Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Added Variable and Partial Residual Plots for the Detection of Influential Observations in Generalized Linear Models

The added variable plots proposed by Pregibon and Wang and the partial residual plots proposed by Pregibon and Landwehr and co-workers for generalized linear models have been found useful for examining the relationship between the dependent variable and an independent variable; however, they can give misleading impressions about influential observations. Alternative procedures in which the plots are based on the full rather than the reduced model, or on weighted rather than unweighted variables, prove to be more informative about such observations, giving information which is consistent with Pregibon's influence diagnostics in generalized linear models.
A Profile of Positive and Negative Caregiving Experiences Among Canadian Older Adults: The Relevance of Demographic and Care Contexts

This study examines the predictors of burdens and benefits of informal caregiving to caregivers by examining how demographic characteristics and care contexts simultaneously predict separate scales of positive and negative caregiving experiences. The Caregiving, Aging, and Financial Experiences study is a national survey which examines a representative sample of 4010 Canadians between the ages of 65 and 85, including 1641 informal caregivers that are the focus of the current analysis. Seemingly unrelated regression analyses show that there are similarities as well as differences in predictors between the two caregiving experiences. More frequent involvement in caregiving is associated with greater negative caregiving experiences but those are not significant predictors for less positive caregiving experiences. This study demonstrates that there are some overlaps of determinants of the two caregiving experiences, and a few of them are distinct. Further studies should warrant to identify additional, unobserved factors explaining variance in positive caregiving experience.
The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization

Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
Identification and sex-specific expression of chemosensory genes in the antennal transcriptomes of Pachyrhinus yasumatsui (Coleoptera: Curculionidae)

Abstract Pachyrhinus yasumatsui Kono et Morimoto is a major pest of Chinese jujube, which is widespread in northern China and causes severe economic losses in the jujube industry. Chemosensory genes play crucial roles in insect behaviors. Currently, little is known about chemosensory genes in P. yasumatsui. In the present study, antennal transcriptomes of female and male adult P. yasumatsui were annotated. In total, 113 genes involved in chemosensory functions were identified, including 41 odorant receptors, 28 odorant-binding proteins, 16 ionotropic receptors, 15 chemosensory proteins, 9 gustatory receptors, and 4 sensory neuron membrane proteins. Subsequently, the phylogenetic analyses of these olfactory-related proteins in P. yasumatsui were conducted using multiple sequence alignment. Furthermore, sex-specific expression levels of 113 genes were analyzed based on fragments per kilobase of transcript per million mapped reads (FPKM). Then, the quantitative real-time PCR (RT-qPCR) was used to quantify gene expression profiles of 28 P. yasumatsui OBPs (PyasOBPs) and 15 CSPs (PyasCSPs). The results revealed that 20 PyasOBPs and 13 PyasCSPs exhibited significantly higher expression in the antennae than in the bodies, suggesting that they might have functions in olfaction. Moreover, some OBPs and CSPs (PyasOBP6, PyasOBP7, PyasOBP16, PyasOBP21, and PyasCSP4) exhibited female-biased expression, indicating that they might take part in several female-specific behaviors. This study will promote the understanding of olfactory mechanism in P. yasumatsui, and our findings lay the groundwork for developing environmentally friendly pest management measures.
Wang Tilings in Numerical Homogenization

Stochastic Wang tiling has been shown to bring unexpected insights to microstructure representation efforts as it generalizes the conventional unit-cell approach. It allows to reconstruct stochastic realizations of the compressed medium without prior periodic assumptions on microstructural patterns. Moreover, once the microstructure is compressed, its realizations of various sizes can be generated at almost negligible cost. In this paper, we follow the standard numerical homogenization procedure and make use of the realizations as domains over which local quantities are computed and averaged subsequently. In order to alleviate computational cost, a domain decomposition method is adopted such that it benefits from the fact that the computational domains are composed of limited number of repetitive patterns -- tiles.
Shape-defining alginate shells as semi-permeable culture chambers for soft cell-laden hydrogels

Soft hydrogels have a porous structure that promotes viability and growth of resident cells. However, due to their low structural stability, these materials are fragile and difficult to culture in vitro. Here we present a novel approach for the 3D culture of such materials, where a shape-defining, semi-permeable hydrogel shell is used to provide mechanical stability. These thin hydrogel shells enclose and stabilize the soft materials while still permitting gas and nutrient exchange. Custom alginate-shaped shells were prepared using a thermosetting, ion-eluting hydrogel mold. In a second step, the hydrogel shells were filled with cell-laden infill materials. As an example of the versatility of this technique, materials previously not available for tissue engineering, such as non-annealed microgels or low crosslinked and mechanically unstable hydrogels, were used for tissue culture. Primary human chondrocytes were cultured using this platform, to evaluate its potential for cartilage tissue engineering. To prove the scalability of this technique, anatomically-shaped ears were cultured for 3 weeks. This novel approach has the potential to radically change the material property requirements in the field of tissue engineering: thanks to the shape definition and stability provided by the hydrogel shells, a wide range of materials previously inaccessible for the manufacture of 3D tissue grafts can be re-evaluated.
Creation of a structured molecular genomics report for Germany as a local adaption of HL7’s Genomic Reporting Implementation Guide

Abstract Objective The objective was to develop a dataset definition, information model, and FHIR® specification for key data elements contained in a German molecular genomics (MolGen) report to facilitate genomic and phenotype integration in electronic health records. Materials and Methods A dedicated expert group participating in the German Medical Informatics Initiative reviewed information contained in MolGen reports, determined the key elements, and formulated a dataset definition. HL7’s Genomics Reporting Implementation Guide (IG) was adopted as a basis for the FHIR® specification which was subjected to a public ballot. In addition, elements in the MolGen dataset were mapped to the fields defined in ISO/TS 20428:2017 standard to evaluate compliance. Results A core dataset of 76 data elements, clustered into 6 categories was created to represent all key information of German MolGen reports. Based on this, a FHIR specification with 16 profiles, 14 derived from HL7®’s Genomics Reporting IG and 2 additional profiles (of the FamilyMemberHistory and RiskAssessment resources), was developed. Five example resource bundles show how our adaptation of an international standard can be used to model MolGen report data that was requested following oncological or rare disease indications. Furthermore, the map of the MolGen report data elements to the fields defined by the ISO/TC 20428:2017 standard, confirmed the presence of the majority of required fields. Conclusions Our report serves as a template for other research initiatives attempting to create a standard format for unstructured genomic report data. Use of standard formats facilitates integration of genomic data into electronic health records for clinical decision support.
Regulation of Macrophage Cell Surface GAPDH Alters LL-37 Internalization and Downstream Effects in the Cell

Mycobacterium tuberculosis (M.tb), the major causative agent of tuberculosis, has evolved mechanisms to evade host defenses and persist within host cells. Host-directed therapies against infected cells are emerging as an effective option. Cationic host defense peptide LL-37 is known to internalize into cells and induce autophagy resulting in intracellular killing of M.tb. This peptide also regulates the immune system and interacts with the multifunctional protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) inside macrophages. Our investigations revealed that GAPDH moonlights as a mononuclear cell surface receptor that internalizes LL-37. We confirmed that the surface levels of purinergic receptor 7, the receptor previously reported for this peptide, remained unaltered on M.tb infected macrophages. Upon infection or cellular activation with IFNγ, surface recruited GAPDH bound to and internalized LL-37 into endocytic compartments via a lipid raft-dependent process. We also discovered a role for GAPDH in LL-37-mediated autophagy induction and clearance of intracellular pathogens. In infected macrophages wherein GAPDH had been knocked down, we observed an inhibition of LL-37-mediated autophagy which was rescued by GAPDH overexpression. This process was dependent on intracellular calcium and p38 MAPK pathways. Our findings reveal a previously unknown process by which macrophages internalize an antimicrobial peptide via cell surface GAPDH and suggest a moonlighting role of GAPDH in regulating cellular phenotypic responses of LL-37 resulting in reduction of M.tb burden.
Graphical solution of turbulent‐flow diffusion equations

Linear partial-differential eqations are often encountered when thermal or material diffusion in flowing systems is considered. Analytic solutions of such equations are known for only the simplest situations. In two examples a graphical method of solution is presented and demonstrated which makes feasible, without excessive labor or special computing facilities, the use of available knowledge concerning turbulent flow in the prediction of thermal or material transfers in complex situations involving linear steady flow.
Transition metal–catalyzed remote C─H borylation: An emerging synthetic tool

Transition metal–catalyzed C─H bond activation and borylation is a powerful synthetic method that offers versatile synthetic transformation from organoboron compounds to virtually all other functional groups. Compared to the ortho-borylation, remote borylation remains more challenging owing to the inaccessibility of these C─H bonds. Enforcing the metal catalyst toward the remote C─H bonds needs well-judged catalyst design through proper ligand development. This review article aims to summarize the recent discoveries for the remote C─H borylation by the employment of new catalyst/ligand design with the help of steric of the ligand, noncovalent interactions. It has been found that C─H borylation now takes part in the total synthesis of natural products in a shorter route. Whereas, Ir-catalyzed C─H borylation is predominant, cobalt catalyst has also started to affect this field for sustainable and cost-effective development.
Outlier Mining Based on Variance of Angle Technology Research in High-Dimensional Data

Outlier mining in high dimensional data is currently one of the hot areas of data mining. The existing outlier mining methods are based on the distance in the full-dimensional Euclidean space. In high-dimensional data, these methods are bound to deteriorate due to the notorious "dimension disaster" which leads to distance measure can not express the original physical meaning and the low computational efficiency. This paper improves the method of anglebased outlier factor outlier and proposes the method of variance of angle-based outlier factor outlier. It introduces the related theories to guarantee the reliability of the method. The empirical experiments on synthetic data sets show that the method is efficient and scalable to large high-dimensional data sets.
Magnetic Resonance Elastography in the Study of Neurodegenerative Diseases

Neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD) present a major health burden to society. Changes in brain structure and cognition are generally only observed at the late stage of the disease. Although advanced magnetic resonance imaging (MRI) techniques such as diffusion imaging may allow identification of biomarkers at earlier stages of neurodegeneration, early diagnosis is still challenging. Magnetic resonance elastography (MRE) is a noninvasive MRI technique for studying the mechanical properties of tissues by measuring the wave propagation induced in the tissues using a purpose‐built actuator. Here, we present a systematic review of preclinical and clinical studies in which MRE has been applied to study neurodegenerative diseases. Actuator systems for data acquisition, inversion algorithms for data analysis, and sample demographics are described and tissue stiffness measures obtained for the whole brain and internal structures are summarized. A total of six animal studies and eight human studies have been published. The animal studies refer to 123 experimental animals (68 AD and 55 PD) and 121 wild‐type animals, while the human studies refer to 142 patients with neurodegenerative disease (including 56 AD and 17 PD) and 166 controls. The animal studies are consistent in the reporting of decreased stiffness of the hippocampal region in AD mice. However, in terms of disease progression, although consistent decreases in either storage modulus or shear modulus magnitude are reported for whole brain, there is variation in the results reported for the hippocampal region. The clinical studies are consistent in reports of a significant decrease in either whole brain storage modulus or shear modulus magnitude, in both AD and PD and with different brain structures affected in different neurodegenerative diseases. MRE studies of neurodegenerative diseases are still in their infancy, and in future it will be interesting to investigate potential relationships between brain mechanical properties and clinical measures, which may help elucidate the mechanisms underlying onset and progression of neurodegenerative diseases.
Why people engage in corrupt collaboration: an observation at the multi-brain level

Abstract Recent studies suggest that corrupt collaboration (i.e. acquiring private benefits with joint immoral acts) represents a dilemma between the honesty and reciprocity norms. In this study, we asked pairs of participants (labeled as A and B) to individually toss a coin and report their outcomes; their collective benefit could be maximized by dishonestly reporting (a corrupt behavior). As expected, the likelihood of corrupt behavior was high; this probability was negatively correlated with player A’s moral judgment ability but positively correlated with player B’s empathic concern (EC). Functional near-infrared spectroscopy data revealed that the brain-to-brain synchronization in the right dorsolateral prefrontal cortex was associated with fewer corrupt behaviors, and that it mediated the relationship between player A’s moral judgment ability and corrupt collaboration. Meanwhile, the right temporal–parietal junction synchronization was associated with more corrupt behaviors, and that it mediated the relationship between player B’s EC and corrupt collaboration. The roles of these 2 regions are interpreted according to the influence of the honesty and reciprocity norms on corrupt collaboration. In our opinion, these findings provide insight into the underlying mechanisms and modulating factors of corrupt collaboration.
Complement Activation by Adeno-Associated Virus-Neutralizing Antibody Complexes

Treatment of monogenetic disorders using vectors based on adeno-associated virus (AAV) is an area of intense interest. AAV is non-pathogenic human virus, and preexisting capsid antibodies are prevalent in the population posing a challenge to the safety and efficacy of AAV-mediated gene therapies. In this study, we investigated the risk of AAV-mediated complement activation when sera from a cohort of human donors were exposed to AAV9 capsid. Seropositive donor sera carrying neutralizing antibodies from a previous environmental exposure activated complement when admixed with AAV9 capsids and complement activation was associated with donors who had higher levels of anti-AAV IgG1 antibodies. These findings were consistent with mass spectrometry analysis that identified increased binding of immunoglobulins and complement factors when AAV9 capsids were admixed with seropositive sera. Finally, complement activation was abrogated after IgG-depletion using affinity columns or serum pretreatment with an IgG degrading enzyme. Overall, these results demonstrate an important role of preexisting neutralizing antibodies in activating complement; a risk that can be mitigated by using adequate immunosuppression strategies when dosing seropositive patients with vector.
Disrupted resting-sate brain network dynamics in children born extremely preterm

Abstract The developing brain has to adapt to environmental and intrinsic insults after extremely preterm (EPT) birth. Ongoing maturational processes maximize their fit to the environment and this can provide a substrate for neurodevelopmental failures. Resting-state functional magnetic resonance imaging was used to scan 33 children born EPT, at < 27 weeks of gestational age, and 26 full-term controls at 10 years of age. We studied the capability of a brain area to propagate neural information (intrinsic ignition) and its variability across time (node-metastability). This framework was computed for the dorsal attention network (DAN), frontoparietal, default-mode network (DMN), and the salience, limbic, visual, and somatosensory networks. The EPT group showed reduced intrinsic ignition in the DMN and DAN, compared with the controls, and reduced node-metastability in the DMN, DAN, and salience networks. Intrinsic ignition and node-metastability values correlated with cognitive performance at 12 years of age in both groups, but only survived in the term group after adjustment. Preterm birth disturbed the signatures of functional brain organization at rest in 3 core high-order networks: DMN, salience, and DAN. Identifying vulnerable resting-state networks after EPT birth may lead to interventions that aim to rebalance brain function.
γ*-SEMI-OPEN SETS IN TOPOLOGICAL SPACES

The concept of generalized open sets in generalized topological spaces was introduced by A. Csaszar [6,7]. In this paper, we introduce the concept of γ*-semi-open sets and investigate the related topological properties of the associated topologies SOγ*(X) and τγ. We also introduce the concepts of -sets and Λsγ-sets which generalize g· Λs-sets and g· νs-sets respectively introduced by Minguel Caldas and Julian Dontchev [5].
Fault Diagnosis Method for Distribution Networks Based on the Rough Sets and Decision Tree Theory

To improve the indeterminacy and imperfection of distribution networks fault information that make it difficult to obtain accuracy fault diagnosis results,a new fault diagnosis algorithm based on the rough sets and decision tree theory is proposed,which can extract diagnosis rules directly from reduced decision table.The rough sets theory as a new mathematical tool is used to deal with inexact and uncertain knowledge for pattern recognition.The target is mainly to remove redundant information and to seek for reduced decision tables by use of discernible matrix.As a quickly learning theory and classification tool,according to the value of the information entropy,the decision tree is used to extract diagnosis rules directly from reduced decision table.The rules from decision tree can be with clear relationship and easy to explain.With the proposed method the blindness and redundancy of ruling can be avoided and the space for decision table is evidently diminished.According to the value of information entropy,the priority of different characteristic information can be conducive to acquiring quick and satisfactory results for distribution networks without looking up the whole rules.In addition when the fault information is imperfect,the results can be still acquired according to the remained information, so the proposed method possesses strong tolerant ability.This method is thus developed to ensure diagnosis precision and speed up the implementation of distribution fault diagnosis system.Finally,examples are given to verify its effectiveness,and the comparison with the former method shows its advantages.
Single-cell transcriptomics of a dynamic cell behavior in murine airways

Despite advances in high-dimensional cellular analysis, the molecular profiling of dynamic behaviors of cells in their native environment remains a major challenge. We present a method that allows us to couple the physiological behaviors of cells in an intact murine tissue to deep molecular profiling of individual cells. This method enabled us to establish a novel molecular signature for a striking migratory cellular behavior following injury in murine airways.