Miracle-dz/UniFAR-FTUs huggingface dataset:
Terpenoid Emissions of Two Mediterranean Woody Species in Response to Drought Stress

Drought is a major environmental constrain affecting plant performance and survival, particularly in Mediterranean ecosystems. Terpenoids may play a protective role under these conditions, however, observations of drought effects on plant terpenoid emissions are controversial ranging from decreased emissions to unaffected or increased release of terpenoids. In the present study we investigated terpenoid emissions of cork oak (Quercus suber) and gum rockrose (Cistus ladanifer) in response to summer drought stress in 2017. Pre-dawn leaf water potential (ΨPD) decreased from -0.64 to -1.72 MPa in Q. suber and from -1.69 to -4.05 MPa in C. ladanifer, indicating a transition from mild to severe drought along summer. Total terpenoid emissions decreased with drought, but differed significantly between species (p < 0.001) and in response to ΨPD, air temperature and assimilation rates. C. ladanifer emitted a large variety of >75 compounds comprising monoterpenes, sesquiterpenes and even diterpenes, which strongly decreased from 1.37 ± 0.23 μg g-1h-1 to 0.40 ± 0.08 μg g-1h-1 (p < 0.001) in response to drought. Total emission rates were positively correlated to air temperature (p < 0.001). C. ladanifer behavior points toward terpenoid leaf storage depletion and reduced substrate availability for terpenoid synthesis with increasing drought, most likely accelerated by high air temperatures. Q. suber emitted mainly monoterpenes and emissions declined significantly from June (0.50 ± 0.08 μg g-1h-1) to August (0.29 ± 0.02 μg g-1h-1) (p < 0.01). Emission rates were weakly correlated with net assimilation rates (R2 = 0.19, p < 0.001), but did not respond strongly to ΨPD and air temperature. Early onset of drought in 2017 most likely reduced plant metabolism in Q. suber, resulting in diminished, but stable terpenoid fluxes. Calculation of standard emission factors (at 30°C) revealed contrasting emission patterns of decreasing, unaffected, or increasing fluxes of single terpenoid compounds. Unaffected or drought-enhanced emissions of compounds such as α-pinene, camphene or manoyl oxide may point toward a specific role of these terpenoids in abiotic stress adaptation. In conclusion, these results suggest a strong negative, but species- and compound-specific effect of severe drought on terpenoid fluxes in Mediterranean ecosystems.
Variation in Seed Allergen Content From Three Varieties of Soybean Cultivated in Nine Different Locations in Iowa, Illinois, and Indiana

Soybean (Glycine max) is an important food stock, and also considered an allergenic food with at least eight well characterized allergens. However, it is a less prevalent allergen source than many other foods and is rarely life-threatening. Soybean is incorporated into commonly consumed foods, and therefore, the allergens pose a potential concern for individuals already sensitized. The protein profile of soybean can be affected by several factors including genetic and environmental. To investigate how soybean allergen content may be affected by genetics and/or environment, nine soy allergens were quantified from three commercial soybean varieties grown at nine locations in three states within a single climate zone in North America; Iowa, Illinois, and Indiana, United States. Quantitation was achieved using liquid chromatography-selected reaction monitoring (LC-SRM) tandem mass spectrometry with AQUA peptide standards specific to the nine target allergens. Quantitation of allergen concentration indicated that both genetics and location affected specific allergen content. Seven of the nine allergens were significantly influenced by genetics, with the exceptions of glycinin G4 and KTI 3. The allergens P34, Gly m Bd 28k, glycinin G3, and KTI 1 showed statistically significant impact from location as well, but at a lower threshold of significance compared with genetics (cultivar/variety). This dataset contributes to our understanding of the natural variation of endogenous allergens, as it represents a sampling of soybeans grown in a controlled, distributed plot design under agronomic conditions common for commercial soybean food and feed production. The aim was to build upon our recent understanding of how allergens are expressed as part of the overall soybean proteome.
Semi-Generative Modelling: Domain Adaptation with Cause and Effect Features

This paper presents a novel, causally-inspired approach to domain adaptation which aims to also include unlabelled data in the model fitting when labelled data is scarce. We consider a case of covariate-shift adaptation with cause and effect features, and--drawing from recent ideas in causal modelling and invariant prediction--show how this setting leads to, what we will refer to as, a semi-generative model: P(Y, X_eff; X_cau,\theta). Our proposed approach is robust to changes in the distribution over causal features, and naturally allows to impose model constraints by unsupervised learning of a map from causes to effects. In experiments on synthetic datasets we demonstrate a significant improvement in classification performance of our semi-generative model over purely-supervised and importance-weighting baselines when the amount of labelled data is small. Moreover, we apply our approach for regression on real-world protein-count data and compare it to feature transformation methods.
miR-19b serves as a prognostic biomarker of breast cancer and promotes tumor progression through PI3K/AKT signaling pathway

Background MicroRNAs (miRNAs) are involved in tumor progression of various human malignancies. MicroRNA-19b (miR-19b) has been described as serving a crucial role in tumorigenesis of breast cancer. The purpose of this study was to investigate the expression patterns, clinical value, and functional role of miR-19b in breast cancer. Methods Expression of miR-19b was estimated by quantitative real time PCR. Kaplan–Meier survival analysis and Cox regression assay were performed to explore the prognostic value of miR-19b. The functional role of miR-19b was verified using cell experiments. Results Upregulated miR-19b expression was observed in breast cancer tissues and cells compared with the controls (all P<0.05). The miR-19b expression was associated with distant metastasis and TNM stage. The survival curves showed that high miR-19b was correlated with poor overall survival of the patients (log-rank P=0.002). Furthermore, miR-19b was proven to be an independent prognostic factor for patients. By using miR-19b mimic and inhibitor, cell proliferation, migration, and invasion were enhanced by miR-19b overexpression but were suppressed by reduction of miR-19b (all P<0.05). Besides, PI3K/AKT was demonstrated to be activated by miR-19b in breast cancer cells. Conclusion The overexpression of miR-19b serves as a candidate prognostic biomarker of breast cancer and may be involved in the tumor progression through PI3K/AKT pathway.
The Ability of Prostate Health Index (PHI) to Predict Gleason Score in Patients With Prostate Cancer and Discriminate Patients Between Gleason Score 6 and Gleason Score Higher Than 6—A Study on 320 Patients After Radical Prostatectomy

Aim: The purpose of this study was to investigate the Prostate Health Index as a marker for tumor aggressiveness in prostate biopsy and the optimization of indication for treatment options. Methods: Our cohort consisted of 320 patients indicated for radical prostatectomy with preoperative measurements of total prostate-specific antigen, free prostate-specific antigen, [-2]proPSA, calculated %freePSA, and Prostate Health Index. The Gleason score was determined during biopsy and after radical prostatectomy. Using the Gleason score, we divided the group of patients into the 2 subgroups: Gleason score ≤6 and Gleason score >6. This division was performed according to the biopsy Gleason score and according to the postoperative Gleason score. We compared total prostate-specific antigen, [-2]proPSA, %freePSA, and Prostate Health Index in the subgroups Gleason score ≤6 and Gleason score >6 after biopsy and the definitive score. Results: On evaluation of the subgroups created by Gleason score ≤6 and Gleason score >6, we observed agreement between biopsy Gleason score and definitive Gleason score in only 45.3% of cases. Of the calculated biopsy, Gleason score ≤6 and Gleason score >6 subgroups, [-2]proPSA, and Prostate Health Index (P = .0003 and P = .0005) were statistically significant. Of the definitive Gleason score ≤6 and Gleason score >6 subgroups, Prostate Health Index, [-2]proPSA, %freePSA, and PSA (P < .0001, P < .0001, P = .0003, and P = .0043) were statistically significant. The best area under the curve value (0.7496) was achieved by Prostate Health Index when the subgroups were established according to the postoperative Gleason score. Conclusion: Prostate Health Index is the best of the tested markers for the categorization of Gleason score 6 tumors and for facilitating the management of patients with prostate cancer. Prostate Health Index can be a helpful marker for indication of active surveillance or radical prostatectomy. Prostate health index can also simplify the decision of whether to perform nerve-sparing radical prostatectomy.
Up-To-Date Review About Minipuberty and Overview on Hypothalamic-Pituitary-Gonadal Axis Activation in Fetal and Neonatal Life

Minipuberty consists of activation of the hypothalamic-pituitary-gonadal (HPG) axis during the neonatal period, resulting in high gonadotropin and sex steroid levels, and occurs mainly in the first 3–6 months of life in both sexes. The rise in the levels of these hormones allows for the maturation of the sexual organs. In boys, the peak testosterone level is associated with penile and testicular growth and the proliferation of gonadic cells. In girls, the oestradiol levels stimulate breast tissue, but exhibit considerable fluctuations that probably reflect the cycles of maturation and atrophy of the ovarian follicles. Minipuberty allows for the development of the genital organs and creates the basis for future fertility, but further studies are necessary to understand its exact role, especially in girls. Nevertheless, no scientific study has yet elucidated how the HPG axis turns itself off and remains dormant until puberty. Additional future studies may identify clinical implications of minipuberty in selected cohorts of patients, such as premature and small for gestational age infants. Finally, minipuberty provides a fundamental 6-month window of the possibility of making early diagnoses in patients with suspected sexual reproductive disorders to enable the prompt initiation of treatment rather than delaying treatment until pubertal failure.
Learning Heuristics for Automated Reasoning through Deep Reinforcement Learning

We demonstrate how to learn efficient heuristics for automated reasoning algorithms through deep reinforcement learning. We consider search algorithms for quantified Boolean logics, that already can solve formulas of impressive size - up to 100s of thousands of variables. The main challenge is to find a representation which lends to making predictions in a scalable way. The heuristics learned through our approach significantly improve over the handwritten heuristics for several sets of formulas.
T-Synthase Deficiency Enhances Oncogenic Features in Human Colorectal Cancer Cells via Activation of Epithelial-Mesenchymal Transition

Background Immature truncated O-glycans such as Tn antigen are frequently detected in human colorectal cancer (CRC); however, the precise pathological consequences of Tn antigen expression on CRC are unknown. T-synthase is the key enzyme required for biosynthesis of mature O-glycans. Here we investigated the functional roles of Tn antigen expression mediated by T-synthase deficiency in CRC cells. Methods To knock out T-synthase, we used CRISPR-Cas9 technology to target C1GALT1, the gene encoding T-synthase, in a CRC cell line (HCT116). Deletion of T-synthase was confirmed by western blotting, and expression of Tn antigen was determined by flow cytometry in HCT116 cells. We then assessed the biological effects of T-synthase deficiency on oncogenic behaviors in HCT116 cells. Furthermore, we analyzed the mechanistic role of T-synthase deficiency in cancer cells by determining the epithelial-mesenchymal transition (EMT) pathway. Results We showed that forced knockout of T-synthase in HCT116 cells significantly induced Tn antigen expression, which represented the occurrence of aberrant O-glycosylation. Loss of T-synthase significantly enhanced cell proliferation and adhesion, as well as migration and invasiveness in culture. More importantly, we demonstrated that T-synthase deficiency directly induced classical EMT characteristics in cancer cells. E-cadherin, a typical epithelial cell marker, was markedly decreased in T-synthase knockout HCT 116 cells, accompanied by an enhanced expression of mesenchymal markers including snail and fibronectin (FN). Conclusions These findings indicate that T-synthase deficiency in CRC cells not only is responsible for aberrant O-glycosylation, but also triggers the molecular process of EMT pathway, which may translate to increased invasiveness and metastasis in cancers.
Speech Understanding With Various Maskers in Cochlear-Implant and Simulated Cochlear-Implant Hearing: Effects of Spectral Resolution and Implications for Masking Release

The purpose of this study was to investigate the relationship between psychophysical spectral resolution and sentence reception in various types of interfering backgrounds for listeners with cochlear implants and normal-hearing subjects listening to vocoded speech. Spectral resolution was measured with a spectral modulation detection (SMD) task. For speech testing, maskers included stationary speech-shaped noise (SSN), four-talker babble, multitone noise, and a competing talker. To explore the possible trade-offs between spectral resolution and susceptibility to different types of maskers, the degree of simulated current spread was varied within the vocoder group, achieving a range of performance for SMD and speech tasks. Greater simulated current spread was detrimental to both spectral resolution and speech recognition, suggesting that interventions that decrease current spread may improve performance for both tasks. Better SMD sensitivity was significantly correlated with improved sentence reception. In addition, differences in sentence reception across the four maskers were significantly associated with SMD across the combined group of cochlear-implant and vocoder subjects. Masking release (MR) was quantified as the signal-to-noise ratio difference in speech reception threshold between the SSN and competing talker. Several individual cochlear-implant subjects demonstrated substantial MR, in contrast to previous studies, and the degree of MR increased with better SMD thresholds across subjects. The results of this study suggest that alternative masker types, particularly competing talkers, are more sensitive than stationary SSN to differences in spectral resolution in the cochlear-implant population.
TIE2-expressing monocytes and M2-polarized macrophages impact survival and correlate with angiogenesis in adenocarcinoma of the pancreas

Introduction M2-polarized tumor-associated macrophages (TAMs) and TIE2-expressing monocytes (TEMs) are associated with angiogenesis and have been identified as a potential prognostic marker in several solid tumors, including hepatobiliary malignancies. However, little is known regarding their influence on tumor progression and patient survival in pancreatic ductal adenocarcinoma (PDAC). Results Patients with tumors characterized by the presence of CD163+ TAMs or TEMs in TCA or TIF, respectively, showed a significantly decreased 1-, 3- and 5-year overall and recurrence-free survival compared to patients without CD163+ TAMs or TEMs (all ρ < 0.05). Patients with TEMs in TCA showed a higher incidence of tumor recurrence (ρ < 0.05). Furthermore, the presence of CD163+ TAMs was associated with a higher tumor MVD (ρ < 0.05). Conclusions Presence of M2-polarized TAMs and TEMs is associated with a decreased overall and recurrence-free survival of patients with PDAC. Materials and methods The localization and density of CD163+ M2-polarized TAMs and TEMs were quantified in the tumor central area (TCA) and tumor-infiltrating front (TIF) in human PDAC tissue (n = 106) and correlated to clinicopathological characteristics, tumor recurrence rates and patient survival. In parallel, tumor microvascular density (MVD) and the density of angiopoietin-positive tumor cells were quantified. Statistical analysis was performed using SPSS software.
Association of Nonalcoholic Fatty Liver Disease With Osteoporotic Fractures: A Cross-Sectional Retrospective Study of Chinese Individuals

Objective: Nonalcoholic fatty liver disease (NAFLD) is related to several inflammatory or metabolic diseases. However, findings of previous studies investigating the association between NAFLD and BMD are inconsistent. Only one study reported a potential association between NAFLD and osteoporotic fracture. This study investigated whether NAFLD in older participants (>55 years) was associated with osteoporotic fracture risk. Materials and Methods: This cross-sectional, observational study included 2,695 participants (35.7% men, 614 cases of NAFLD, and 383 fractures). Standardized questionnaires, laboratory tests, and physical and ultrasonic examinations were completed. Results: After adjusting for various factors including serum triglycerides (TG), high-density cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), multivariate logistic regression models revealed a marginal association between NAFLD and osteoporotic fracture risk in men (odds ratio [OR], 1.86; 95% confidence interval [CI], 1.06–3.27; P = 0.030) but no association in women (OR, 1.05; 95% CI, 0.74–1.48; P = 0.800). Further stratified analyses showed a significant association between NAFLD and osteoporotic fracture risk in men without high TG, low HDL-C, and high LDL-C. Conclusions: There was a significant association between NAFLD and osteoporotic fracture risk in older Chinese men, particularly men without dyslipidemia.
Multimodal MRI-Based Triage for Acute Stroke Therapy: Challenges and Progress

Revascularization therapies have been established as the treatment mainstay for acute ischemic stroke. However, a substantial number of patients are either ineligible for revascularization therapy, or the treatment fails or is futile. At present, non-contrast computed tomography is the first-line neuroimaging modality for patients with acute stroke. The use of magnetic resonance imaging (MRI) to predict the response to early revascularization therapy and to identify patients for delayed treatment is desirable. MRI could provide information on stroke pathophysiologies, including the ischemic core, perfusion, collaterals, clot, and blood–brain barrier status. During the past 20 years, there have been significant advances in neuroimaging as well as in revascularization strategies for treating patients with acute ischemic stroke. In this review, we discuss the role of MRI and post-processing, including machine-learning techniques, and recent advances in MRI-based triage for revascularization therapies in acute ischemic stroke.
The Effect of Background Music on Inhibitory Functions: An ERP Study

The influence of background music on cognitive functions is still a matter of debate. In this study, we investigated the influence of background music on executive functions (particularly on inhibitory functions). Participants completed a standardized cued Go/NoGo task during three different conditions while an EEG was recorded (1: with no background music, 2: with relaxing, or 3: with exciting background music). In addition, we collected reaction times, omissions, and commissions in response to the Go and NoGo stimuli. From the EEG data, event-related potentials (ERPs) were calculated for the Go and NoGo trials. From these ERPs, the N2 and P3 components were specifically analyzed since previous studies have shown that these components (and particularly the Go-NoGo difference waves) are strongly associated with inhibitory functions. The N2 and P3 components of the difference waves (N2d and P3d) were used for statistical analyses. The statistical analyses revealed no differences between the three conditions in terms of amplitudes and latencies of the N2d and P3d components. In addition, reaction times, omissions, and commissions were comparable across all conditions. Our results suggest that in the context of this paradigm, music as background acoustic stimulation has no detrimental effects on the performance of a Go/NoGo task and neural underpinnings.
SOCS3 Suppression Promoted the Recruitment of CD11b+Gr-1−F4/80−MHCII− Early-Stage Myeloid-Derived Suppressor Cells and Accelerated Interleukin-6-Related Tumor Invasion via Affecting Myeloid Differentiation in Breast Cancer

Interleukin-6 (IL-6) is an important trigger for the expansion and recruitment of myeloid-derived suppressor cells (MDSCs), which are regarded to be major coordinators of the immunosuppressive tumor microenvironment. In this study, we constructed IL-6-knockdown breast cancer mice models to explore the molecular events involved in the IL-6-mediated effects on MDSC development. We defined a subset of early-stage MDSCs (e-MDSCs) with the phenotype of CD11b+Gr-1−F4/80−MHCII− in IL-6 high-expressing 4T1 mice mammary carcinoma models, which were the precursors of CD11b+Gr-1+ conventional MDSCs. Furthermore, sustained suppression of SOCS3 and aberrant hyperactivation of the JAK/STAT signaling pathway was exclusively detected in wide-type 4T1 tumor-bearing mice, which promoted the accumulation of e-MDSCs in situ and their immunosuppressive capability in vitro. After blocking the IL-6/STAT3 signaling pathway with the IL-6 receptor antibody or STAT3 antagonist JSI-124 in tumor-bearing mice, significant shrinkage of primary tumors and decrease in lung metastatic nodules were observed in vivo, accompanied by the dramatic decrease of e-MDSC recruitment and recovery of anti-tumor T cell immunity. Thus, SOCS3 suppression accelerated the IL-6-mediated growth and metastasis of mammary carcinoma via affecting myeloid differentiation in breast cancer. Moreover, the IL-6/STAT3 signaling pathway might be a promising candidate target in developing novel therapeutic strategies to eliminate e-MDSCs and improve breast cancer prognosis.
Dialectical GAN for SAR Image Translation: From Sentinel-1 to TerraSAR-X

With more and more SAR applications, the demand for enhanced high-quality SAR images has increased considerably. However, high-quality SAR images entail high costs, due to the limitations of current SAR devices and their image processing resources. To improve the quality of SAR images and to reduce the costs of their generation, we propose a Dialectical Generative Adversarial Network (Dialectical GAN) to generate high-quality SAR images. This method is based on the analysis of hierarchical SAR information and the “dialectical” structure of GAN frameworks. As a demonstration, a typical example will be shown, where a low-resolution SAR image (e.g., a Sentinel-1 image) with large ground coverage is translated into a high-resolution SAR image (e.g., a TerraSAR-X image). A new algorithm is proposed based on a network framework by combining conditional WGAN-GP (Wasserstein Generative Adversarial Network—Gradient Penalty) loss functions and Spatial Gram matrices under the rule of dialectics. Experimental results show that the SAR image translation works very well when we compare the results of our proposed method with the selected traditional methods.