Miracle-dz/UniFAR-FTUs huggingface dataset:
Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2

Abstract A prominent aspect of most, if not all, central nervous systems (CNSs) is that anterior regions (brain) are larger than posterior ones (spinal cord). Studies in Drosophila and mouse have revealed that Polycomb Repressor Complex 2 (PRC2), a protein complex responsible for applying key repressive histone modifications, acts by several mechanisms to promote anterior CNS expansion. However, it is unclear what the full spectrum of PRC2 action is during embryonic CNS development and how PRC2 intersects with the epigenetic landscape. We removed PRC2 function from the developing mouse CNS, by mutating the key gene Eed, and generated spatio-temporal transcriptomic data. To decode the role of PRC2, we developed a method that incorporates standard statistical analyses with probabilistic deep learning to integrate the transcriptomic response to PRC2 inactivation with epigenetic data. This multi-variate analysis corroborates the central involvement of PRC2 in anterior CNS expansion, and also identifies several unanticipated cohorts of genes, such as proliferation and immune response genes. Furthermore, the analysis reveals specific profiles of regulation via PRC2 upon these gene cohorts. These findings uncover a differential logic for the role of PRC2 upon functionally distinct gene cohorts that drive CNS anterior expansion. To support the analysis of emerging multi-modal datasets, we provide a novel bioinformatics package that integrates transcriptomic and epigenetic datasets to identify regulatory underpinnings of heterogeneous biological processes.
Serum uric acid level and all-cause and cardiovascular mortality in peritoneal dialysis patients: A systematic review and dose-response meta-analysis of cohort studies

Background The association between serum uric acid (SUA) and all-cause and cardiovascular disease (CVD) mortality in peritoneal dialysis (PD) patients is controversial. Therefore, we aimed to determine the relationship between SUA and all-cause and CVD mortality in PD patients. Method Web of Science, EMBASE, PubMed and the Cochrane Library databases were searched from their inception to 7 April 2021. Effect estimates were presented as hazard ratios (HRs) with 95% confidence intervals (95% CIs) and pooled using random effects model. Result Thirteen cohort studies with 22418 patients were included in this systematic review, of which 9 were included in the meta-analysis. Before switching the reference group, pooled result for the highest SUA category was significantly greater than the median for all-cause mortality (HR = 2.41, 95% CI: 1.37–4.26). After switching the reference group, the highest SUA category did not demonstrate an increased all-cause (HR = 1.40, 95% CI: 0.95–2.05) or CVD (HR = 1.30, 95% CI: 0.72–2.34) mortality compared with the lowest SUA category. Dose-response analysis suggested a nonlinear association between SUA and all-cause mortality risk (Pnonlinearity = 0.002). Conclusion This meta-analysis didn’t find the relationship between SUA levels and all-cause and CVD mortality risk in PD patients. More rigorously designed studies are warranted in the future.
Aortic arch type, a novel morphological indicator and the risk for acute type B aortic dissection

Abstract OBJECTIVES Aortic arch type is a readily recognizable and obtainable morphological feature of the aorta that does not require complex measurements. The goal of this study was to evaluate whether aortic arch type is a comparable and alternative morphological parameter for predicting acute type B aortic dissection (aTBAD) by comparing the prognostic value of the aortic arch type with that of other morphological parameters such as aortic length, angulation and tortuosity index. METHODS The patients with aTBAD (n = 216) were matched 1:1 with a control group (n = 263) by propensity score matching. The morphological data of the ascending aorta and the aortic arch, which included diameter, length, angulation and tortuosity index, were collected on a three-dimensional aortic model using 3mensio Vascular software. The aortic arch type was identified by the vertical distance from the origin of the brachiocephalic trunk to the top of the arch. The binary logistic regression models were analysed to determine the independent geometric variables related to the aTBAD. The nonparametric approach was performed to assess whether there were statistical differences between the area under the receiver operating characteristic curves (AUC) of the models. RESULTS After propensity score matching, 151 matched pairs of patients were selected. The diameters at the sinotubular junction and the mid-ascending aorta, the ascending aorta length and the ascending aorta angulation in the aTBAD group were significantly greater than those of the controls. Compared with the control group, the diameters at the proximal aortic arch, mid-aortic arch and distal aortic arch, the angulation and the tortuosity index of the aortic arch were significantly greater in the aTBAD group. The proportion of the type III arch in the patients with aTBAD is higher than that of the type I arch and the type II arch (χ2 = 70.187; P < 0.001). Binary logistic regression analysis showed that the diameter at the mid-aortic arch, the ascending aorta length, the aortic arch angulation and the tortuosity index were independently related to the aTBAD with an AUC value of 0.887. Another binary logistic regression analysis indicated that the diameter at the mid-aortic arch and the aortic arch type were independent correlative variables associated with the aTBAD with an AUC of 0.874. No significant difference was observed in the prognostic value of receiver operating characteristic curves between the 2 models (P = 0.716). CONCLUSIONS The type III arch, which has the characteristics of aortic elongation, incremental angulation and tortuosity index, is a comparable and alternative identifier for patients at high risk for aTBAD.
A complex network of interactions governs DNA methylation at telomeric regions

Abstract DNA methylation modulates telomere function. In Arabidopsis thaliana, telomeric regions have a bimodal chromatin organization with unmethylated telomeres and methylated subtelomeres. To gain insight into this organization we have generated TAIR10-Tel, a modified version of the Arabidopsis reference genome with additional sequences at most chromosome ends. TAIR10-Tel has allowed us to analyse DNA methylation at nucleotide resolution level in telomeric regions. We have analysed the wild-type strain and mutants that encode inactive versions of all currently known relevant methyltransferases involved in cytosine methylation. These analyses have revealed that subtelomeric DNA methylation extends 1 to 2 kbp from Interstitial Telomeric Sequences (ITSs) that abut or are very near to telomeres. However, DNA methylation drops at the telomeric side of the telomere-subtelomere boundaries and disappears at the inner part of telomeres. We present a comprehensive and integrative model for subtelomeric DNA methylation that should help to decipher the mechanisms that govern the epigenetic regulation of telomeres. This model involves a complex network of interactions between methyltransferases and subtelomeric DNA sequences.
The fork protection complex recruits FACT to reorganize nucleosomes during replication

Abstract Chromosome replication depends on efficient removal of nucleosomes by accessory factors to ensure rapid access to genomic information. Here, we show this process requires recruitment of the nucleosome reorganization activity of the histone chaperone FACT. Using single-molecule FRET, we demonstrate that reorganization of nucleosomal DNA by FACT requires coordinated engagement by the middle and C-terminal domains of Spt16 and Pob3 but does not require the N-terminus of Spt16. Using structure-guided pulldowns, we demonstrate instead that the N-terminal region is critical for recruitment by the fork protection complex subunit Tof1. Using in vitro chromatin replication assays, we confirm the importance of these interactions for robust replication. Our findings support a mechanism in which nucleosomes are removed through the coordinated engagement of multiple FACT domains positioned at the replication fork by the fork protection complex.
Acceptability of an extended duration vaginal ring for HIV prevention and interest in a multi-purpose ring

Given challenges with adherence to existing HIV prevention products, the development of an extended duration vaginal ring could improve adherence while reducing patient and provider burden. Additionally, women have other interlinked sexual health concerns such as unintended pregnancy. We evaluated acceptability of a 90-day ring to prevent HIV and hypothetical preferences for a dual (HIV and contraceptive) indication. This was a secondary analysis of a Phase 1, two-arm, multi-site, placebo-controlled randomized trial evaluating safety and pharmacokinetics of a 90-day vaginal ring containing tenofovir for HIV prevention (N = 49). We used a mixed methods approach to assess quantitative data on acceptability (n = 49) and used qualitative data from a random subset to explain the quantitative findings (N = 25). The 3-month extended duration tenofovir ring was highly acceptable. Participants perceived the ring to be easy to use, comfortable and reported liking it more over time. About half felt the ring during sex but most of those participants said it bothered them only a little. Concerns about hygiene increased over the study period but were often outweighed by the benefits of an extended duration ring. Interest in a multi-purpose ring was high (77%) and even higher among those who were sexually active and had male partners. The 3-month extended duration tenofovir ring for HIV prevention was highly acceptable among women and interest in an MPT was high.
End-effector control for bipedal locomotion

Biped locomotion can be formulated as goal-directed tasks in the low-dimensional end-effector space, with the upper body and the two feet as end effectors. Based on this observation and the neuroscience hypothesis about hierarchical control in human for tasks such as arm reaching and handwriting, I design a framework for the automatic synthesis of hierarchical controllers for biped locomotion. The controller consists of two components: a per-footstep end-effector path planner at the higher level, and a per-timestep generalized-force solver at the lower level. At the start of each footstep, the planner performs short-term planning in the space of end-effector trajectories. These trajectories at run-time adapt to the interactive task goals and the features of the surrounding uneven terrain in the virtual environment. Using the per-footstep plan, the generalized-force solver takes ground contacts into consideration and solves a quadratic program at each simulation timestep to obtain joint torques that drive the biped. The framework solves for the parameters of the planner and the generalized-force solver for different tasks in offline optimizations. I demonstrate the capabilities of the controllers in navigation tasks where they perform gradual and sharp turns and transition between moving forwards, backwards, and sideways on uneven terrain according to the interactive task goals. I show that the resulting controllers are capable of handling certain morphology changes to the character. To verify that such hierarchical end-effector controllers can potentially be used in real-world mechanical systems, I also show that the controllers are robust to disturbances such as actuator and sensor noise, and changes in the friction coefficient. Because human locomotion is routinely subject to these disturbances, robustness against these disturbances also suggests that the hierarchical control hypothesis about human arm reaching and handwriting control may be a good candidate hypothesis for human locomotion control as well.
Evolution of hospitalized patient characteristics through the first three COVID-19 waves in Paris area using machine learning analysis

Characteristics of patients at risk of developing severe forms of COVID-19 disease have been widely described, but very few studies describe their evolution through the following waves. Data was collected retrospectively from a prospectively maintained database from a University Hospital in Paris area, over a year corresponding to the first three waves of COVID-19 in France. Evolution of patient characteristics between non-severe and severe cases through the waves was analyzed with a classical multivariate logistic regression along with a complementary Machine-Learning-based analysis using explainability methods. On 1076 hospitalized patients, severe forms concerned 29% (123/429), 31% (66/214) and 18% (79/433) of each wave. Risk factors of the first wave included old age (≥ 70 years), male gender, diabetes and obesity while cardiovascular issues appeared to be a protective factor. Influence of age, gender and comorbidities on the occurrence of severe COVID-19 was less marked in the 3rd wave compared to the first 2, and the interactions between age and comorbidities less important. Typology of hospitalized patients with severe forms evolved rapidly through the waves. This evolution may be due to the changes of hospital practices and the early vaccination campaign targeting the people at high risk such as elderly and patients with comorbidities.
A space-time adaptive method for flows in oil reservoirs

This work presents a space-time adaptive framework for simulating multi-phase flows through porous media, with specific applications to flows in oil reservoirs. A fully unstructured discretization of space and time is used instead of a conventional timemarching approach. For d-dimensional spatial problems, this requires the generation of (d+1)-dimensional meshes, where time is treated as an additional spatial dimension. Anisotropic mesh adaptation is performed based on a posteriori error estimation to reduce the error of a specified output of interest. This work makes use of the DWR method for error estimation and the MOESS algorithm for metric-based mesh optimization. A discontinuous Galerkin finite element discretization is used to solve on simplex meshes with arbitrary anisotropy, and thereby obtain solutions of higher order accuracy in both space and time. The adaptive framework has been applied to single-phase and two-phase flow test problems in a one-dimensional reservoir, and the results were compared to those obtained from a time-marching finite volume method that is representative of a typical industrial simulator. Thesis Supervisor: David Darmofal Title: Professor of Aeronautics and Astronautics
Leader-Follower Formation Control of Autonomous Underwater Vehicles

Cooperation of multiple autonomous underwater vehicles(AUVs)has become a hotspot of current AUVs,in which formation control is the typical problem,and a basis of other cooperative control problems.A mathematic model of the formation control for AUVs was established,the feedback linearization was then used to simplify the model to a one order dynamic system,and the control law was derived.Stabilization of the control law and the inner dynamic system were proved.Furthermore,the formation errors of two leader-follower formation controls under different topologies were compared.Simulation results show validation of the algorithm,and the formation error in parallel connection mode is smaller than that in serial connection mode.
Finite element analysis between Hunsuck/Epker and novel modification of Low Z plasty technique of mandibular sagittal split osteotomy

A novel modification of the Low Z plasty (NM-Low Z) technique for bilateral sagittal split osteotomy was recently proposed. The osteotomy line was modified more inferiorly than in the conventional Hunsuck–Epker (HE) approach. The NM-Low Z technique enhances the mandibular setback distance and degree of rotation in severe skeletal discrepancies. This study aimed to investigate the biomechanical behavior under simulated forces, and to compare the NM-Low Z and HE techniques on the mandible with Class III skeletal deformity at 1 week, 3 weeks, and 6 weeks post-operation. Physiological muscular and occlusal loads were simulated using the finite element (FE) method. Stresses on the miniplate, screws, and bone were observed and compared between the two models. The elastic strain at the fracture site was observed for the optimal bone-healing capacity. The NM-Low Z model exhibited a lower stress than the HE model at every stage post-operation. Both models demonstrated elastic strains within the normal range for bone healing. In summary, the biomechanical behavior of the NM-Low Z technique is comparable to that of the conventional EH technique. NM-Low Z could facilitate post-operation skeletal stability by reducing the stress on fixation materials during bone healing.
Characteristics of Nursing Home Resident Movement Patterns: Results from the TEAM-UP Trial

ABSTRACT OBJECTIVE To determine movement patterns of nursing home residents, specifically those with dementia or obesity, to improve repositioning approaches to pressure injury (PrI) prevention. METHODS A descriptive exploratory study was conducted using secondary data from the Turn Everyone And Move for Ulcer Prevention (TEAM-UP) clinical trial examining PrI prevention repositioning intervals. K-means cluster analysis used the average of each resident’s multiple days’ observations of four summary mean daily variables to create homogeneous movement pattern clusters. Growth mixture models examined movement pattern changes over time. Logistic regression analyses predicted resident and nursing home cluster group membership. RESULTS Three optimal clusters partitioned 913 residents into mutually exclusive groups with significantly different upright and lying patterns. The models indicated stable movement pattern trajectories across the 28-day intervention period. Cluster profiles were not differentiated by residents with dementia (n = 450) or obesity (n = 285) diagnosis; significant cluster differences were associated with age and Braden Scale total scores or risk categories. Within clusters 2 and 3, residents with dementia were older (P < .0001) and, in cluster 2, were also at greater PrI risk (P < .0001) compared with residents with obesity; neither group differed in cluster 1. CONCLUSIONS Study results determined three movement pattern clusters and advanced understanding of the effects of dementia and obesity on movement with the potential to improve repositioning protocols for more effective PrI prevention. Lying and upright position frequencies and durations provide foundational knowledge to support tailoring of PrI prevention interventions despite few significant differences in repositioning patterns for residents with dementia or obesity.
Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

ABSTRACT Purpose While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease intervention. Materials and Methods Three microarray datasets associated with MM were downloaded from the Gene Expression Omnibus (GEO) database. GSE125364 and GSE39754 were used as the training set, and GSE13591 was used as the verification set. The differentially expressed genes (DEGs) were obtained from the training set, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate their functions. The hub genes were derived from the combined results of a protein–protein interaction (PPI) network and weighted gene coexpression network analysis (WGCNA). The receiver operating characteristic (ROC) curves of hub genes were plotted to evaluate their clinical diagnostic value. Biological processes and signaling pathways associated with hub genes were explained by gene set enrichment analysis (GSEA). Results A total of 1759 DEGs were identified. GO and KEGG pathway analyses suggested that the DEGs were related to the process of protein metabolism. RPN1, SEC61A1, SPCS1, SRPR, SRPRB, SSR1 and TRAM1 were proven to have clinical diagnostic value for MM. The GSEA results suggested that the hub genes were widely involved in the N-glycan biosynthesis pathway. Conclusion The hub genes identified in this study can partially explain the potential molecular mechanisms of MM and serve as candidate biomarkers for disease diagnosis.
Asperbenzophenone A and Versicolamide C, New Fungal Metabolites from the Soft Coral Derived Aspergillus sp. SCSIO 41036

Two new compounds, asperbenzophenone A (1) and versicolamide C (5), together with fifteen known compounds were isolated from a soft coral derived fungus Aspergillus sp. SCSIO 41036. Their structures were elucidated by spectroscopic methods, ECD analysis, and by a comparison with data from the literature. In bioassay, compound 8 showed significant inhibitory activity against lipopolysaccharide‐inducted nitric oxide (NO) in RAW264.7 cells at the concentration of 10 μM. Additionally, the anti‐acetylcholinesterase activity assay showed that 14 exhibited weak inhibition with an IC50 value of 157.8 μM.
Research of the Equipment on Integration Testing and Analyzing Time Parameters of Electromagnetic Relay

The equipment was designed for the research based on industrial control computer. Ten channel signals of coil or contact of electromagnetic relay can be sampled synchronously through the way of hardware logic controlling memeory mapping, and the maximum time resolution is 0.25 μs. The equipment also can be used to test the neutral position of magnetic latch relay. The test result shows that the equipment has very strong application value.
CLOUD COMPUTING: A CROSS-CULTURAL COMPARATIVE STUDY BETWEEN COMPUTER AND INFORMATION SYSTEMS FACULTY AT A UNIVERSITY IN THE UNITED STATES AND A UNIVERSITY IN SAUDI ARABIA

Cloud computing is similar to any new technology and can cause major challenges and opportunities for faculty in institutions of Higher Education. This study was undertaken to determine how Computer and Information Systems (CIS) faculty at two universities view the acceptance and use of cloud computing technology within their respective departments. One university is located in the United States and the other is located in Saudi Arabia. Specifically, this study sought to examine the commonalities and differences between these diverse universities as related to the advantages and disadvantages of using cloud computing, identify the key factors that influence adopting/using cloud computing, and determine each university’s overall perception of cloud computing. This study also sought to determine if there are differences between CIS faculty in a U.S.-based university and in a Saudi Arabian-based university regarding perceived knowledge of Cloud Computing and the status of adoption of Cloud Computing