tuan Thai Thanh , Chung Yong Suk , Mansoor Sheikh
Published: January 2024

Citrus fruit yield is essential for market stability, as it allows businesses to plan for production and distribution. However, yield estimation is a complex and time-consuming process that often requires a large number of field samples to ensure representativeness. To address this challenge, we investigated the optimal altitude for unmanned aerial vehicle (UAV) imaging to estimate the yield of Citrus unshiu fruit. We captured images from five different altitudes (30 m, 50 m, 70 m, 90 m, and 110 m), and determined that a resolution of approximately 5 pixels/cm is necessary for reliable estimation of fruit size based on the average diameter of C. unshiu fruit (46.7 mm). Additionally, we found that histogram equalization of the images improved fruit count estimation compared to using untreated images. At the images from 30 m height, the normal image estimates fruit numbers as 73, 55, and 88. However, the histogram equalized image estimates 88, 71, 105. The actual number of fruits is 124, 88, and 141. Using a Vegetation Index such as IPCA showed a similar estimation value to histogram equalization, but I1 estimation represents a gap to actual yields. Our results provide a valuable database for future UAV field investigations of citrus fruit yield. Using flying platforms like UAVs can provide a step towards adopting this sort of model spanning ever greater regions at a cheap cost, with this system generating accurate results in this manner.
Early parental deprivation during primate infancy has a lifelong impact on gene expression in the male marmoset brain
Authors: Shinohara Haruka , Meguro-Horike Makiko , Inoue Takashi , Shimazu Miyuki , Hattori Machiko , Hibino Hitoshi , Fukasawa Kazumasa , Sasaki Erika , Horike Shin-ichi
Published: January 2024

Adverse early life experiences are well-established risk factors for neurological disorders later in life. However, the molecular mechanisms underlying the impact of adverse experiences on neurophysiological systems throughout life remain incompletely understood. Previous studies suggest that social attachment to parents in early development are indispensable for infants to grow into healthy adults. In situations where multiple offspring are born in a single birth in common marmosets, human hand-rearing is employed to ensure the survival of the offspring in captivity. However, hand-reared marmosets often exhibit behavioral abnormalities, including abnormal vocalizations, excessive attachment to the caretaker, and aggressive behavior. In this study, comprehensive transcriptome analyses were conducted on hippocampus tissues, a neuroanatomical region sensitive to social attachment, obtained from human hand-reared (N = 6) and parent-reared male marmosets (N = 5) at distinct developmental stages. Our analyses revealed consistent alterations in a subset of genes, including those related to neurodevelopmental diseases, across different developmental stages, indicating their continuous susceptibility to the effects of early parental deprivation. These findings highlight the dynamic nature of gene expression in response to early life experiences and suggest that the impact of early parental deprivation on gene expression may vary across different stages of development.
Genotype by environment and genotype by yield*trait interactions in sugar beet: analyzing yield stability and determining key traits association
Authors: Hassani Mahdi , Mahmoudi Seyed Bagher , Saremirad Ali , Taleghani Dariush
Published: January 2024

The genotype by environment interaction significantly influences plant yield, making it imperative to understand its nature for the creation of breeding programs to enhance crop production. However, this is not the only obstacle in the yield improvement process. Breeders also face the significant challenge of unfavorable and negative correlations among key traits. In this study, the stability of root yield and white sugar yield, and the association between the key traits of root yield, sugar content, nitrogen, sodium, and potassium were examined in 20 sugar beet genotypes. The study was conducted using a randomized complete block design with four replications over two consecutive years across five locations. The combined analysis of variance results revealed significant main effects of year, location, and genotype on both root yield and white sugar yield. Notably, two-way and three-way interactions between these main effects on root yield and white sugar yield resulted in a significant difference. The additive main effect and multiplicative interaction analysis revealed that the first five interaction principal components significantly impacted both the root yield and white sugar yield. The linear mixed model results for root yield and white sugar yield indicated that the genotype effect and the genotype by environment interaction were significant. The weighted average absolute scores of the best linear unbiased predictions biplot demonstrated that genotypes 20, 4, 7, 2, 16, 3, 6, 1, 14, and 15 were superior in terms of root yield. For white sugar yield, genotypes 4, 16, 3, 7, 5, 1, 10, 20, 2, and 6 stood out. These genotypes were not only stable but also had a yield value higher than the total average. All key traits, which include sugar content, sodium, potassium, and alpha amino nitrogen, demonstrated a negative correlation with root yield. Based on the genotype by yield*trait analysis results, genotypes 20, 19, and 16 demonstrated optimal performance when considering the combination of root yield with sugar content, sodium, alpha amino nitrogen, and potassium. The multi-trait stability study, genotype 13 ranked first, and genotypes 10, 8, and 9 were identified as the most ideal stable genotypes across all traits. According to the multi-trait stability index, genotype 13 emerged as the top-ranking genotype. Additionally, genotypes 10, 8, and 9 were recognized as the most stable genotypes.
An attenuation field network for dedicated cone beam breast CT with short scan and offset detector geometry
Authors: Fu Zhiyang , Tseng Hsin Wu , Vedantham Srinivasan
Published: January 2024

The feasibility of full-scan, offset-detector geometry cone-beam CT has been demonstrated for several clinical applications. For full-scan acquisition with offset-detector geometry, data redundancy from complementary views can be exploited during image reconstruction. Envisioning an upright breast CT system, we propose to acquire short-scan data in conjunction with offset-detector geometry. To tackle the resulting incomplete data, we have developed a self-supervised attenuation field network (AFN). AFN leverages the inherent redundancy of cone-beam CT data through coordinate-based representation and known imaging physics. A trained AFN can query attenuation coefficients using their respective coordinates or synthesize projection data including the missing projections. The AFN was evaluated using clinical cone-beam breast CT datasets (n = 50). While conventional analytical and iterative reconstruction methods failed to reconstruct the incomplete data, AFN reconstruction was not statistically different from the reference reconstruction obtained using full-scan, full-detector data in terms of image noise, image contrast, and the full width at half maximum of calcifications. This study indicates the feasibility of a simultaneous short-scan and offset-detector geometry for dedicated breast CT imaging. The proposed AFN technique can potentially be expanded to other cone-beam CT applications.
ROX index as a predictor of failure of high-flow nasal cannula in infants with bronchiolitis
Authors: Nascimento Milena Siciliano , Zólio Bianca Agostini , Vale Luciana Assis Pires Andrade , Silva Patrícia Angelica de Lima , Souza Thereza Silva , Gonçalves Louise Helena Rodrigues , Fascina Linus Pauling , do Prado Cristiane
Published: January 2024

High-flow nasal cannula (HFNC) is a relatively recent therapy that has been used to treat respiratory failure. Until now, the criterion for failure requiring escalation to other forms of ventilatory support has remained unclear. This study evaluated how the ROX index predicts the success or failure of HFNC in infants with bronchiolitis. A prospective, observational, multicenter study was conducted in 2 pediatric ICUs. The data were collected at 7 moments. Patients were categorized into failure and success groups according to HFNC. A total of 102 infants were included, 18(17.6%) of whom failed HFNC therapy. For the ROX index, significant differences were observed between the failure 5.8(95%CI 4.7–7.1) and success 7.7(95%CI 7.2–8.2) groups (p = 0.005) at the 12 h evaluation. According to the analysis of the performance of the ROX index, the AUC at 12 h was 0.716(95%CI 0.591–0.842; p = 0.016). The best cutoff range for the ROX index at 12 h was 6.50–7.18, with a sensitivity of 42% and a specificity of 66% at the cutoff of 6.50, and a sensitivity of 92% and a specificity of 54% at the cutoff of 7.18. We concluded that the ROX index could be effective at predicting the failure of HFNC therapy in infants with bronchiolitis beginning at 12 h after installation.
Boosting effect of strong western pole of the Indian Ocean Dipole on the decay of El Niño events
Authors: Wu Jia , Fan Hanjie , Lin Shuheng , Zhong Wenxiu , He Shan , Keenlyside Noel , Yang Song
Published: January 2024

The Indian Ocean Basin (IOB) mode is believed to favor the decay of El Niño via modulating the zonal wind anomalies in the western equatorial Pacific, while the contribution of the Indian Ocean Dipole (IOD) mode to the following year’s El Niño remains highly controversial. In this study, we use the evolution of fast and slow decaying El Niño events during 1950–2020 to demonstrate that the positive IOD with a strong western pole prompts the termination of El Niño, whereas a weak western pole has no significant effect. The strong western pole of a positive IOD leads to a strong IOB pattern peaking in the late winter (earlier than normal), enhancing local convection and causing anomalous rising motions over the tropical Indian Ocean and sinking motions over the western tropical Pacific. The surface equatorial easterly wind anomalies on the western flank of the sinking motions stimulate oceanic equatorial upwelling Kelvin waves, which shoal the thermocline in the eastern equatorial Pacific and rapidly terminate the equatorial warming during El Niño. However, a weak western pole of the IOD induces a weak IOB mode that peaks in the late spring, and the above-mentioned cross-basin physical processes do not occur.
X-ray phase contrast reveals soft tissue and shell growth lines in mollusks
Authors: Häggmark Ilian , Hoshino Masato , Uesugi Kentaro , Sasaki Takenori
Published: January 2024

High-resolution 3D imaging of species with exoskeletons such as shell-bearing mollusks typically involves destructive steps. Nondestructive alternatives are desirable since samples can be rare and valuable, and destructive steps are time-consuming and may distort the tissue. Here, we show for the first time that propagation-based phase-contrast X-ray imaging can significantly increase contrast in mollusks with intact shells. By using the recently upgraded monochromator at the SPring-8 BL20B2 synchrotron beamline, we imaged six species of mollusks, showing that X-ray phase contrast enhances soft-tissue contrast. Features that are almost invisible in conventional attenuation-based micro-computed tomography (micro-CT) are clearly reproduced with phase-contrast imaging under the same scan conditions. Furthermore, this method can reveal features such as growth rings in the shell and differentiate between calcite and aragonite crystal forms. Phase-contrast imaging can thus serve as a compelling alternative when destructive methods are not an option.
Single-cell transcriptomics enable the characterization of local extension in retinoblastoma
Authors: Liu Yaoming , Hu Wei , Xie Yanjie , Tang Junjie , Ma Huan , Li Jinmiao , Nie Jiahe , Wang Yinghao , Gao Yang , Cheng Chao , Li Cheng , Ma Yujun , Su Shicai , Zhang Zhihui , Bao Yuekun , Ren Yi , Wang Xinyue , Sun Fengyu , Li Shengli , Lu Rong
Published: January 2024

Retinoblastoma (RB) is the most prevalent ocular tumor of childhood, and its extraocular invasion significantly increases the risk of metastasis. Nevertheless, a single-cell characterization of RB local extension has been lacking. Here, we perform single-cell RNA sequencing on four RB samples (two from intraocular and two from extraocular RB patients), and integrate public datasets of five normal retina samples, four intraocular samples, and three extraocular RB samples to characterize RB local extension at the single-cell level. A total of 128,454 qualified cells are obtained in nine major cell types. Copy number variation inference reveals chromosome 6p amplification in cells derived from extraocular RB samples. In cellular heterogeneity analysis, we identified 10, 8, and 7 cell subpopulations in cone precursor like cells, retinoma like cells, and MKI67+ photoreceptorness decreased (MKI67+ PhrD) cells, respectively. A high expression level of SOX4 was detected in cells from extraocular samples, especially in MKI67+ PhrD cells, which was verified in additional clinical RB samples. These results suggest that SOX4 might drive RB local extension. Our study presents a single-cell transcriptomic landscape of intraocular and extraocular RB samples, improving our understanding of RB local extension at the single-cell resolution and providing potential therapeutic targets for RB patients.
STAT3 and SOX-5 induce BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells
Authors: Wang Xian , Han Chao , Yang Di , Zhou Jian , Dong Hui , Wei Zhiyuan , Xu Shuai , Xu Chen , Zhang Yiwei , Sun Yi , Ni Bing , Guo Sheng , Zhang Jingbo , Zhao Tingting , Chen Xiangmei , Luo Jie , Wu Yuzhang , Tian Yi
Published: January 2024

Retinoid-related orphan receptor gamma t (RORγt) is the lineage-specific transcription factor for T helper 17 (Th17) cells. Our previous study demonstrated that STAT3 likely participates in the activation of RORCE2 (a novel enhancer of the RORγt gene) in Th17 cells. However, the detailed mechanism is still unclear. Here, we demonstrate that both STAT3 and SOX-5 mediate the enhancer activity of RORCE2 in vitro. Deletion of the STAT3 binding site (STAT3-BS) in RORCE2 impaired RORγt expression and Th17 differentiation, resulting in reduced severity of experimental autoimmune encephalomyelitis (EAE). Mechanistically, STAT3 and SOX-5 bind the RORCE2 region and recruit the chromatin remodeling factor BRG1 to remodel the nucleosomes positioned at this region. Collectively, our data suggest that STAT3 and SOX-5 mediate the differentiation of Th17 cells through the induction of BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells.
Structural basis and selectivity of sulfatinib binding to FGFR and CSF-1R
Authors: Lin Qianmeng , Dai Shuyan , Qu Lingzhi , Lin Hang , Guo Ming , Wei Hudie , Chen Yongheng , Chen Xiaojuan
Published: January 2024

Acquired drug resistance poses a challenge for single-target FGFR inhibitors, leading to the development of dual- or multi-target FGFR inhibitors. Sulfatinib is a multi-target kinase inhibitor for treating neuroendocrine tumors, selectively targeting FGFR1/CSF-1R. To elucidate the molecular mechanisms behind its binding and kinase selectivity, we determined the crystal structures of sulfatinib with FGFR1/CSF-1R. The results reveal common structural features and distinct conformational adaptability of sulfatinib in response to FGFR1/CSF-1R binding. Further biochemical and structural analyses disclose sensitivity of sulfatinib to FGFR/CSF-1R gatekeeper mutations. The insensitivity of sulfatinib to FGFR gatekeeper mutations highlights the indispensable interactions with the hydrophobic pocket for FGFR selectivity, whereas the rotatory flexibility may enable sulfatinib to overcome CSF-1RT663I. This study not only sheds light on the structural basis governing sulfatinib’s FGFR/CSF-1R inhibition, but also provides valuable insights into the rational design of dual- or multi-target FGFR inhibitors with selectivity for CSF-1R and sensitivity to gatekeeper mutations.
Bridging the incompatibility gap in dual asymmetric catalysis over a thermoresponsive hydrogel-supported catalyst
Authors: Huang Renfu , Yang Shoujin , Hu Zhipeng , Peng Bangtai , Zhu Yuanli , Cheng Tanyu , Liu Guohua
Published: January 2024

The integration of dual asymmetric catalysis is highly beneficial for the synthesis of organic molecules with multiple stereocenters. However, two major issues that need to be addressed are the intrinsic deactivation of dual-species and the extrinsic conflict of reaction conditions. To overcome these concerns, we have utilized the compartmental and thermoresponsive properties of poly(N-isopropylacrylamide) (PNIPAM) to develop a cross-linked PNIPAM-hydrogel-supported bifunctional catalyst. This catalyst is designed with Rh(diene) species situated on the outer surface and Ru(diamine) species positioned within the interior of the hydrogel. The compartmental function of PNIPAM in the middle overcomes intrinsic mutual deactivations between the dual-species. The thermoresponsive nature of PNIPAM allows for precise control of catalytic pathways in resolving external conflicts by controlling the reaction switching between an Rh-catalyzed enantioselective 1,4-addition at 50°C and a Ru-catalyzed asymmetric transfer hydrogenation (ATH) at 25°C. As we envisioned, this sequential 1,4-addition/reduction dual enantioselective cascade reaction achieves a transformation from incompatibility to compatibility, resulting in direct access to γ-substituted cyclic alcohols with dual stereocenters in high yields and enantio/diastereoselectivities. Mechanistic investigation reveals a reversible temperature transition between 50°C and 25°C, ensuring a cascade process comprising a 1,4-addition followed by the ATH process.
A systematic review of the definitions, narratives and paths forwards for a protein transition in high-income countries
Authors: Duluins Océane , Baret Philippe Vincent
Published: January 2024

The protein transition, aiming to rebalance protein intake between animal and alternative proteins, is gaining momentum in scientific and policy discussions on food system transformation. Here, using a systematic review approach, we identified 33 articles that address challenges in reducing the environmental impacts of protein production and consumption, providing healthy diets for a growing population and preventing adverse effects of industrial livestock production systems. We found unclear definitions of the protein transition, conflicting views on reduction or replacement of dietary protein and a lack of attention to systemic change by reducing protein to its macronutrient function. Three narratives were identified, namely, the consumer narrative focusing on consumption-based solutions targeting dietary changes; the techno-centred narrative developing new, more resource-efficient protein production systems; and the socio-technological narrative that intends to transition the agri-food system from an animal-dominated regime to an alternative protein regime. We conclude that solutions should consider factors such as scale, initiating actors and expected impact to support complementary protein transition approaches.
Unlocking the potential of ordinary Portland cement with hydration control additive enabling low-carbon building materials
Authors: Li Xuerun , Grassl Harald , Hesse Christoph , Dengler Joachim
Published: January 2024

Ordinary Portland cement (OPC) is the core ingredient of many construction materials. In 2022, 4.1 billion tons were used worldwide, contributing to ~8% of CO2 emissions ( ~ 3 Gt/year). Nevertheless, the complete strength-generating capacity of OPC remains unrealized due to the restricted conversion of aluminates to ettringite, caused by conventional hydration kinetics. Here we show a hydration control additive that selectively modifies the hydration kinetics, thereby facilitating enhanced dissolution of aluminates (calcium aluminoferrite and tricalcium aluminate) in OPC, which promotes ettringite formation at a desired time. Increasing ettringite content improves packing of the hardened cement, resulting in ~50% higher specific strength and enabling cement reduction. It also increases OPC strength development efficiency, reducing carbon footprint by ~30%. The use of this additive can be combined with methods such as reducing water and/or using supplementary cementitious materials (SCMs) to prepare building materials with significantly fewer CO2 emissions than those from conventional OPC.
Indian interstate trade exacerbates nutrient pollution in food production hubs
Authors: Goyal Shekhar Sharan , Dave Raviraj , Kumar Rohini , Bhatia Udit
Published: January 2024

Intensive agricultural practices have powered green revolutions, helping nations attain self-sufficiency. However, these fertilizer-intensive methods and exploitative trade systems have created unsustainable agricultural systems. To probe the environmental consequences on production hubs, we map the fate of Nitrogen and Phosphorus in India’s interstate staple crop trade over the recent decade. The nation’s food bowls, while meeting national food demand, are becoming pollution-rich, sustaining around 50% of the total surplus from trade transfer, accounting for 710 gigagrams of nitrogen per year and 200 gigagrams of phosphorus per year. In combination with water balance analysis, surplus nutrient conversion to a graywater footprint further highlights an aggravated situation in major producer regions facing long-term water deficits. Given India’s role in global food security, identifying the nation’s environmental vulnerability can help in designing appropriate policy interventions for sustainable development.
Auditory-motor synchronization and perception suggest partially distinct time scales in speech and music
Authors: Barchet Alice Vivien , Henry Molly J. , Pelofi Claire , Rimmele Johanna M.
Published: January 2024

Speech and music might involve specific cognitive rhythmic timing mechanisms related to differences in the dominant rhythmic structure. We investigate the influence of different motor effectors on rate-specific processing in both domains. A perception and a synchronization task involving syllable and piano tone sequences and motor effectors typically associated with speech (whispering) and music (finger-tapping) were tested at slow (~2 Hz) and fast rates (~4.5 Hz). Although synchronization performance was generally better at slow rates, the motor effectors exhibited specific rate preferences. Finger-tapping was advantaged compared to whispering at slow but not at faster rates, with synchronization being effector-dependent at slow, but highly correlated at faster rates. Perception of speech and music was better at different rates and predicted by a fast general and a slow finger-tapping synchronization component. Our data suggests partially independent rhythmic timing mechanisms for speech and music, possibly related to a differential recruitment of cortical motor circuitry.
Silicon-containing nanomedicine and biomaterials: materials chemistry, multi-dimensional design, and biomedical application
Authors: Chen Liang , Zhang Shanshan , Duan Yanqiu , Song Xinran , Chang Meiqi , Feng Wei , Chen Yu
Published: January 2024

Silicon-based biomaterials have been extensively developed in the past decades. The classification, characteristics, multi-dimensional design, and biomedical applications of silicon-containing biomaterials are comprehensively elaborated.
A novel nanoprobe for visually investigating the controversial role of miRNA-34a as an oncogene or tumor suppressor in cancer cells
Authors: Chen Zhe , Ge Chuandong , Zhu Xiaokai , Sun Ping , Sun Zeyuan , Derkach Tetiana , Zhou Mingyang , Wang Yaoguang , Luan Mingming
Published: January 2024

Identify the controversial role of miRNA-34a as an oncogene or tumor suppressor. Simultaneous fluorescence imaging of miRNA-34a and caspase-3 in living cells.
One-step synthesis of a dual-functional AIE-active probe for ClO− detection and photodynamic therapy
Authors: Liu Yiping , Fu Juan , Wan Jiaxing , Huang Tongsheng , Zhu Weifeng , Tian Jianwen , Liu Meiying , Zhang Xiaoyong , Wei Yen
Published: January 2024

An amphiphilic fluorescent probe (BHSMP) with aggregation-induced emission (AIE) features was synthesized via a one-step route.
Can cage-like cations function as antagonistic ions towards pentazolate anions?
Authors: Jiang Tianyu , Xia Honglei , Zhang Wenquan , Cai Ziwu , Song Siwei , Liu Tianlin
Published: January 2024

In this work, we synthesized and studied two cyclo-N5− salts based on the cage-like cations. The results suggest that selecting cage-like cations as antagonistic ions to cyclo-N5− anions may be a better choice compared to the chain-like cations with similar structures.
Photodynamics of azaindoles in polar media: the influence of the environment
Authors: Lamas Iker , Montero Raúl , Martínez-Martínez Virginia , Longarte Asier
Published: January 2024

We have studied the relaxation dynamics of a family of azaindole (AI) structural isomers, 4-, 5-, 6- and 7-AI, by steady-state and time-resolved methods (fs-transient absorption and fluorescence up-conversion), in solvents of different polarity.
Coupling at the molecular scale between the graphene nanosheet and water and its effect on the thermal conductivity of the nanofluid
Authors: Pan Xiong , Jin Hanhui , Ku Xiaoke , Guo Yu , Fan Jianren
Published: January 2024

A preferential orientation angle of GNSs inside the nanofluid is discovered, that is, the unrestrained GNSs tend to be parallel to the heat flow direction.
Single-layer PtSe2 adsorbed with non-metallic atoms: geometrical, mechanical, electronic and optical properties and strain effects
Authors: Li Xinyan , Li Zhanhai , Han Jianing , Cao Shengguo , Zhang Zhenhua
Published: January 2024

Single-layer PtSe2 was functionalized via the adsorption of various non-metallic atoms X, and the related geometrical, mechanical, electronic, and optical properties as well as strain tuning effects were studied deeply.
Therapeutic synthetic and natural materials for immunoengineering
Authors: Slezak Anna , Chang Kevin , Hossainy Samir , Mansurov Aslan , Rowan Stuart J. , Hubbell Jeffrey A. , Guler Mustafa O.
Published: January 2024

This review discusses the balance of inflammation in immunity and biomaterials strategies to modulate immunity in cases of imbalance such as autoimmune disease, infection, and cancer. Adapted from “Balanced Energy State”, by BioRender.com (2023).
Efficient iron-catalyzed direct acylation of amines with carboxylic acids and esters under oxygenated conditions
Authors: Obieta Maria , Urgoitia Garazi , Herrero María Teresa , SanMartin Raul
Published: January 2024

A new use for dioxygen at atmospheric pressure as an inducer of a highly efficient iron-catalyzed direct amidation between amines and carboxylic acids or esters in a biodegradable greener solvent such as diethyl carbonate has been discovered.