Miracle-dz/UniFAR-FTUs huggingface dataset:
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response

Abstract Immune checkpoint blockade (ICB) therapy has been successfully applied to clinically therapeutics in multiple cancers, but its efficacy varies greatly among different patients and cancer types. Therefore, the construction of gene signatures to identify patients who could benefit from ICB therapy is particularly important for precision cancer treatment. However, due to the lack of a user-friendly platform, the construction of such gene signatures is a great challenge for clinical investigators who have limited programming skills. In light of this challenge, we developed a web server called Tumor Immunotherapy Response Signature Finder(TIRSF) for the construction of gene signatures to predict ICB therapy response in cancer patients. TIRSF consists of three functional modules. The first module is the Signature Discovery module which provides signature construction and performance evaluation functionalities. The second is a module for response prediction based on the TIRSF signatures, which enables response prediction and prognostic analysis of immunotherapy samples. The last is a module for response prediction based on existing signatures. This module currently integrates 24 published signatures for ICB therapy response prediction. Together, all of above features can be freely accessed at http://tirsf.renlab. org/.
Theta oscillatory dynamics of inhibitory control, error processing, and post‐error adjustments: Neural underpinnings and alcohol‐induced dysregulation in social drinkers

Abstract Background Alcohol intoxication impairs inhibitory control, resulting in disinhibited, impulsive behavior. The anterior cingulate cortex (ACC) plays an essential role in a range of executive functions and is sensitive to the effects of alcohol, which contributes to the top‐down cognitive dysregulation. This study used a multimodal approach to examine the acute effects of alcohol on the neural underpinnings of inhibitory control, inhibition failures, and neurobehavioral optimization as reflected in trial‐to‐trial dynamics of post‐error adjustments. Methods Adult social drinkers served as their own controls by participating in the Go/NoGo task during acute alcohol and placebo conditions in a multi‐session, counterbalanced design. Distributed source modeling of the magnetoencephalographic signal was combined with structural magnetic resonance imaging to characterize the spatio‐temporal dynamics of inhibitory control in the time‐frequency domain. Results Successful response inhibition (NoGo) elicited right‐lateralized event‐related theta power (4 to 7 Hz). Errors elicited a short‐latency increase in theta power in the dorsal (dACC), followed by activity in the rostral (rACC), which may underlie an affective “oh, no! ” orienting response to errors. Error‐related theta in the dACC was associated with subsequent activity of the motor areas on the first post‐error trial, suggesting the occurrence of post‐error output adjustments. Importantly, a gradual increase of the dACC theta across post‐error trials closely tracked improvements in accuracy under placebo, which may reflect cognitive control engagement to optimize response accuracy. In contrast, alcohol increased NoGo commission errors, dysregulated theta during correct NoGo withholding, and abolished the post‐error theta enhancement of cognitive control. Conclusions Confirming the sensitivity of frontal theta to inhibitory control and error monitoring, the results support functional and temporal dissociation along the dorso‐rostral axis of the ACC and the deleterious effects of alcohol on the frontal circuitry subserving top‐down regulation. Over time, alcohol‐induced disinhibition may give rise to compulsive drinking and contribute to alcohol misuse.
Auxin response factors in plant adaptation to drought and salinity stress.

Salinity and drought stresses affect plant growth worldwide and limit crop production. Auxin is crucial in regulating plants' salinity and drought stress adaptative response. As a chemical messenger, auxin influences gene expression through a family of functionally distinct transcription factors, the DNA-binding AUXIN RESPONSE FACTORS (ARFs). Various studies have revealed the important roles of ARFs in regulating drought and salinity stress responses in plants. Different ARFs regulate soluble sugar content, promote root development and maintain chlorophyll content under drought and saline stress conditions to help plants adapt to these stresses. The functional characterization of ARFs pertaining to the regulation of drought and salinity stress responses is still in its infancy. Interestingly, the small RNA-mediated post-transcriptional regulation of ARF expression has been shown to influence plant responses to both stresses. The current knowledge on the diverse roles of ARFs in conferring specificity to auxin-mediated drought and salinity stress responses has not been reviewed to date. In this review, we summarize the recent research concerning the role of ARFs in response to drought and salinity stresses: gene expression patterns, functional characterization and post-transcriptional regulation under drought and salinity stresses. We have also reviewed the modulation of ARF expression by other molecular regulators in the context of drought and salt stress signalling.
Deepened snow loosens temporal coupling between plant and microbial N utilization and induces ecosystem N losses

Seasonal differences in plant and microbial nitrogen (N) acquisition are believed to be a major mechanism that maximizes ecosystem N retention. There is also a concern that climate change may interrupt the delicate balance in N allocation between plants and microbes. Yet, convincing experimental evidence is still lacking. Using a 15N tracer, we assessed how deepened snow affects the temporal coupling between plant and microbial N utilization in a temperate Mongolian grassland. We found that microbial 15N recovery peaked in winter, accounting for 22% of the total ecosystem 15N recovery, and then rapidly declined during the spring thaw. By stimulating N loss via N2O emission and leaching, deepened snow reduced the total ecosystem 15N recovery by 42% during the spring thaw. As the growing season progresses, the 15N released from microbial biomass was taken up by plants, and the competitive advantage for N shifted from microbes to plants. Plant 15N recovery reached its peak in August, accounting for 17% of the total ecosystem 15N recovery. The Granger causality test showed that the temporal dynamics of plant 15N recovery can be predicted by microbial 15N recovery under ambient snow but not under deepened snow. In addition, plant 15N recovery in August was positively correlated with and best explained by microbial 15N recovery in March. The lower microbial 15N recovery under deepened snow in March reduced plant 15N recovery by 73% in August. Together, our results provide direct evidence of seasonal differences in plant and microbial N utilization that are conducive to ecosystem N retention; however, deepened snow disrupted the temporal coupling between plant–microbial N use and turnover. These findings suggest that changes in snowfall patterns may significantly alter ecosystem N cycling and N‐based greenhouse gas emissions under future climate change. We highlight the importance of better representing winter processes and their response to winter climate change in biogeochemical models when assessing N cycling under global change.
Association of white mater lesions with orthostatic hypotension.

OBJECTIVE To reveal the cerebral hypoperperfusion characteristics of White matter lesions (WMLs), we monitored the blood pressure (BP) fluctuation in patients with orthostatic hypotension (OH) and WMLs. METHODS A total of 2265 syncope patients were enrolled in this retrospective study. Clinical outcomes of brain MRI or CT, tilt test and continuous electrocardiogram monitoring were reviewed. All patients were divided into two groups according to WMLs status, and the WMLs group was further classified into three subgroups according to Fazekas grade (1-3). BP fluctuation in these subgroups was compared. The risk factors of WMLs and OH were determined by a multivariate logistic regression test. RESULTS A total of 2265 syncope patients were enrolled, among which 56% patients were male. The average age of patients with WMLs was (61±12) years old. ΔTIME (Odds ratio [OR]: 1.014, 95% confidence interval [CI]: (1.005, 1.023), P=0.0015) and ΔSBP1 (OR: 0.990, 95% CI: (0.980, 1.000), P=0.0579) were demonstrated to be the risk factors of WMLs. The number of cases of repeated drops in blood pressure was twice as high as the cases with only drop in BP . The median and mean ΔSBP and ΔTIME of patients with WMLs were higher than those without WMLs. The incidence of diabetes, hypertension, age and Parkinson Plus Syndromes in patients with WMLs significantly decreased in comparison to those without WMLs (OR-diabetes: 2.558, OR-hypertension: 1.713, OR-age: 0.924 and OR-Parkinson Plus Syndromes: 0.476, P<0.05). CONCLUSION WMLs occurs in patients with hypoperfusion of recurrent OH. Vascular WMLs is associated with diabetes, hypertension, and age is at higher risk than WMLs associated with Parkinson Plus Syndromes.
Tuning electronic, magnetic and catalytic behaviors of biphenylene network by atomic doping

Recently, a new two-dimensional allotrope of carbon named biphenylene has been experimentally synthesized. First-principles calculations are preformed to investigate the electronic properties of biphenylene and the doping effect is also considered to tune its electronic, magnetic, and catalytic properties. The metallic nature with an n-type Dirac cone is observed in the biphenylene. The magnetism can be induced by Fe, Cl, Cr, and Mn doping. More importantly, the doping position dependence of hydrogen evolution reaction (HER) performance of biphenylene is addressed, which can be significantly improved by atomic doping. In particular, the barrier for HER of Fe doping case is only −0.03 eV, denoting its great potential in HER catalysis.
Increased Supply of Methionine During a Heat-Stress Challenge in Lactating Holstein Cows Alters Mammary Tissue mTOR Signaling and its Response to Lipopolysaccharide.

The first objective was to investigate the effects of feeding rumen-protected methionine (RPM) during a heat stress (HS) challenge on abundance and phosphorylation of mechanistic target of rapamycin (mTOR)-related signaling proteins in mammary gland. The second objective was to investigate how HS and RPM may modulate the response of mammary gland explants to lipopolysaccharide (LPS) stimulation. Thirty-two multiparous, lactating Holstein cows (184 ± 59 DIM) were randomly assigned to 1 of 2 environmental treatment groups, and 1 of 2 dietary treatments [TMR with RPM (Smartamine M; Adisseo Inc.; 0.105% DM as top dress) or TMR without RPM (CON)] in a crossover design. There were 2 periods with 2 phases per period. In phase 1 (9 d), all cows were in thermoneutral conditions (TN) and fed ad libitum. During phase 2 (9 d), group 1 (n = 16) was exposed to HS using electric heat blankets while group 2 (n = 16) remained in TN but were pair-fed to HS counterparts to control for DMI decreases associated with HS. After a washout period (14 d), the study was repeated (period 2). Environmental treatments were inverted in period 2 (sequence), while dietary treatments remained the same. Mammary tissue was harvested via biopsy at the end of both periods. Tissue was used for protein abundance analysis and also for incubation with 0 or 3 μg/mL of LPS for 2 h and subsequently used for mRNA abundance. Data were analyzed using PROC MIXED in SAS. Analysis of protein abundance data included the effects of diet, environment and their interaction, and period and sequence to account for the crossover design. The explant data model also included the effect of LPS and its interaction with environment and diet. Abundance of phosphorylated mTOR and ratio of phosphorylated eukaryotic translation elongation factor 2 (p-EEF2) to total EEF2 in non-challenged tissue was greater with RPM supplementation (P = 0.04 for both) and in both cases tended to be greater with HS (P = 0.08 for both). Regardless of RPM supplementation, incubation with LPS upregulated mRNA abundance of IL8, IL6, IL1B, CXCL2, TNF, NFKB1 and TLR2 (P < 0.05). An environment × LPS interaction was observed for NFKB1 (P = 0.03); abundance was greater in LPS-treated explants from non-HS compared with HS cows. Abundance of CXCL2, NFKB1, NOS2, NOS1, and SOD2 was lower with HS (P < 0.05). While LPS did not alter abundance of mRNA associated with the antioxidant transcription factor NFE2L2 signaling (P = 0.59), explants from HS cows had lower abundance of NFE2L2 (P < 0.001) and CUL3 (P = 0.04). Overall, RPM supplementation may alter mTOR activation. Additionally, while HS reduced explant immune and antioxidant responses, RPM did not attenuate the inflammatory response induced by LPS in vitro.
Hyperspectral and LiDAR Data Classification Based on Structural Optimization Transmission

With the development of the sensor technology, complementary data of different sources can be easily obtained for various applications. Despite the availability of adequate multisource observation data, for example, hyperspectral image (HSI) and light detection and ranging (LiDAR) data, existing methods may lack effective processing on structural information transmission and physical properties alignment, weakening the complementary ability of multiple sources in the collaborative classification task. The complementary information collaboration manner and the redundancy exclusion operator need to be redesigned for strengthening the semantic relatedness of multisources. As a remedy, we propose a structural optimization transmission framework, namely, structural optimization transmission network (SOT-Net), for collaborative land-cover classification of HSI and LiDAR data. Specifically, the SOT-Net is developed with three key modules: 1) cross-attention module; 2) dual-modes propagation module; and 3) dynamic structure optimization module. Based on above designs, SOT-Net can take full advantage of the reflectance-specific information of HSI and the detailed edge (structure) representations of multisource data. The inferred transmission plan, which integrates a self-alignment regularizer into the classification task, enhances the robustness of the feature extraction and classification process. Experiments show consistent outperformance of SOT-Net over baselines across three benchmark remote sensing datasets, and the results also demonstrate that the proposed framework can yield satisfying classification result even with small-size training samples.
What Happened When? Cerebral Processing of Modified Structure and Content in Episodic Cueing

Abstract Episodic memories are not static but can change on the basis of new experiences, potentially allowing us to make valid predictions in the face of an ever-changing environment. Recent research has identified prediction errors during memory retrieval as a possible trigger for such changes. In this study, we used modified episodic cues to investigate whether different types of mnemonic prediction errors modulate brain activity and subsequent memory performance. Participants encoded episodes that consisted of short toy stories. During a subsequent fMRI session, participants were presented videos showing the original episodes, or slightly modified versions thereof. In modified videos, either the order of two subsequent action steps was changed or an object was exchanged for another. Content modifications recruited parietal, temporo-occipital, and parahippocampal areas reflecting the processing of the new object information. In contrast, structure modifications elicited activation in right dorsal premotor, posterior temporal, and parietal areas, reflecting the processing of new sequence information. In a post-fMRI memory test, the participants' tendency to accept modified episodes as originally encoded increased significantly when they had been presented modified versions already during the fMRI session. After experiencing modifications, especially those of the episodes' structure, the recognition of originally encoded episodes was impaired as well. Our study sheds light onto the neural processing of different types of episodic prediction errors and their influence on subsequent memory recall.
Correlation of 68Ga-RM2 PET with Postsurgery Histopathology Findings in Patients with Newly Diagnosed Intermediate- or High-Risk Prostate Cancer

Visual Abstract 68Ga-RM2 targets gastrin-releasing peptide receptors (GRPRs), which are overexpressed in prostate cancer (PC). Here, we compared preoperative 68Ga-RM2 PET to postsurgery histopathology in patients with newly diagnosed intermediate- or high-risk PC. Methods: Forty-one men, 64.0 ± 6.7 y old, were prospectively enrolled. PET images were acquired 42–72 min (median ± SD, 52.5 ± 6.5 min) after injection of 118.4–247.9 MBq (median ± SD, 138.0 ± 22.2 MBq) of 68Ga-RM2. PET findings were compared with preoperative multiparametric MRI (mpMRI) (n = 36) and 68Ga-PSMA11 PET (n = 17) and correlated to postprostatectomy whole-mount histopathology (n = 32) and time to biochemical recurrence. Nine participants decided to undergo radiation therapy after study enrollment. Results: All participants had intermediate- (n = 17) or high-risk (n = 24) PC and were scheduled for prostatectomy. Prostate-specific antigen was 8.8 ± 77.4 (range, 2.5–504) and 7.6 ± 5.3 ng/mL (range, 2.5–28.0 ng/mL) when participants who ultimately underwent radiation treatment were excluded. Preoperative 68Ga-RM2 PET identified 70 intraprostatic foci of uptake in 40 of 41 patients. Postprostatectomy histopathology was available in 32 patients in which 68Ga-RM2 PET identified 50 of 54 intraprostatic lesions (detection rate = 93%). 68Ga-RM2 uptake was recorded in 19 nonenlarged pelvic lymph nodes in 6 patients. Pathology confirmed lymph node metastases in 16 lesions, and follow-up imaging confirmed nodal metastases in 2 lesions. 68Ga-PSMA11 and 68Ga-RM2 PET identified 27 and 26 intraprostatic lesions, respectively, and 5 pelvic lymph nodes each in 17 patients. Concordance between 68Ga-RM2 and 68Ga-PSMA11 PET was found in 18 prostatic lesions in 11 patients and 4 lymph nodes in 2 patients. Noncongruent findings were observed in 6 patients (intraprostatic lesions in 4 patients and nodal lesions in 2 patients). Sensitivity and accuracy rates for 68Ga-RM2 and 68Ga-PSMA11 (98% and 89% for 68Ga-RM2 and 95% and 89% for 68Ga-PSMA11) were higher than those for mpMRI (77% and 77%, respectively). Specificity was highest for mpMRI with 75% followed by 68Ga-PSMA11 (67%) and 68Ga-RM2 (65%). Conclusion: 68Ga-RM2 PET accurately detects intermediate- and high-risk primary PC, with a detection rate of 93%. In addition, 68Ga-RM2 PET showed significantly higher specificity and accuracy than mpMRI and a performance similar to 68Ga-PSMA11 PET. These findings need to be confirmed in larger studies to identify which patients will benefit from one or the other or both radiopharmaceuticals.
Determination of 52 hidden chemical pesticides in biopesticide products by GC-MS/MS and LC-MS/MS

Abstract Addition of chemical pesticides in biopesticides are expected to be common, due to effect of pest control during plant protection. These hidden chemical pesticides may cause various food safety problems if consumed. The purpose of our study was to develop a method to determine 52 hidden chemical pesticides in three formulation biopesticide products. Optimizations of different parameters, such as the instrument analysis condition for target, the extraction, and the composition of clean-up materials were carried out. The developed method used acetonitrile as an extraction solvent for all biopesticide formulations. The composition of adsorbents was based on QuEChERS, called QuSEL which was a needle filter head, containing PSA, GCB, and MgSO4. Fifty-two chemical pesticides residues were then analyzed by GC-MS/MS and LC-MS/MS. The present results showed good linearity by correlation coefficients of more than 0.99 for all analyses. The LOQ ranged from 5.0 to 20.0 μg kg−1. Recoveries of 32 chemical pesticides ranged from 71.9% to 118.4% at the spiked level of 10, 50, and 100 μg kg−1, and 20 chemical pesticides ranged from 75.3% to 119.8% at the spiked level of 5, 25, and 50 μg kg−1. The developed method was applied for biopesticide products, and 9 samples were positive in 20 samples.
Testing Feature Economy

Why do speech sounds tend to be organized along just a few phonetic dimensions in each language, such as “nasals”, “voiced fricatives”, etc.? The classic answer to this question was proposed by Martinet [8]: “Une nouvelle economie est realisee en faisant resulter [les phonemes] de combinaisons de traits phoniques non-successifs, ce qui reduit encore le nombre des elements de base” (p. 95). In other words, features introduce a further level of economy by allowing the set of phonemes P to be defined in terms of a smaller set of features, F. Economy exerts pressure on systems to maximize the combinatory possibilities of features by increasing the ratio P/F. This paper outlines a method for testing feature economy, and presents illustrative results involving the patterning of labial consonants.
Synthesis, Biological Activity and Molecular Docking Studies of Novel Sulfonate Derivatives Bearing Salicylaldehyde

Enzyme activity alterations have been associated with many metabolism disorders and have crucial roles in the pathogenesis of some diseases. Tyrosinase is a key enzyme in melanin biosynthesis, which is responsible for skin pigmentation to protect the skin from solar radiation. Pancreatic lipase has been considered a key enzyme for the treatment of obesity. Herein, we reported the synthesis and enzyme inhibitions of a series of sulfonates as possible tyrosinase and pancreatic lipase inhibitors. According to the calculated IC50 values, compound 3f (74.1±11.1 μM) and compound 3c (86.6±6.9 μM) were determined to be the best inhibitors among the synthesized compounds for the tyrosinase and pancreatic lipase enzymes, respectively. The approach yielded at extremely high level by creating very flexible structural domains for the chemically modified groups. The structural characterization of the target molecules was implemented by 1H‐NMR, 13C‐NMR, and HR‐MS analyses. Also, molecular docking studies of the synthesized compounds with tyrosinase and pancreatic lipase enzymes were conducted using AutoDock Vina software. Additionally, the studies of the absorption distribution, metabolism, and excretion (ADME) were performed to uncover the target compounds′ pharmacokinetics, drug similarities, and medicinal properties of the novel sulfonate derivatives bearing salicylaldehyde.