Miracle-dz/UniFAR-FTUs huggingface dataset:
Sedimentary Nitrogen and Sulfur Reduction Functional-Couplings Interplay With the Microbial Community of Anthropogenic Shrimp Culture Pond Ecosystem

Sediment nitrogen and sulfur cycles are essential biogeochemical processes that regulate the microbial communities of environmental ecosystems, which have closely linked to environment ecological health. However, their functional couplings in anthropogenic aquaculture sedimentary ecosystems remain poorly understood. Here, we explored the sediment functional genes in shrimp culture pond ecosystems (SCPEs) at different culture stages using the GeoChip gene array approach with 16S amplicon sequencing. Dissimilarity analysis showed that the compositions of both functional genes and bacterial communities differed at different phases of shrimp culture with the appearance of temporal distance decay (p < 0.05). During shrimp culture, the abundances of nitrite and sulfite reduction functional genes decreased (p < 0.05), while those of nitrate and sulfate reduction genes were enriched (p < 0.05) in sediments, implying the enrichment of nitrites and sulfites from microbial metabolism. Meanwhile, nitrogen and sulfur reduction genes were found to be linked with carbon degradation and phosphorous metabolism (p < 0.05). The influence pathways of nutrients were demonstrated by structural equation modeling through environmental factors and the bacterial community on the nitrogen and sulfur reduction functions, indicating that the bacterial community response to environmental factors was facilitated by nutrients, and led to the shifts of functional genes (p < 0.05). These results indicate that sediment nitrogen and sulfur reduction functions in SCPEs were coupled, which are interconnected with the SCPEs bacterial community. Our findings will be helpful for understanding biogeochemical cycles in anthropogenic aquaculture ecosystems and promoting sustainable management of sediment environments through the framework of an ecological perspective.
Patient-Specific Cerebral Blood Flow Simulation Based on Commonly Available Clinical Datasets

Cerebral hemodynamics play an important role in the development of cerebrovascular diseases. In this work, we propose a numerical framework for modeling patient-specific cerebral blood flow, using commonly available clinical datasets. Our hemodynamic model was developed using Simscape Fluids library in Simulink, based on a block diagram language. Medical imaging data obtained from computerized tomography angiography (CTA) in 59 patients with aneurysmal subarachnoid hemorrhage was used to extract arterial geometry parameters. Flow information obtained from transcranial Doppler (TCD) measurement was employed to calibrate input parameters of the hemodynamic model. The results show that the proposed numerical model can reproduce blood flow in the circle of Willis (CoW) per patient per measurement set. The resistance at the distal end of each terminal branch was the predominant parameter for the flow distribution in the CoW. The proposed model may be a promising tool for assessing cerebral hemodynamics in patients with cerebrovascular disease.
Performance of Impedance Control-Based Strategies in Power-Assisted Wheelchairs: A Predictive Simulation Study

Manual wheelchair propulsion is known to be inefficient and causes upper extremity pain, fatigue, and injury. Power-assisted wheelchairs can mitigate these effects through motors that reduce users' effort and load during propulsion. Among the different control strategies proposed to govern the user-wheelchair interaction, impedance control-based ones appear to be the most natural and effective. It can change the apparent dynamical properties of the wheelchair, particularly mass and friction, and automatically compensate for external disturbances such as terrain conditions. This study investigates the advantages and disadvantages of this control strategy employing predictive simulations of locomotion with power-assisted wheelchairs in different scenarios. The simulations are generated using a biomechanically realistic model of the upper extremities and their interaction with the power-assisted wheelchair by solving an optimal control problem. Investigated scenarios include steady-state locomotion vs. a transient maneuver starting from rest, movement on a ramp vs. a level surface, and different choices of reference model parameters. The results reveal that the investigated impedance control-based strategy can effectively reproduce the reference model and reduce the user's effort, with a more significant effect of inertia in the transient maneuver and of friction in steady-state locomotion. However, the simulations also show that imposing a first-order, linear reference model with constant parameters can produce disadvantageous locomotion patterns, particularly in the recovery phase, leading to unnecessary energy dissipation and consequent increase in energy consumption from the batteries. These observations indicate there is room for improvement, for instance, by exploring energy regeneration in the recovery phase or by switching reference model nature or parameters along the cycle. To the best of our knowledge, this is the first investigation of impedance control-based strategies for power-assisted wheelchairs using predictive simulations and a realistic, nonlinear model of the user-wheelchair system.
Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women

Background Bacterial colonization and associations with bacterial vaginosis (BV) signs and symptoms (Amsel criteria) may vary between populations. We assessed relationships between vaginal bacteria and Amsel criteria among two populations. Methods Kenyan participants from the placebo arm of the Preventing Vaginal Infections (PVI) trial and participants from a Seattle-based cross-sectional BV study were included. Amsel criteria were recorded at study visits, and the vaginal microbiota was characterized using 16S rRNA gene sequencing. Logistic regression models, accounting for repeat visits as appropriate, were fit to evaluate associations between bacterial relative abundance and each Amsel criterion. Results Among 84 PVI participants (496 observations) and 220 Seattle participants, the prevalence of amine odor was 25% and 40%, clue cells 16% and 37%, vaginal discharge 10% and 52%, elevated vaginal pH 69% and 67%, and BV 13% and 44%, respectively. BV-associated bacterium 1 (BVAB1) was positively associated with all Amsel criteria in both populations. Eggerthella type 1, Fannyhessea (Atopobium) vaginae, Gardnerella spp. , Sneathia amnii, and Sneathia sanguinegens were positively associated with all Amsel criteria in the Seattle study, and all but discharge in the PVI trial. Conclusions Core vaginal bacteria are consistently associated with BV signs and symptoms across two distinct populations of women.
Transparent Interaction Based Learning for Human-Robot Collaboration

The number of collaborative robots that perform different tasks in close proximity to humans is increasing. Previous studies showed that enabling non-expert users to program a cobot reduces the cost of robot maintenance and reprogramming. Since this approach is based on an interaction between the cobot and human partners, in this study, we investigate whether making this interaction more transparent can improve the interaction and lead to better performance for non-expert users. To evaluate the proposed methodology, an experiment with 67 participants is conducted. The obtained results show that providing explanation leads to higher performance, in terms of efficiency and efficacy, i.e., the number of times the task is completed without teaching a wrong instruction to the cobot is two times higher when explanations are provided. In addition, providing explanation also increases users’ satisfaction and trust in working with the cobot.
Benefits of Targeted Molecular Therapy to Immune Infiltration and Immune-Related Genes Predicting Signature in Breast Cancer

Background This study aimed to investigate the tumor-related infiltrating lymphocytes (TILs) affecting the response of trastuzumab and identify potential biomarkers based on immune-related genes to improve prognosis and clinical outcomes of targeted therapies in breast cancer. Methods Estimation of stromal and immune cells in malignant tumors using expression data (ESTIMATE) was adopted to infer the fraction of stromal and immune cells through utilizing gene expression signatures in breast tumor samples. Cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT) algorithm was applied to characterize cell composition of 22 lymphocytes from breast cancer tissues using their gene expression profiles. Immune-related genes were collected from the Immunology Database and Analysis (ImmPort). Univariate and multivariate Cox regression analyses were performed to identify the significant independent risk factors associated with poor overall survival (OS) and breast cancer-specific survival (BCSS) of breast cancer patients. Hub genes were identified based on the protein–protein interaction (PPI) network analysis. Results Based on the ESTIMATE algorithm, a significant reduction of stromal scores was observed in tumor tissues and pretreated tumor tissues compared with nontumor and posttreated tumor tissues, respectively, while immune scores failed to present notably statistical differences between both groups. However, from the results of the univariate Cox regression analysis, the immune score was identified to be remarkably associated with the poor OS for breast cancer patients. Subsequently, the infiltrating lymphocytes were evaluated in tumor tissues based on the CIBERSORT algorithm. Furthermore, significance analysis identified 1,244 differentially expressed genes (DEGs) from the GSE114082 dataset, and then 91 overlapping immune-related DEGs were screened between GSE114082 and ImmPort datasets. Subsequently, 10 top hub genes were identified and five (IGF1, ADIPOQ, PPARG, LEP, and NR3C1) significantly correlated with worse OS and BCSS on response to trastuzumab in breast cancer patients. Conclusions This study provided an insight into the immune score based on the tumor-related infiltrating lymphocytes in breast cancer tissues and demonstrates the benefits of immune infiltration on the treatment of trastuzumab. Meanwhile, the study established a novel five immune-related gene signature to predict the OS and BCSS of breast cancer treated by trastuzumab.
High Resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1, and ∼DQB1 Diversity in South African Populations

Background: Lack of HLA data in southern African populations hampers disease association studies and our understanding of genetic diversity in these populations. We aimed to determine HLA diversity in South African populations using high resolution HLA ∼A, ∼B, ∼C, ∼DRB1, ∼DQA1 and ∼DQB1 data, from 3005 previously typed individuals. Methods: We determined allele and haplotype frequencies, deviations from Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and neutrality test. South African HLA class I data was additionally compared to other global populations using non-metrical multidimensional scaling (NMDS), genetic distances and principal component analysis (PCA). Results: All loci strongly (p < 0.0001) deviated from HWE, coupled with excessive heterozygosity in most loci. Two of the three most frequent alleles, HLA ∼DQA1*05:02 (0.2584) and HLA ∼C*17:01 (0.1488) were previously reported in South African populations at lower frequencies. NMDS showed genetic distinctness of South African populations. Phylogenetic analysis and PCA clustered our current dataset with previous South African studies. Additionally, South Africans seem to be related to other sub-Saharan populations using HLA class I allele frequencies. Discussion and Conclusion: Despite the retrospective nature of the study, data missingness, the imbalance of sample sizes for each locus and haplotype pairs, and induced methodological difficulties, this study provides a unique and large HLA dataset of South Africans, which might be a useful resource to support anthropological studies, disease association studies, population based vaccine development and donor recruitment programs. We additionally provide simulated high resolution HLA class I data to augment the mixed resolution typing results generated from this study.
Unity Assumption in Audiovisual Emotion Perception

We experience various sensory stimuli every day. How does this integration occur? What are the inherent mechanisms in this integration? The “unity assumption” proposes a perceiver’s belief of unity in individual unisensory information to modulate the degree of multisensory integration. However, this has yet to be verified or quantified in the context of semantic emotion integration. In the present study, we investigate the ability of subjects to judge the intensities and degrees of similarity in faces and voices of two emotions (angry and happy). We found more similar stimulus intensities to be associated with stronger likelihoods of the face and voice being integrated. More interestingly, multisensory integration in emotion perception was observed to follow a Gaussian distribution as a function of the emotion intensity difference between the face and voice—the optimal cut-off at about 2.50 points difference on a 7-point Likert scale. This provides a quantitative estimation of the multisensory integration function in audio-visual semantic emotion perception with regards to stimulus intensity. Moreover, to investigate the variation of multisensory integration across the population, we examined the effects of personality and autistic traits of participants. Here, we found no correlation of autistic traits with unisensory processing in a nonclinical population. Our findings shed light on the current understanding of multisensory integration mechanisms.
Impact of Interest Congruence on Study Outcomes

Grounding on Holland’s RIASEC model of vocational interests and the respective assumptions on person-environment fit (congruence), this paper focuses on how congruence is related to study outcomes, especially students’ persistence, performance, and satisfaction. The paper distinguishes the measure of congruence with respect to social congruence (SOC) (interest fit with the study mates) and aspirational congruence (ASP) (interest fit with the occupation aspired) and also distinguishes the effects of congruence for gender and six different study areas including Science, Technology, Engineering, Mathematics (STEM), medicine, economics, education, and languages. The paper analyses 10,226 university freshmen of the German National Educational Panel Study (NEPS) and follows them longitudinally with respect to their study outcomes. The results show that students’ persistence was more related to SOC than to ASP, especially for male students. Furthermore, SOC was particularly important for students in STEM areas. Regarding performance, however, ASP was more important. Here, we notably found correlations for STEM subjects with a balanced proportion of female students. Regarding satisfaction, mainly marginal correlations could be found. The results indicate conceptual differences between social and aspirational congruence as well as specific effects for gender and study area. While research might take this into account by specifically developing their models for different study areas, career counseling may reflect on the different significance of the interest-based person-environment fit for different study areas. Initiatives for raising young people’s participation in STEM should therefore specifically focus on students that have high chances to develop interest profiles that are congruent to STEM rather than students who show profiles which already indicate a low congruence.
Long-Term Limitation Effects of Se(VI), Zn(II), and Ni(II) on Start-Up of the Anammox Process Using Gel Carrier

Anaerobic ammonia oxidation (anammox) bacteria are inhibited by heavy metals at high concentrations but require trace amounts of some heavy-metal elements for growth and activity maintenance. The present study evaluates the long-term limitation effects of Se(VI), Zn(II), and Ni(II) on the start-up period of an anammox reactor. To strictly limit the levels of heavy metals in the reactor, all tests used ultrapure water as the influent synthetic wastewater and all reactors were installed in a clean booth. The anammox biomass was maintained through the gel entrapment technique. In the absence of Se(VI) and Ni(II), the anammox reactor start-up was 18.9 kg-N (m3-carrier d)−1 (nitrogen conversion rate (NCR) per gel carriers), indicating that Se(VI) and Ni(II) are not required or need not be continuously added to maintain the anammox process. Under Zn(II) limitation, the anammox process failed to start-up and the NCR tended to decrease rapidly. After readdition of 0.005 mg L−1 of Zn(II), the NCR did not decline further and instead partially recovered at a very slow rate. The NCR was completely recovered after adding 0.020 mg L−1 of Zn(II). These results reveal that Zn(II) limitation seriously affects the start-up of the anammox process while Se(VI) and Ni(II) are not required or need not be continuously added to the anammox process.
Lactobacillus plantarum HFY05 Attenuates Carrageenan-Induced Thrombosis in Mice by Regulating NF-κB Pathway-Associated Inflammatory Responses

In this study, a carrageenan-induced thrombus model was established in mice to observe the ability of Lactobacillus plantarum KFY05 (LP-KFY05) to inhibit thrombosis through an NF-κB-associated pathway. Biochemical analysis, microscopical observations, quantitative polymerase chain reactions (qPCR) and western blot analysis were used to examine relevant serum and tissue indexes, and the composition of intestinal microorganisms was determined by examining the abundance of microorganisms in feces. The results showed that LP-KFY05 could markedly reduce the degree of black tail in thrombotic mice; increase the activated partial thromboplastin time (APTT); and decrease the thrombin time (TT), fibrinogen (FIB) level, and prothrombin time (PT). LP-KFY05 could also reduce tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and interleukin-1 beta (IL-1β) levels in sera and renal tissues of thrombotic mice. Hematoxylin and eosin staining showed that LP-KFY05 could alleviate renal tissue lesions and tail vein thrombosis. qPCR results showed that LP-KFY05 could down-regulate nuclear factor kappa-B (NF-κB) p65, IL-6, TNF-α, and interferon γ (IFN-γ) mRNA expression in renal tissues, as well as NF-κB p65, intercellular cell adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), and E-selectin mRNA expression in tail vein vascular tissues of thrombotic mice. Western blot analysis showed that LP-KFY05 also down-regulated NF-κB protein expression in renal and tail vein vascular tissues of thrombotic mice. Lastly, LP-KFY05 increased the abundances of Bacteroidetes, Lactobacillus, and Bifidobacterium, as well as decreased the abundance of Firmicutes. These results show that LP-KFY05 can reduce inflammation and inhibit thrombosis in thrombotic mice, and the effects of high concentrations of LP-KFY05 were most pronounced, which were similar to the effects of dipyridamole.
Efficient Cholesterol Transport in Dendritic Cells Defines Optimal Exogenous Antigen Presentation and Toxoplasma gondii Proliferation

Dendritic cells are the most powerful antigen-presenting cells of the immune system. They present exogenous antigens associated with Major Histocompatibility Complex (MHC) Class II molecules through the classical pathway to stimulate CD4+ T cells, or with MHC-I to activate CD8+ T lymphocytes through the cross-presentation pathway. DCs represent one of the main cellular targets during infection by Toxoplasma gondii. This intracellular parasite incorporates essential nutrients, such as cholesterol, to grow and proliferate inside a highly specialized organelle, the parasitophorous vacuole (PV). While doing so, T. gondii modulates the host immune response through multiple interactions with proteins and lipids. Cholesterol is an important cellular component that regulates cellular physiology at the structural and functional levels. Although different studies describe the relevance of cholesterol transport for exogenous antigen presentation, the molecular mechanism underlying this process is not defined. Here, we focus our study on the inhibitor U18666A, a drug widely used to arrest multivesicular bodies biogenesis that interrupts cholesterol trafficking and changes the lipid composition of intracellular membranes. Upon bone marrow-derived DC (BMDC) treatment with U18666A, we evidenced a drastic disruption in the ability to present exogenous soluble and particulate antigens to CD4+ and CD8+ T cells. Strikingly, the presentation of T. gondii-associated antigens and parasite proliferation were hampered in treated cells. However, neither antigen uptake nor BMDC viability was significantly affected by the U18666A treatment. By contrast, this drug altered the transport of MHC-I and MHC-II molecules to the plasma membrane. Since U18666A impairs the formation of MVBs, we analyzed in T. gondii infected BMDCs the ESCRT machinery responsible for the generation of intraluminal vesicles. We observed that different MVBs markers, including ESCRT proteins, were recruited to the PV. Surprisingly, the main ESCRT-III component CHMP4b was massively recruited to the PV, and its expression level was upregulated upon BMDC infection by T. gondii. Finally, we demonstrated that BMDC treatment with U18666A interrupted cholesterol delivery and CHMP4b recruitment to the PV, which interfered with an efficient parasite replication. Altogether, our results highlight the importance of cholesterol trafficking and MVBs formation in DCs for optimal antigen presentation and T. gondii proliferation.