bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics
Authors: Cosentino Matheus Augusto Calvano , D’arc Mirela , Moreira Filipe Romero Rebello , Cavalcante Liliane Tavares de Faria , Mouta Ricardo , Coimbra Amanda , Schiffler Francine Bittencourt , Miranda Thamiris dos Santos , Medeiros Gabriel , Dias Cecilia A. , Souza Antonizete R. , Tavares Maria Clotilde Henriques , Tanuri Amilcar , Soares Marcelo Alves , Santos André Felipe Andrade dos
Published: September 2022

The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.
Impact of an arbuscular mycorrhizal fungal inoculum and exogenous methyl jasmonate on the performance of tall fescue under saline-alkali condition
Authors: Liu Hui , Tang Huimin , Ni Xiaozhen , Zhang Yajie , Wang Yingchao
Published: September 2022

Hormonal regulation and symbiotic relationships provide benefits for plants to overcome stress conditions. The aim of this study was to elucidate the effects of arbuscular mycorrhizal fungal (AMF) inoculum, methyl jasmonate (MeJA), and saline-alkali effects on the growth and physiology of tall fescue (Festuca elata “Crossfire II”). Treatments included AMF-inoculation, and non-AMF inoculation, four MeJA application concentrations (0, 50, 100, and 200 mg/L), and two saline-alkali levels (0 and 200 mmol/L). The results showed that AMF inoculation significantly enhanced saline-alkali resistance of the plants, and the beneficial effects were increased by MeJA at a concentration of 50 mg/L (50 MeJA) and decreased by MeJA at a concentration both of 100 (100 MeJA) and 200 mg/L (200 MeJA). AMF inoculation plants when treated with 50 MeJA accumulated significantly more biomass, had greater proline and total phenolic concentration, and lower malondialdehyde (MDA) concentration than plants only treated either with AMF or 50 MeJA. However, no significant differences in growth or physiological characteristics were observed between AMF and non-AMF plants when treated either with 100 or 200 MeJA. All of these results suggest that the interaction between a certain concentration of MeJA and AMF can significantly increase saline-alkali resistance of the tall fescue by regulating the biomass, proline, total phenolic, and MDA. Our findings provide new information on the effect of biological and chemical priming treatments on plant performance under saline-alkali stress.
Effects of extracellular polymeric substances on the aggregation of Aphanizomenon flos-aquae under increasing temperature
Authors: Deng Dailan , Meng Han , Ma You , Guo Yongqi , Wang Zixuan , He Huan , Liu Jin-e , Zhang Limin
Published: September 2022

Aphanizomenon flos-aquae (A. flos-aquae) blooms are serious environmental and ecological problems. Extracellular polymeric substances (EPSs) are among the most important indicators for the growth and aggregation of A. flos-aquae. In this study, the secretion of the EPS matrix under temperature rise (7–37°C) was investigated and the role of this matrix in A. flos-aquae aggregation was quantified. First, when the temperature increased, the aggregation ratio increased from 41.85 to 91.04%. Meanwhile, we found that when soluble EPSs (S-EPSs), loosely bound EPSs (LB-EPSs), and tightly bound EPSs (TB-EPSs) were removed successively, the aggregation ratio decreased from 69.29 to 67.45%, 61.47%, and 41.14%, respectively. Second, the content of polysaccharides in the EPS matrix was higher than the content of proteins under temperature change. The polysaccharide in TB-EPSs was closely related to the aggregation ability of A. flos-aquae (P < 0.01). Third, PARAFAC analysis detected two humic-like substances and one protein-like substance in EPSs. Furthermore, Fourier transforms infrared spectroscopy (FTIR) showed that with increasing temperature, the polysaccharide-related functional groups increased, and the absolute value of the zeta potential decreased. In conclusion, these results indicated that a large number of polysaccharides in TB-EPSs were secreted under increasing temperature, and the polysaccharide-related functional groups increased correspondingly, which reduced the electrostatic repulsion between algal cells, leading to the destruction of the stability of the dispersion system, and then the occurrence of aggregation. This helps us to understand the process of filamentous cyanobacterial aggregation in lakes.
nifH gene expression and diversity in geothermal springs of Tengchong, China
Authors: Song Zhao-Qi , Wang Li , Liang Feng , Zhou Qingfeng , Pei Dongli , Jiang Hongchen , Li Wen-Jun
Published: September 2022

Terrestrial hot springs have been suggested to harbor diverse diazotrophic lineages by using DNA-based nifH gene phylogenetic analysis. However, only a small amount of diazotrophs were ever confirmed to perform nitrogen fixation. In order to explore the compositions of active diazotrophic populations in hot springs, the in situ expression and diversity of nifH and 16S rRNA genes were investigated in the sediments of hot springs (pH 4.3-9.1; temperature 34-84°C) in Tengchong, China, by using high-throughput sequencing. The results showed that active diazotrophs were diverse in the studied Tengchong hot springs. The main active diazotrophs in high-temperature hot springs were affiliated with Aquificae, while those in low-temperature hot springs belonged to Cyanobacteria and Nitrospirae. Such dominance of Aquificae and Nitrospirae of diazotrophs has not been reported in other ecosystems. This suggests that hot springs may harbor unique active diazotrophs in comparison with other type of ecosystems. Furthermore, there were significant differences in the phylogenetic lineages of diazotrophs between hot springs of Tengchong and other regions, indicating that diazotrophs have geographical distribution patterns. Statistical analysis suggests that the expression and distribution of nifH gene were influenced by temperature and concentrations of ammonia and sulfur seem in Tengchong hot springs. These findings avail us to understand element cycling mediated by diazotrophs in hot spring ecosystems.
Wheat blast: A review from a genetic and genomic perspective
Authors: Hossain Md. Motaher
Published: September 2022

The newly emerged wheat blast fungus Magnaporthe oryzae Triticum (MoT) is a severe threat to global wheat production. The fungus is a distinct, exceptionally diverse lineage of the M. oryzae, causing rice blast disease. Genome-based approaches employing MoT-specific markers are used to detect MoT field isolates. Sequencing the whole genome indicates the presence of core chromosome and mini-chromosome sequences that harbor effector genes and undergo divergent evolutionary routes. Significant genetic and pathotype diversity within the fungus population gives ample potential for evolutionary change. Identifying and refining genetic markers allows for tracking genomic regions with stable blast resistance. Introgression of quantitative and R gene resistance into popular cultivars is crucial to controlling disease in areas where the pathogen population is diverse and well established. Novel approaches such as CRISPR/Cas-9 genome editing could generate resistant varieties in wheat within a short time. This chapter provides an extensive summary of the genetic and genomic aspects of the wheat blast fungus MoT and offers an essential resource for wheat blast research in the affected areas.
DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images
Authors: Hamitouche Ilyes , Jonic Slavica
Published: September 2022

Single-particle cryo-electron microscopy (cryo-EM) is a technique for biomolecular structure reconstruction from vitrified samples containing many copies of a biomolecular complex (known as single particles) at random unknown 3D orientations and positions. Cryo-EM allows reconstructing multiple conformations of the complexes from images of the same sample, which usually requires many rounds of 2D and 3D classifications to disentangle and interpret the combined conformational, orientational, and translational heterogeneity. The elucidation of different conformations is the key to understand molecular mechanisms behind the biological functions of the complexes and the key to novel drug discovery. Continuous conformational heterogeneity, due to gradual conformational transitions giving raise to many intermediate conformational states of the complexes, is both an obstacle for high-resolution 3D reconstruction of the conformational states and an opportunity to obtain information about multiple coexisting conformational states at once. HEMNMA method, specifically developed for analyzing continuous conformational heterogeneity in cryo-EM, determines the conformation, orientation, and position of the complex in each single particle image by image analysis using normal modes (the motion directions simulated for a given atomic structure or EM map), which in turn allows determining the full conformational space of the complex but at the price of high computational cost. In this article, we present a new method, referred to as DeepHEMNMA, which speeds up HEMNMA by combining it with a residual neural network (ResNet) based deep learning approach. The performance of DeepHEMNMA is shown using synthetic and experimental single particle images.
Assess and rehabilitate body representations via (neuro)robotics: An emergent perspective
Authors: Risso Gaia , Bassolino Michela
Published: September 2022

The perceptions of our own body (e.g., size and shape) do not always coincide with its real characteristics (e.g., dimension). To track the complexity of our perception, the concept of mental representations (model) of the body has been conceived. Body representations (BRs) are stored in the brain and are maintained and updated through multiple sensory information. Despite being altered in different clinical conditions and being tightly linked with self-consciousness, which is one of the most astonishing features of the human mind, the BRs and, especially, the underlying mechanisms and functions are still unclear. In this vein, here we suggest that (neuro)robotics can make an important contribution to the study of BRs. The first section of the study highlights the potential impact of robotics devices in investigating BRs. Far to be exhaustive, we illustrate major examples of its possible exploitation to further improve the assessment of motor, haptic, and multisensory information building up the BRs. In the second section, we review the main evidence showing the contribution of neurorobotics-based (multi)sensory stimulation in reducing BRs distortions in various clinical conditions (e.g., stroke, amputees). The present study illustrates an emergent multidisciplinary perspective combining the neuroscience of BRs and (neuro)robotics to understand and modulate the perception and experience of one's own body. We suggest that (neuro)robotics can enhance the study of BRs by improving experimental rigor and introducing new experimental conditions. Furthermore, it might pave the way for the rehabilitation of altered body perceptions.
Effective cloth folding trajectories in simulation with only two parameters
Authors: De Gusseme Victor-Louis , wyffels Francis
Published: September 2022

Robotic cloth folding remains challenging for robots due to its highly deformable nature. In order to deal with these deformations, several strategies with varying amounts of adaptability have been proposed. We study robotic cloth folding by simulating and evaluating a trajectory search space with only two parameters: one parameter for the trajectory's height and one parameter to tilt it. We extensively analyzed folding a long-sleeved shirt in a high-fidelity simulator. To demonstrate that the trajectory is sufficiently adaptable and robust, we test several cloth shapes, cloth materials, an entire folding sequence and different folding velocities. We can deal with every folding scenario by tuning the two parameters correctly. The trajectories' simplicity and their robustness in simulation make them ideal candidates for future transfer to real-world robotic setups.
Peri-lead edema and local field potential correlation in post-surgery subthalamic nucleus deep brain stimulation patients
Authors: Prenassi Marco , Borellini Linda , Bocci Tommaso , Scola Elisa , Barbieri Sergio , Priori Alberto , Ferrucci Roberta , Cogiamanian Filippo , Locatelli Marco , Rampini Paolo , Vergari Maurizio , Pastore Stefano , Datola Bianca , Marceglia Sara
Published: September 2022

Implanting deep brain stimulation (DBS) electrodes in patients with Parkinson’s disease often results in the appearance of a non-infectious, delayed-onset edema that disappears over time. However, the time window between the DBS electrode and DBS stimulating device implant is often used to record local field potentials (LFPs) which are used both to better understand basal ganglia pathophysiology and to improve DBS therapy. In this work, we investigated whether the presence of post-surgery edema correlates with the quality of LFP recordings in eight patients with advanced Parkinson’s disease implanted with subthalamic DBS electrodes. The magnetic resonance scans of the brain after 8.5 ± 1.5 days from the implantation surgery were segmented and the peri-electrode edema volume was calculated for both brain hemispheres. We found a correlation (ρ = −0.81, p < 0.0218, Spearman’s correlation coefficient) between left side local field potentials of the low beta band (11–20 Hz) and the edema volume of the same side. No other significant differences between the hemispheres were found. Despite the limited sample size, our results suggest that the effect on LFPs may be related to the edema localization, thus indicating a mechanism involving brain networks instead of a simple change in the electrode-tissue interface.
Age-related decrease in motor contribution to multisensory reaction times in primary school children
Authors: Alhamdan Areej A. , Murphy Melanie J. , Crewther Sheila G.
Published: September 2022

Traditional measurement of multisensory facilitation in tasks such as speeded motor reaction tasks (MRT) consistently show age-related improvement during early childhood. However, the extent to which motor function increases with age and hence contribute to multisensory motor reaction times in young children has seldom been examined. Thus, we aimed to investigate the contribution of motor development to measures of multisensory (auditory, visual, and audiovisual) and visuomotor processing tasks in three young school age groups of children (n = 69) aged (5−6, n = 21; 7−8, n = 25.; 9−10 n = 18 years). We also aimed to determine whether age-related sensory threshold times for purely visual inspection time (IT) tasks improved significantly with age. Bayesian results showed decisive evidence for age-group differences in multisensory MRT and visuo-motor processing tasks, though the evidence showed that threshold time for visual identification IT performance was only slower in the youngest age group children (5−6) compared to older groups. Bayesian correlations between performance on the multisensory MRT and visuo-motor processing tasks indicated moderate to decisive evidence in favor of the alternative hypothesis (BF10 = 4.71 to 91.346), though not with the threshold IT (BF10 < 1.35). This suggests that visual sensory system development in children older than 6 years makes a less significant contribution to the measure of multisensory facilitation, compared to motor development. In addition to this main finding, multisensory facilitation of MRT within race-model predictions was only found in the oldest group of children (9−10), supporting previous suggestions that multisensory integration is likely to continue into late childhood/early adolescence at least.
Frontal lobe hemodynamics detected by functional near-infrared spectroscopy during head-up tilt table tests in patients with electrical burns
Authors: Kim Yoo Hwan , Kim Youngmin , Yoon Jaechul , Cho Yong Suk , Kym Dohern , Hur Jun , Chun Wook , Kim Byung-Jo
Published: September 2022

Significance

Electrical burns can cause severe damage to the nervous system, resulting in autonomic dysfunction with reduced cerebral perfusion. However, few studies have investigated these consequences.

Aim

To elucidate changes in prefrontal cerebral hemodynamics using functional near-infrared spectroscopy (fNIRS) during the head-up tilt table test (HUT) for patients with electrical burns.

Approach

We recruited 17 patients with acute electrical burns within 1 week after their accidents and 10 healthy volunteers. The NIRS parameters acquired using an fNIRS device attached to the forehead were analyzed in five distinct HUT phases.

Results

Based on their HUT response patterns, patients with electrical burns were classified into the group with abnormal HUT results (APG, n = 4) or normal HUT results (NPG, n = 13) and compared with the healthy control (HC, n = 10) participants. We found trends in hemodynamic changes during the HUT that distinguished HC, NPG, and APG. Reduced cerebral perfusion and decreased blood oxygenation during the HUT were found in both the NPG and APG groups. Patients with electrical burns had autonomic dysfunction compared to the HC participants.

Conclusions

Using fNIRS, we observed that acute-stage electrical burn injuries could affect cerebral perfusion.
Beyond the brain-computer interface: Decoding brain activity as a tool to understand neuronal mechanisms subtending cognition and behavior
Authors: Loriette Célia , Amengual Julian L. , Ben Hamed Suliann
Published: September 2022

One of the major challenges in system neurosciences consists in developing techniques for estimating the cognitive information content in brain activity. This has an enormous potential in different domains spanning from clinical applications, cognitive enhancement to a better understanding of the neural bases of cognition. In this context, the inclusion of machine learning techniques to decode different aspects of human cognition and behavior and its use to develop brain–computer interfaces for applications in neuroprosthetics has supported a genuine revolution in the field. However, while these approaches have been shown quite successful for the study of the motor and sensory functions, success is still far from being reached when it comes to covert cognitive functions such as attention, motivation and decision making. While improvement in this field of BCIs is growing fast, a new research focus has emerged from the development of strategies for decoding neural activity. In this review, we aim at exploring how the advanced in decoding of brain activity is becoming a major neuroscience tool moving forward our understanding of brain functions, providing a robust theoretical framework to test predictions on the relationship between brain activity and cognition and behavior.
The learning-relative hemodynamic modulation of cortical plasticity induced by a force-control motor training
Authors: Wang Yongrong , Feng Shuai , Yang Rui , Hou Wensheng , Wu Xiaoying , Chen Lin
Published: September 2022

Background

Novel motor skills are generally acquired through repetitive practices which are believed to be strongly related to neural plasticity mechanisms. This study aimed to investigate the learning-relative hemodynamic modulation of cortical plasticity induced by long-term motor training.

Methods

An 8-day participation-control program was conducted. Eighteen right-handed healthy participants were recruited and randomly assigned into the training (12) and control groups (6). The training group were arranged to undergo the 8-day block-designed motor training which required to repeat a visuomotor force-control task. The functional near-infrared spectroscopy (fNIRS) was used to continuously monitor the cortical hemodynamic response during training. Two transcranial magnetic stimulation (TMS) measurements were performed before and after training to evaluate the cortical excitability changes. The transfer effects of learning were also investigated.

Results

The behavior performance was quantified via score execution accuracy to illustrate the fast/slow learning stages as experience cumulated. The cortical hemodynamic activations mapped by fNIRS exhibited a temporal evolution trends that agreed the expansion–renormalization model, which assumed the brain modulation against skill acquisition includes complex mechanisms of neural expansion, selection, and renormalization. Functional connectivity (FC) analysis showed the FC strength was maintained, while the measured homodynamic activation returned to baseline after certain level of skill acquisition. Furthermore, the TMS results demonstrated a significant increase of motor evoked potential (MEP) on the targeted muscle for the trained participants, who significantly outperformed the untrained subjects in learning transfer investigation.

Conclusion

The study illustrated the expansion–renormalization trends during continuous motor training, and relative analysis showed the functional connectivity enhancement may be maintained after amplitude renormalization of cortical hemodynamic activations. The TMS findings further gave an implication of neural facilitations on the descending motor pathway when brain activation returned to renormalization status after certain level of learning stages was achieved, and the learning can transfer to enhance the performance while encountering similar tasks.
13C metabolic flux analysis: Classification and characterization from the perspective of mathematical modeling and application in physiological research of neural cell
Authors: Tian Birui , Chen Meifeng , Liu Lunxian , Rui Bin , Deng Zhouhui , Zhang Zhengdong , Shen Tie
Published: September 2022

13C metabolic flux analysis (13C-MFA) has emerged as a forceful tool for quantifying in vivo metabolic pathway activity of different biological systems. This technology plays an important role in understanding intracellular metabolism and revealing patho-physiology mechanism. Recently, it has evolved into a method family with great diversity in experiments, analytics, and mathematics. In this review, we classify and characterize the various branch of 13C-MFA from a unified perspective of mathematical modeling. By linking different parts in the model to each step of its workflow, the specific technologies of 13C-MFA are put into discussion, including the isotope labeling model (ILM), isotope pattern measuring technique, optimization algorithm and statistical method. Its application in physiological research in neural cell has also been reviewed.
Triglyceride glucose index and its combination with the Get with the Guidelines-Heart Failure score in predicting the prognosis in patients with heart failure
Authors: Han Su , Wang Chuanhe , Tong Fei , Li Ying , Li Zhichao , Sun Zhaoqing , Sun Zhijun
Published: September 2022

Background

Heart failure (HF) is associated with generalized insulin resistance (IR). Recent studies demonstrated that triglyceride glucose (TyG) is an effective alternative index of IR. However, the relationship between the TyG index and in-hospital mortality in patients with HF is unclear. In the present study, we aimed to clarify the association between the TyG index and in-hospital mortality in patients with HF.

Methods

A retrospective study consisting of 4,411 patients diagnosed with HF from 2015 to 2018 was conducted. All-cause mortality during hospitalization was the primary endpoint. The association between the TyG index and in-hospital mortality was assessed using the logistic regression analysis.

Results

The risk of in-hospital mortality was significantly associated with increased TyG index (OR: 1.886, 95% CI: 1.421–2.501, p < 0.001) under logistic regression with multivariable adjustment. When divided into three groups based on the TyG index, Tertile 3 demonstrated significantly higher in-hospital mortality than the other two Tertiles (OR: 2.076, 95% CI: 1.284–3.354, p = 0.001). Moreover, the TyG index improved the prediction efficiency of the Get with the Guidelines-Heart Failure (GWTG-HF) score (absolute integrated discrimination improvement = 0.006, p < 0.001; category-free net reclassification improvement = 0.075, p = 0.005). In subgroup analysis, the TyG index exhibited similar predictive performance of in-hospital mortality when groups were stratified based on type 2 diabetes mellitus (T2DM) and coronary artery disease (CAD).

Conclusion

TyG is a potential index for predicting in-hospital mortality in patients with HF, independent of T2DM or CAD status. The TyG index may be combined with the GWTG-HF score to further improve its predictive efficacy.
Prediction value of 18F-FDG PET/CT intratumor metabolic heterogeneity parameters for recurrence after radical surgery of stage II/III colorectal cancer
Authors: Liu Xin , Zhang Yi-Fan , Shi Qin , Yang Yi , Yao Ben-Hu , Wang Shi-Cun , Geng Guang-Yong
Published: September 2022

Purpose

We explored the predictive effect of intratumor metabolic heterogeneity indices extracted from 18F-FDG PET/CT on recurrence in stage II/III colorectal cancer after radical surgery.

Methods

A total of 140 stage II/III colorectal cancer patients who received preoperative 18F-FDG PET/CT and radical resection were enrolled. 18F-FDG traditional parameters including the maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG) under different thresholds; heterogeneity indices including the coefficient of variation with SUV 2.5 as a threshold (CV2.5), CV40%, heterogeneity index-1 (HI-1) calculated by the fixed-threshold method, and HI-2 calculated by the percentage threshold method; and clinicopathological information were collected. We concluded that relationships exist between these data and patients’ disease-free survival (DFS).

Results

Regional lymph node status (P < 0.001), nerve invasion (P = 0.036), tumor thrombus (P = 0.005), and HI-1 (P = 0.010) exhibited significant differences between the relapse and non-relapse groups, while SUVmax, MTV2.5, MTV40%, TLG2.5, TLG40%, CV2.5, CV40%, HI-2, and other clinicopathological factors had no differences between the relapse and non-relapse groups. Multivariate analysis demonstrated that HI-1 (HR = 1.02, 1.00–1.04, P = 0.038), regional lymph node metastasis (HR = 2.95, 1.37–6.38, P = 0.006), and tumor thrombus status (HR = 2.37, 1.13–4.99, P = 0.022) were independent factors significantly related to DFS.

Conclusion

HI-1, tumor thrombus status, and regional lymph node status could predict the recurrence of stage II/III colorectal cancer after radical resection and had an advantage over other 18F-FDG PET/CT conventional parameters and heterogeneity indices.
The angiogenic genes predict prognosis and immune characteristics in esophageal squamous cell carcinoma: Evidence from multi-omics and experimental verification
Authors: Wang Shuaiyuan , Liang Yinghao , Zhang Jiaxin , Wang Wenjia , Hong Yichen , Sun Miaomiao , Shu Jiao , Chen Kuisheng
Published: September 2022

Esophageal squamous cell carcinomas (ESCC) is an aggressive disease with five-year overall survival (OS) <15%. The main cause is metastasis rather than local tumor, and angiogenesis plays an important role. Angiogenesis has a significant impact on tumor metastasis, treatment and prognosis. However, the expression pattern of angiogenic genes, its effect on treatment and its relationship with prognosis in ESCC have not been systematically reported. We performed the first and most comprehensive multi-omics analysis of angiogenic genes in patients with ESCC and identified four angiogenic phenotypes that vary in outcome, tumor characteristics, and immune landscape. These subtypes provide not only patient outcomes but also key information that will help to identify immune blocking therapy. In addition, angiogenesis intensity score (AIS) was proposed to quantify tumor angiogenesis ability, and its accuracy as a predictor of prognosis and immunotherapy was verified by external cohort and corresponding cell lines. Our study provides clinicians with guidance for individualized immune checkpoint blocking therapy and anti-angiogenic therapy for ESCC.
Could fertility-sparing surgery be considered for stage I ovarian sex cord-stromal tumors? A comparison of the Fine-Gray model with Cox model
Authors: Sun Dan , Zhi Zhi F. , Fan Jiang T.
Published: September 2022

Objective

To evaluate the oncologic outcomes in patients with International Federation of Gynecology and Obstetrics (FIGO) stage I ovarian sex cord-stromal tumors (SCSTs) who underwent fertility-sparing surgery (FSS) and the independent risk factors affecting overall survival (OS) and cancer-specific survival (CSS).

Methods

Data were acquired from the Surveillance, Epidemiology, and End Results (SEER) database between 1973 and 2018. A total of 240 patients diagnosed with stage I ovarian SCSTs were divided into the definitive surgery group (N=116) and FSS group (N=124). The Kaplan-Meier analysis and Cox model were used to evaluate the overall survival (OS) and cancer-specific survival (CSS) of the two groups and assess the independent risk factors respectively. The Fine-Gray model evaluated cancer-specific mortality (CSM) and the independent risk factors that affected CSM.

Results

Kaplan-Meier survival analysis showed no statistically significant differences in OS and CSS between the two groups (P>0.05). Univariate analysis of the Fine-Gray model also showed that there was no difference in the CSS between the two groups (P>0.05). However, from the 15th year postoperatively, the CSS of the FSS group decreased by 13.21% compared with that of the control group and by 17.49% in the 20th and 25th years postoperatively. The Cox proportional hazards model found that surgical methods (“defined surgery” vs “FSS”; HR=0.03259, P=0.0196) and FIGO stage (“stage IA” vs “stage IC”; HR=0.03073, P=0.0300) were independent risk factors for OS. The multivariate analysis of Fine-Gray model showed that the cancer-specific mortality of patients receiving definitive surgery was 40.1% lower than that of patients receiving FSS (“definitive surgery” vs “FSS”; HR=0.599, P=0.005), indicating that FSS might lead to higher tumor-specific mortality and lower CSS. However, age, race, laterality, history, FIGO stage, and tumor size had no significant influence on the tumor-specific mortality (P>0.05).

Conclusions

FSS is considered for patients with stage I SCSTs with reproductive needs, but the follow-up period should not be less than 15 years. For patients with stage IC disease, FSS should be selected carefully, and close follow-up is necessary. Perhaps, definitive surgery after birth is a means to improve long-term survival rates.
Calcium dobesilate efficiency in the treatment of diabetic kidney disease through suppressing MAPK and chemokine signaling pathways based on clinical evaluation and network pharmacology
Authors: Du Bingyu , Yin Yanyan , Wang Yuqing , Fu Hui , Sun Helin , Yue Zhaodi , Yu Shaohong , Zhang Zhongwen
Published: September 2022

Aims: To evaluate the effectiveness and potential mechanism of calcium dobesilate (CaD) in diabetic kidney disease (DKD) patients.

Methods: We searched for available randomized controlled studies on DKD patients’ treatment with CaD through open databases. Continuous variables were expressed as standardized mean difference (SMD) with a 95% confidence interval (CI). The putative targets and possible pathways of CaD on DKD were analyzed by network pharmacology. Molecular docking was employed to verify the match between CaD and the target genes.

Results: In the meta-analysis, 42 trials were included, involving 3,671 DKD patients, of which 1,839 received CaD treatment in addition to conventional treatment, while 1,832 received conventional treatment. Compared with routine therapy, the levels of serum creatinine (Scr) and blood urea nitrogen (BUN) significantly decreased in the CaD treatment (early stage of DKD, Scr: p < 0.00001; BUN: p < 0.0001; clinical stage of DKD, Scr: p < 0.00001; BUN: p < 0.00001; kidney failure stage, Scr: p = 0.001; BUN: p = 0.004). The levels of serum cystatin C (Cys-C), urine levels of molecules reflecting kidney function (urinary albumin excretion rate (UAER) and micro glycoprotein), and inflammatory factors [hypersensitive c-reactive protein (hs-CRP)] were reduced compared with control groups, while glomerular filtration rate (GFR) was increased in patients treated with CaD for 12 weeks. CaD also showed a better effect on improving endothelial function. Network pharmacology results showed that the interaction pathway between CaD and DKD was mainly enriched in MAPK and chemokine signaling pathways. AKT1, CASP3, IGF1, MAPK8, and CCL5 might be the key targets for CaD in treating DKD.

Conclusion: Combination with CaD is effective and safe in patients with DKD. Inhibition of MAPK and chemokine signaling pathways might be vital in treating CaD in DKD patients.
Nanogels as target drug delivery systems in cancer therapy: A review of the last decade
Authors: Attama Anthony A. , Nnamani Petra O. , Onokala Ozioma B. , Ugwu Agatha A. , Onugwu Adaeze L.
Published: September 2022

Cancer is an important cause of morbidity and mortality worldwide, irrespective of the level of human development. Globally, it was estimated that there were 19.3 million new cases of cancer and almost 10 million deaths from cancer in 2020. The importance of prevention, early detection as well as effective cancer therapies cannot be over-emphasized. One of the important strategies in cancer therapy is targeted drug delivery to the specific tumor sites. Nanogels are among the several drug delivery systems (DDS) being explored as potential candidates for targeted drug delivery in cancer therapy. Nanogels, which are new generation, versatile DDS with the possession of dual characteristics of hydrogels and nanoparticles have shown great potential as targeted DDS in cancer therapy. Nanogels are hydrogels with a three-dimensional (3D) tunable porous structure and a particle size in the nanometre range, from 20 to 200 nm. They have been visualized as ideal DDS with enormous drug loading capacity, and high stability. Nanogels can be modified to achieve active targeting and enhance drug accumulation in disease sites. They can be designed to be stimulus-responsive, and react to internal or external stimuli such as pH, temperature, light, redox, thus resulting in the controlled release of loaded drug. This prevents drug accumulation in non-target tissues and minimizes the side effects of the drug. Drugs with severe adverse effects, short circulation half-life, and easy degradability by enzymes, such as anti-cancer drugs, and proteins, are suitable for delivery by chemically cross-linked or physically assembled nanogel systems. This systematic review summarizes the evolution of nanogels for targeted drug delivery for cancer therapy over the last decade. On-going clinical trials and recent applications of nanogels as targeted DDS for cancer therapy will be discussed in detail. The review will be concluded with discussions on safety and regulatory considerations as well as future research prospects of nanogel-targeted drug delivery for cancer therapy.
Exploring the oncogenic roles of LINC00857 in pan-cancer
Authors: Ren Xiaomin , Liu Jing , Wang Rui , Liu Xinling , Ma Xiaolin , Lu Zhong , Hu Zhenbo , Zheng Mingzhu , Ma Jingang , Li Jiaqiu
Published: September 2022

Although aberrant LINC00857 expression may play a key role in oncogenesis, no research has analyzed the pan-cancer oncogenic roles of LINC00857, particularly in tumor immunology. Here, we integrated data from several databases to analyze the characteristics of LINC00857 in pan-cancer. We found that LINC00857 was overexpressed and correlated with a poor prognosis in a variety of cancers. Furthermore, high-expression of LINC00857 was negatively associated with immune cell infiltration and immune checkpoint gene expression. Notably, LINC00857 expression was negatively related to microsatellite instability and tumor mutation burden in colorectal cancer, implying poor reaction to immunotherapy when LINC00857 was highly expressed. Targeting LINC00857 could dramatically impair the proliferative ability of colorectal cancer cells. After RNA-sequencing in HCT116 cells, gene set enrichment analysis showed that LINC00857 may accelerate cancer progression by inhibiting the ferroptosis pathway and promoting glycolipid metabolism in colorectal cancer. Screening by weighted gene co-expression network analysis determined PIWIL4 as a target of LINC00857, which also performed an immunosuppressive role in colorectal cancer. Based on the structure of PIWIL4, a number of small molecule drugs were screened out by virtual screening and sensitivity analysis. In summary, LINC00857 expression was closely correlated with an immunosuppressive microenvironment and may be a novel diagnostic and prognostic biomarker for diverse cancers. The LINC00857/PIWIL4 axis may be predictive biomarkers for immunotherapy and valuable molecular targets for malignant tumors.
Long-range interference of localized electromagnetic field enhancement in plasmonic nanofinger lattices
Authors: Sui Yunxia , Hu Pan , Pan Dalong , Jiang Zhanshuo , Song Qianliang , Su Guangxu , Wu Wei , Liu Fanxin
Published: September 2022

Sub-wavelength strongly confined electromagnetic field induced by surface plasmon resonance offers a promising method to enhance the light-matter interactions, which has wide applications in the fields of enhanced spectroscopy, photovoltaic conversion, and photocatalysis. For periodic metal nanostructures, the localized surface plasmon resonance (LSPR) can couple with the long-range diffractive interaction, causing a narrow linewidth. Here, we report a new family of plasmonic nanostructure fabricated through nanoimprint lithograph, which enables completely uniform, reproducible, and low-cost Au nanofinger multimer arrays with high aspect ratio at the manufacturing scale. Through adjusting the lattice spacing and the angle of incident light, the different collective coupling strengths between the diffraction modes and the LSPR of trimer or pentamer Au nanofingers arrays are observed experimentally by angle-resolved reflection spectroscopy. According to the numerical simulation based on the finite element method, the dynamic evolution of collective coupled modes is demonstrated. The typical surface charge distribution and electric field distribution of the coupled dipole resonance show a significant electromagnetic field enhancement. By adjusting the height of nanofingers, lattice spacing and gap size of adjacent nanofingers, the feasibility of the coupled modes is further investigated. This work provides an excellent candidate for the localization of light as chip-scale plasmonic devices.
Crystallization kinetics of charged PNIPAM microgels dispersions at low volume fractions
Authors: Bocanegra-Flores J. , Haro-Pérez C. , Reyes-Contreras D. , Rojas-Ochoa L. F.
Published: September 2022

This work studies the kinetics of crystallization of charged microgels suspensions of Poly-N-Isopropylacrylamide (PNIPAM) at low ionic strength. The liquid-crystal transition is induced by suddenly decreasing the temperature of the microgel dispersion, and the crystallization process is monitored by measuring the temporal evolution of the static structure factor of the dispersion using light scattering. We find that the crystal growth rate, indicated by the temporal evolution of the crystallinity factor, strongly depends on the quenching temperature.
Using a competitive counterflow assay to identify novel cationic substrates of OATP1B1 and OATP1B3
Authors: Schnegelberger Regina D. , Steiert Brianna , Sandoval Philip J. , Hagenbuch Bruno
Published: September 2022

OATP1B1 and OATP1B3 are two drug transporters that mediate the uptake of multiple endo- and xenobiotics, including many drugs, into human hepatocytes. Numerous inhibitors have been identified, and for some of them, it is not clear whether they are also substrates. Historically radiolabeled substrates or LC-MS/MS methods were needed to test for transported substrates, both of which can be limiting in time and money. However, the competitive counterflow (CCF) assay originally described for OCT2 and, more recently, for OCT1, OATP2B1, and OATP1A2 does not require radiolabeled substrates or LC-MS/MS methods and, as a result, is a more cost-effective approach to identifying substrates of multidrug transporters. We used a CCF assay based on the stimulated efflux of the common model substrate estradiol-17β-glucuronide (E17βG) and tested 30 compounds for OATP1B1- and OATP1B3-mediated transport. Chinese Hamster Ovary (CHO) cells stably expressing OATP1B1 or OATP1B3 were preloaded with 10 nM [3H]-estradiol-17β-glucuronide. After the addition of known substrates like unlabeled estradiol-17β-glucuronide, estrone-3-sulfate, bromosulfophthalein, protoporphyrin X, rifampicin, and taurocholate to the outside of the preloaded CHO cells, we observed efflux of [3H]-estradiol-17β-glucuronide due to exchange with the added compounds. Of the tested 30 compounds, some organic cation transporter substrates like diphenhydramine, metformin, and salbutamol did not induce [3H]-estradiol-17β-glucuronide efflux, indicating that the two OATPs do not transport them. However, 22 (for OATP1B1) and 16 (for OATP1B3) of the tested compounds resulted in [3H]-estradiol-17β-glucuronide efflux, suggesting that they are OATP substrates. Among these compounds, we further tested clarithromycin, indomethacin, reserpine, and verapamil and confirmed that they are substrates of the two OATPs. These results demonstrate that the substrate spectrum of the well-characterized organic anion transporting polypeptides includes several organic cations. Furthermore, as for other drug uptake transporters, the CCF assay is an easy-to-use screening tool to identify novel OATP substrates.
DCNet: DenseNet-77-based CornerNet model for the tomato plant leaf disease detection and classification
Authors: Albahli Saleh , Nawaz Marriam
Published: September 2022

Early recognition of tomato plant leaf diseases is mandatory to improve the food yield and save agriculturalists from costly spray procedures. The correct and timely identification of several tomato plant leaf diseases is a complicated task as the healthy and affected areas of plant leaves are highly similar. Moreover, the incidence of light variation, color, and brightness changes, and the occurrence of blurring and noise on the images further increase the complexity of the detection process. In this article, we have presented a robust approach for tackling the existing issues of tomato plant leaf disease detection and classification by using deep learning. We have proposed a novel approach, namely the DenseNet-77-based CornerNet model, for the localization and classification of the tomato plant leaf abnormalities. Specifically, we have used the DenseNet-77 as the backbone network of the CornerNet. This assists in the computing of the more nominative set of image features from the suspected samples that are later categorized into 10 classes by the one-stage detector of the CornerNet model. We have evaluated the proposed solution on a standard dataset, named PlantVillage, which is challenging in nature as it contains samples with immense brightness alterations, color variations, and leaf images with different dimensions and shapes. We have attained an average accuracy of 99.98% over the employed dataset. We have conducted several experiments to assure the effectiveness of our approach for the timely recognition of the tomato plant leaf diseases that can assist the agriculturalist to replace the manual systems.
Calcium channels and transporters: Roles in response to biotic and abiotic stresses
Authors: Park Chang-Jin , Shin Ryoung
Published: September 2022

Calcium (Ca2+) serves as a ubiquitous second messenger by mediating various signaling pathways and responding to numerous environmental conditions in eukaryotes. Therefore, plant cells have developed complex mechanisms of Ca2+communication across the membrane, receiving the message from their surroundings and transducing the information into cells and organelles. A wide range of biotic and abiotic stresses cause the increase in [Ca2+]cytas a result of the Ca2+influx permitted by membrane-localized Ca2+permeable cation channels such asCYCLICNUCLEOTIDE-GATECHANNELs (CNGCs), and voltage-dependentHYPERPOLARIZATION-ACTIVATEDCALCIUM2+PERMEABLECHANNELs (HACCs), as well asGLUTAMATE RECEPTOR-LIKERECEPTORs (GLRs) andTWO-PORECHANNELs (TPCs). Recently, resistosomes formed by someNUCLEOTIDE-BINDINGLEUCINE-RICHREPEAT RECEPTORs (NLRs) are also proposed as a new type of Ca2+permeable cation channels. On the contrary, some Ca2+transporting membrane proteins, mainly Ca2+-ATPase and Ca2+/H+exchangers, are involved in Ca2+efflux for removal of the excessive [Ca2+]cytin order to maintain the Ca2+homeostasis in cells. The Ca2+efflux mechanisms mediate the wide ranges of cellular activities responding to external and internal stimuli. In this review, we will summarize and discuss the recent discoveries of various membrane proteins involved in Ca2+influx and efflux which play an essential role in fine-tuning the processing of information for plant responses to abiotic and biotic stresses.