Miracle-dz/UniFAR-FTUs huggingface dataset:
Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder

Significance KRas is the most frequently mutated oncogene in human cancer, and its critical role in tumorigenesis is well established. Historical challenges in targeting KRas have led to its characterization as an “undruggable” target, but recent advances in drug discovery approaches have revealed promising avenues toward the development of small molecule Ras inhibitors. This study describes the successful implementation of second harmonic generation (SHG) as a screening platform to identify a conformational modulator of KRas that binds to a single distinct pocket. This work demonstrates how SHG screening can be applied to both the discovery and characterization of ligands for a high-value oncogenic target. Second harmonic generation (SHG) is an emergent biophysical method that sensitively measures real-time conformational change of biomolecules in the presence of biological ligands and small molecules. This study describes the successful implementation of SHG as a primary screening platform to identify fragment ligands to oncogenic Kirsten rat sarcoma (KRas). KRas is the most frequently mutated driver of pancreatic, colon, and lung cancers; however, there are few well-characterized small molecule ligands due to a lack of deep binding pockets. Using SHG, we identified a fragment binder to KRasG12D and used 1H 15N transverse relaxation optimized spectroscopy (TROSY) heteronuclear single-quantum coherence (HSQC) NMR to characterize its binding site as a pocket adjacent to the switch 2 region. The unique sensitivity of SHG furthered our study by revealing distinct conformations induced by our hit fragment compared with 4,6-dichloro-2-methyl-3-aminoethyl-indole (DCAI), a Ras ligand previously described to bind the same pocket. This study highlights SHG as a high-throughput screening platform that reveals structural insights in addition to ligand binding.
Real-Time Cardiac Beat Detection and Heart Rate Monitoring from Combined Seismocardiography and Gyrocardiography

Cardiography is an indispensable element of health care. However, the accessibility of at-home cardiac monitoring is limited by device complexity, accuracy, and cost. We have developed a real-time algorithm for heart rate monitoring and beat detection implemented in a custom-built, affordable system. These measurements were processed from seismocardiography (SCG) and gyrocardiography (GCG) signals recorded at the sternum, with concurrent electrocardiography (ECG) used as a reference. Our system demonstrated the feasibility of non-invasive electro-mechanical cardiac monitoring on supine, stationary subjects at a cost of $100, and with the SCG–GCG and ECG algorithms decoupled as standalone measurements. Testing was performed on 25 subjects in the supine position when relaxed, and when recovering from physical exercise, to record 23,984 cardiac cycles at heart rates in the range of 36–140 bpm. The correlation between the two measurements had r2 coefficients of 0.9783 and 0.9982 for normal (averaged) and instantaneous (beat identification) heart rates, respectively. At a sampling frequency of 250 Hz, the average computational time required was 0.088 s per measurement cycle, indicating the maximum refresh rate. A combined SCG and GCG measurement was found to improve accuracy due to fundamentally different noise rejection criteria in the mutually orthogonal signals. The speed, accuracy, and simplicity of our system validated its potential as a real-time, non-invasive, and affordable solution for outpatient cardiac monitoring in situations with negligible motion artifact.
The passive leg movement technique for assessing vascular function: defining the distribution of blood flow and the impact of occluding the lower leg

What is the central question of this study? What is the distribution of the hyperaemic response to passive leg movement (PLM) in the common (CFA), deep (DFA) and superficial (SFA) femoral arteries? What is the impact of lower leg cuff‐induced blood flow occlusion on this response? What is the main finding and its importance? Of the total blood that passed through the CFA, the majority was directed to the DFA and this was unaffected by cuffing. As a small fraction does pass through the SFA to the lower leg, cuffing during PLM should be considered to emphasize the thigh‐specific hyperaemia.
Structural and Functional Properties of the Capsid Protein of Dengue and Related Flavivirus

Dengue, West Nile and Zika, closely related viruses of the Flaviviridae family, are an increasing global threat, due to the expansion of their mosquito vectors. They present a very similar viral particle with an outer lipid bilayer containing two viral proteins and, within it, the nucleocapsid core. This core is composed by the viral RNA complexed with multiple copies of the capsid protein, a crucial structural protein that mediates not only viral assembly, but also encapsidation, by interacting with host lipid systems. The capsid is a homodimeric protein that contains a disordered N-terminal region, an intermediate flexible fold section and a very stable conserved fold region. Since a better understanding of its structure can give light into its biological activity, here, first, we compared and analyzed relevant mosquito-borne Flavivirus capsid protein sequences and their predicted structures. Then, we studied the alternative conformations enabled by the N-terminal region. Finally, using dengue virus capsid protein as main model, we correlated the protein size, thermal stability and function with its structure/dynamics features. The findings suggest that the capsid protein interaction with host lipid systems leads to minor allosteric changes that may modulate the specific binding of the protein to the viral RNA. Such mechanism can be targeted in future drug development strategies, namely by using improved versions of pep14-23, a dengue virus capsid protein peptide inhibitor, previously developed by us. Such knowledge can yield promising advances against Zika, dengue and closely related Flavivirus.
Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67

Immunohistochemistry (IHC) of ER, PR, and Ki-67 are routinely used assays in breast cancer diagnostics. Determination of the proportion of stained cells (labeling index) should be restricted on malignant epithelial cells, carefully avoiding tumor infiltrating stroma and inflammatory cells. Here, we developed a deep learning based digital mask for automated epithelial cell detection using fluoro-chromogenic cytokeratin-Ki-67 double staining and sequential hematoxylin-IHC staining as training material. A partially pre-trained deep convolutional neural network was fine-tuned using image batches from 152 patient samples of invasive breast tumors. Validity of the trained digital epithelial cell masks was studied with 366 images captured from 98 unseen samples, by comparing the epithelial cell masks to cytokeratin images and by visual evaluation of the brightfield images performed by two pathologists. A good discrimination of epithelial cells was achieved (AUC of mean ROC = 0.93; defined as the area under mean receiver operating characteristics), and well in concordance with pathologists’ visual assessment (4.01/5 and 4.67/5). The effect of epithelial cell masking on the Ki-67 labeling index was substantial. 52 tumor images initially classified as low proliferation (Ki-67 < 14%) without epithelial cell masking were re-classified as high proliferation (Ki-67 ≥ 14%) after applying the deep learning based epithelial cell mask. The digital epithelial cell masks were found applicable also to IHC of ER and PR. We conclude that deep learning can be applied to detect carcinoma cells in breast cancer samples stained with conventional brightfield IHC.
Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach

ABSTRACT Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life forms. Nevertheless, the analysis of plant proteomes, especially those of samples that contain high-abundance proteins (HAPs), such as soybean seeds, remains challenging. Areas covered: Here, we review recent progress in soybean seed proteomics and highlight advances in HAPs depletion methods and peptide pre-fractionation, identification, and quantification methods. We also suggest a pipeline for future proteomic analysis, in order to increase the dynamic coverage of the soybean seed proteome. Expert opinion: Because HAPs limit the dynamic resolution of the soybean seed proteome, the depletion of HAPs is a prerequisite of high-throughput proteome analysis, and owing to the use of two-dimensional gel electrophoresis-based proteomic approaches, few soybean seed proteins have been identified or characterized. Recent advances in proteomic technologies, which have significantly increased the proteome coverage of other plants, could be used to overcome the current complexity and limitation of soybean seed proteomics.
Ketonuria Is Associated with Changes to the Abundance of Roseburia in the Gut Microbiota of Overweight and Obese Women at 16 Weeks Gestation: A Cross-Sectional Observational Study

The gut microbiome in pregnancy has been associated with various maternal metabolic and hormonal markers involved in glucose metabolism. Maternal ketones are of particular interest due to the rise in popularity of low-carbohydrate diets. We assessed for differences in the composition of the gut microbiota in pregnant women with and without ketonuria at 16 weeks gestation. Fecal samples were obtained from 11 women with fasting ketonuria and 11 matched controls. The samples were analyzed to assess for differences in gut microbiota composition by 16S rRNA sequencing. Supervised hierarchical clustering analysis showed significantly different beta-diversity between women with and without ketonuria, but no difference in the alpha-diversity. Group comparisons and network analysis showed that ketonuria was associated with an increased abundance of the butyrate-producing genus Roseburia. The bacteria that contributed the most to the differences in the composition of the gut microbiota included Roseburia, Methanobrevibacter, Uncl. RF39, and Dialister in women with ketonuria and Eggerthella, Phascolarctobacterium, Butyricimonas, and Uncl. Coriobacteriaceae in women without ketonuria. This study found that the genus Roseburia is more abundant in the gut microbiota of pregnant women with ketonuria. Roseburia is a butyrate producing bacterium and may increase serum ketone levels.
Identification of Sugarcane Host Factors Interacting with the 6K2 Protein of the Sugarcane Mosaic Virus

The 6K2 protein of potyviruses plays a key role in the viral infection in plants. In the present study, the coding sequence of 6K2 was cloned from Sugarcane mosaic virus (SCMV) strain FZ1 into pBT3-STE to generate the plasmid pBT3-STE-6K2, which was used as bait to screen a cDNA library prepared from sugarcane plants infected with SCMV based on the DUALmembrane system. One hundred and fifty-seven positive colonies were screened and sequenced, and the corresponding full-length genes were cloned from sugarcane cultivar ROC22. Then, 24 genes with annotations were obtained, and the deduced proteins were classified into three groups, in which eight proteins were involved in the stress response, 12 proteins were involved in transport, and four proteins were involved in photosynthesis based on their biological functions. Of the 24 proteins, 20 proteins were verified to interact with SCMV-6K2 by yeast two-hybrid assays. The possible roles of these proteins in SCMV infection on sugarcane are analyzed and discussed. This is the first report on the interaction of SCMV-6K2 with host factors from sugarcane, and will improve knowledge on the mechanism of SCMV infection in sugarcane.
Joint RElaxation-Diffusion Imaging Moments (REDIM) to probe neurite microstructure

Joint relaxation-diffusion measurements can provide new insight about the tissue microstructural properties. Most recent methods have focused on inverting the Laplace transform to recover the joint distribution of relaxation-diffusion. However, as is well-known, this problem is notoriously ill-posed and numerically unstable. In this work, we address this issue by directly computing the joint moments of transverse relaxation rate and diffusivity, which can be robustly estimated. To zoom into different parts of the joint distribution, we further enhance our method by applying multiplicative filters to the joint probability density function of relaxation and diffusion and compute the corresponding moments. We propose an approach to use these moments to compute several novel scalar indices to characterize specific properties of the underlying tissue microstructure. Furthermore, for the first time, we propose an algorithm to estimate diffusion signals that are independent of echo time based on the moments of the marginal probability density function of diffusion. We demonstrate its utility in extracting tissue information not contaminated with multiple intra-voxel relaxation rates. We compare the performance of four types of filters that zoom into tissue components with different relaxation and diffusion properties and demonstrate it on an in-vivo human dataset. Experimental results show that these filters are able to characterize heterogeneous tissue microstructure. Moreover, the filtered diffusion signals are also able to distinguish fiber bundles with similar orientations but different relaxation rates. The proposed method thus allows to characterize the neural microstructure information in a robust and unique manner not possible using existing techniques.
Comparing the Diagnostic Accuracy of Two Cognitive Screening Instruments in Different Dementia Subtypes and Clinical Depression

Short but accurate cognitive screening instruments are required in busy clinical practice. Although widely-used, the diagnostic accuracy of the standardised Mini-Mental State Examination (SMMSE) in different dementia subtypes remains poorly characterised. We compared the SMMSE to the Quick Mild Cognitive Impairment (Qmci) screen in patients (n = 3020) pooled from three memory clinic databases in Canada including those with mild cognitive impairment (MCI) and Alzheimer’s, vascular, mixed, frontotemporal, Lewy Body and Parkinson’s dementia, with and without co-morbid depression. Caregivers (n = 875) without cognitive symptoms were included as normal controls. The median age of patients was 77 (Interquartile = ±9) years. Both instruments accurately differentiated cognitive impairment (MCI or dementia) from controls. The SMMSE most accurately differentiated Alzheimer’s (AUC 0.94) and Lewy Body dementia (AUC 0.94) and least accurately identified MCI (AUC 0.73), vascular (AUC 0.74), and Parkinson’s dementia (AUC 0.81). The Qmci had statistically similar or greater accuracy in distinguishing all dementia subtypes but particularly MCI (AUC 0.85). Co-morbid depression affected accuracy in those with MCI. The SMMSE and Qmci have good-excellent accuracy in established dementia. The SMMSE is less suitable in MCI, vascular and Parkinson’s dementia, where alternatives including the Qmci screen may be used. The influence of co-morbid depression on scores merits further investigation.
Cutting Edge: Role of MASP-3 in the Physiological Activation of Factor D of the Alternative Complement Pathway

Key Points MASP-1 is required for physiological LP activation. MASP-3 circulates predominantly in an active form regardless of the role of MASP-1. MASP-3 is pivotal for physiological AP activation via activation of FD. The complement system, a part of the innate immune system, can be activated via three different pathways. In the alternative pathway, a factor D (FD) plays essential roles in both the initiation and the amplification loop and circulates as an active form. Mannose-binding lectin–associated serine proteases (MASPs) are key enzymes of the lectin pathway, and MASP-1 and/or MASP-3 are reported to be involved in the activation of FD. In the current study, we generated mice monospecifically deficient for MASP-1 or MASP-3 and found that the sera of the MASP-1–deficient mice lacked lectin pathway activity, but those of the MASP-3–deficient mice lacked alternative pathway activity with a zymogen FD. Furthermore, the results indicate that MASP-3 but not MASP-1 activates the zymogen FD under physiological conditions and MASP-3 circulates predominantly as an active form. Therefore, our study illustrates that, in mice, MASP-3 orchestrates the overall complement reaction through the activation of FD.
Study on field experiments of forest soil thermoelectric power generation devices

As a new strategy to power forest wireless sensors in remote areas, an environmental microenergy collection device has been improved, and field experiments were carried out under natural conditions for the first time. The thermoelectric power generation devices used a gravity-assisted heat pipe to transmit heat from shallow soil to ground level, and a thermoelectric generator (TEG) was employed to generate electric power from the temperature difference between soil and air. Over the 6-month experimental period at two natural sites, approximately 128.74 J of energy could be harvested in a single day, and 5 209.92 J of energy could be harvested in a generation cycle. The results showed the feasibility of using this green energy to power wireless sensors in remote forests or other environments, This work is relevant to the current acute energy shortages and environmental pollution problems.
Effects of αβ-Blocker Versus β1-Blocker Treatment on Heart Rate Response During Incremental Cardiopulmonary Exercise in Japanese Male Patients with Subacute Myocardial Infarction

A simplified substitute for heart rate (HR) at the anaerobic threshold (AT), i.e., resting HR plus 30 beats per minute or a percentage of predicted maximum HR, is used as a way to determine exercise intensity without cardiopulmonary exercise testing (CPX) data. However, difficulties arise when using this method in subacute myocardial infarction (MI) patients undergoing beta-blocker therapy. This study compared the effects of αβ-blocker and β1-blocker treatment to clarify how different beta blockers affect HR response during incremental exercise. MI patients were divided into αβ-blocker (n = 67), β1-blocker (n = 17), and no-β-blocker (n = 47) groups. All patients underwent CPX one month after MI onset. The metabolic chronotropic relationship (MCR) was calculated as an indicator of HR response from the ratio of estimated HR to measured HR at AT (MCR-AT) and peak exercise (MCR-peak). MCR-AT and MCR-peak were significantly higher in the αβ-blocker group than in the β1-blocker group (p < 0.001, respectively). Multiple regression analysis revealed that β1-blocker but not αβ-blocker treatment significantly predicted lower MCR-AT and MCR-peak (β = −0.432, p < 0.001; β = −0.473, p < 0.001, respectively). Based on these results, when using the simplified method, exercise intensity should be prescribed according to the type of beta blocker used.
Adipose tissue‐derived stem cells upon decellularized ovine small intestine submucosa for tissue regeneration: An optimization and comparison method

The extracellular matrix of different mammalian tissues is commonly used as scaffolds in the field of tissue engineering. One of these tissues, which has frequently been studied due to its structural and biological features, is the small intestine submucosal membrane. These research are mainly done on the porcine small intestine. However, a report has recently been published about a scaffold produced from the submucosal layer of the ovine small intestine. In the present study, ovine small intestine submucosal (OSIS) was decellularized in a modified manner and its histological, morphological, and biomechanical properties were studied. Decellularization was performed in two phases: physical and chemical. In this method, a chloroform‐methanol mixture, enzymatic digestion, and a constant dose of sodium dodecyl sulfate (SDS) was used in the least agitation time and its histological property and biocompatibility were evaluated in the presence of adipose tissue‐derived stem cells (ADSCs); furthermore, ADSCs were isolated with a simple method (modified physical washing non‐enzymatic isolation). The results were showed that the use of OSIS could be effective and operative. Mechanical properties, histological structure and shape, and glycosaminoglycan content were preserved. In the SDS‐treated group, more than 90% of the native cells of tissue were deleted, and also in this group, no toxicity was observed and cell proliferation was supported, compared to the untreated group. Therefore, our results indicate that ADSCs seeded on OSIS scaffold could be used as a new approach in regenerative medicine as hybrid or hydrogel application.
Liver Progenitors and Adult Cell Plasticity in Hepatic Injury and Repair: Knowns and Unknowns.

The liver is a complex organ performing numerous vital physiological functions. For that reason, it possesses immense regenerative potential. The capacity for repair is largely attributable to the ability of its differentiated epithelial cells, hepatocytes and biliary epithelial cells, to proliferate after injury. However, in cases of extreme acute injury or prolonged chronic insult, the liver may fail to regenerate or do so suboptimally. This often results in life-threatening end-stage liver disease for which liver transplantation is the only effective treatment. In many forms of liver injury, bipotent liver progenitor cells are theorized to be activated as an additional tier of liver repair. However, the existence, origin, fate, activation, and contribution to regeneration of liver progenitor cells is hotly debated, especially since hepatocytes and biliary epithelial cells themselves may serve as facultative stem cells for one another during severe liver injury. Here, we discuss the evidence both supporting and refuting the existence of liver progenitor cells in a variety of experimental models. We also debate the validity of developing therapies harnessing the capabilities of these cells as potential treatments for patients with severe and chronic liver diseases. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 15 is January 24, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Analyzing Dynamic Hypergraphs with Parallel Aggregated Ordered Hypergraph Visualization

Parallel Aggregated Ordered Hypergraph(PAOH) is a novel technique to visualize dynamic hypergraphs. Hypergraphs are a generalization of graphs where edges can connect several vertices. Hypergraphs can be used to model networks of business partners or co-authorship networks with multiple authors per article. A dynamic hypergraph evolves over discrete time slots. PAOH represents vertices as parallel horizontal bars and hyperedges as vertical lines, using dots to depict the connections to one or more vertices. We describe a prototype implementation of Parallel Aggregated Ordered Hypergraph, report on a usability study with 9 participants analyzing publication data, and summarize the improvements made. Two case studies and several examples are provided. We believe that PAOH is the first technique to provide a highly readable representation of dynamic hypergraphs. It is easy to learn and well suited for medium size dynamic hypergraphs (50-500 vertices) such as those commonly generated by digital humanities projects—our driving application domain.