Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of cell markers and transcription factors in the avian retina compared with that in the marmoset retina

In the vertebrate retina, amacrine and ganglion cells represent the most diverse cell classes. They can be classified into different cell types by several features, such as morphology, light responses, and gene expression profile. Although birds possess high visual acuity (similar to primates that we used here for comparison) and tetrachromatic color vision, data on the expression of transcription factors in retinal ganglion cells of birds are largely missing. In this study, we tested various transcription factors, known to label subpopulations of cells in mammalian retinae, in two avian species: the common buzzard (Buteo buteo), a raptor with exceptional acuity, and the domestic pigeon (Columba livia domestica), a good navigator and widely used model for visual cognition. Staining for the transcription factors Foxp2, Satb1 and Satb2 labeled most ganglion cells in the avian ganglion cell layer. CtBP2 was established as marker for displaced amacrine cells, which allowed us to reliably distinguish ganglion cells from displaced amacrine cells and assess their densities in buzzard and pigeon. When we additionally compared the temporal and central fovea of the buzzard with the fovea of primates, we found that the cellular organization in the pits was different in primates and raptors. In summary, we demonstrate that the expression of transcription factors is a defining feature of cell types not only in the retina of mammals but also in the retina of birds. The markers, which we have established, may provide useful tools for more detailed studies on the retinal circuitry of these highly visual animals.
Biomarkers for the diagnosis of sepsis-associated acute kidney injury: systematic review and meta-analysis.

BACKGROUND With the development of new techniques, blood and other humoral biomarkers have become increasingly important in the diagnosis of sepsis-associated acute kidney injury (AKI). We aimed to review and summarize the biomarkers associated with the diagnosis of sepsis-associated AKI. METHODS We performed a systematic review in PubMed, Embase, Web of Science, Cochrane and CNKI literature databases. Chinese and English articles published before January 30, 2021. We extracted information on the sensitivity and specificity of biomarkers to diagnose sepsis-associated AKI, the sample size of individuals with sepsis-associated AKI, the demographic variables, the diagnostic criteria and the sample acquisition protocol. Revman 5.3 software was used to analyze data. The sources of heterogeneity of included studies main were different diagnostic criteria for sepsis and AKI, time of sample collection and Patients came from different departments. We defined the inclusion of related studies by using PICOs (Patient, Intervention, Comparison and Outcome) criteria, in particular the design of studies to be included. P: Patients of sepsis. I: Patients of sepsis-associated AKI. C: Patients without sepsis-associated AKI. O: Diagnosis of sepsis associated kidney injury. RESULTS A total of 1,227 articles, including 42 studies, were identified. Increases in urine and serum neutrophil gelatinase-related lipid carrier protein (NGAL), urinary interleukin-18, urinary Kim-1, urinary netrin-1, urinary sCD163, serum estradiol levels, and serum soluble thrombolytic regulatory protein were most strongly correlated with the diagnosis of sepsis-associated AKI. The SROC of urinary KIM-1 ranked first, followed by the other biomarkers: urinary KIM-1 > urinary NGAL > blood NGAL > urinary IL-18. According to the sample size, the SROC values of urinary NGAL, blood NGAL, urinary IL-18 and urinary KIM-1 were 0.907, 0.857, 0.861 and 0.931, respectively. The sequence was still urinary KIM-1 > urinary NGAL > blood NGAL > urinary IL-18. CONCLUSIONS According to the SROC curve area, the diagnostic sequence of sepsis-associated AKI biomarkers was urinary Kim-1 > urinary NGAL > blood NGAL > urinary IL-18. This meta-analysis provided diagnostic features of blood and urine biomarkers based on their association with the diagnosis of sepsis-associated AKI.
A mathematical representation of protein binding sites using structural dispersion of atoms from principal axes for classification of binding ligands

Many researchers have studied the relationship between the biological functions of proteins and the structures of both their overall backbones of amino acids and their binding sites. A large amount of the work has focused on summarizing structural features of binding sites as scalar quantities, which can result in a great deal of information loss since the structures are three-dimensional. Additionally, a common way of comparing binding sites is via aligning their atoms, which is a computationally intensive procedure that substantially limits the types of analysis and modeling that can be done. In this work, we develop a novel encoding of binding sites as covariance matrices of the distances of atoms to the principal axes of the structures. This representation is invariant to the chosen coordinate system for the atoms in the binding sites, which removes the need to align the sites to a common coordinate system, is computationally efficient, and permits the development of probability models. These can then be used to both better understand groups of binding sites that bind to the same ligand and perform classification for these ligand groups. We demonstrate the utility of our method for discrimination of binding ligand through classification studies with two benchmark datasets using nearest mean and polytomous logistic regression classifiers.
Petersen Graph Multi-Orientation Based Multi-Scale Ternary Pattern (PGMO-MSTP): An Efficient Descriptor for Texture and Material Recognition

Classifying and modeling texture images, especially those with significant rotation, illumination, scale, and view-point variations, is a hot topic in the computer vision field. Inspired by local graph structure (LGS), local ternary patterns (LTP), and their variants, this paper proposes a novel image feature descriptor for texture and material classification, which we call Petersen Graph Multi-Orientation based Multi-Scale Ternary Pattern (PGMO-MSTP). PGMO-MSTP is a histogram representation that efficiently encodes the joint information within an image across feature and scale spaces, exploiting the concepts of both LTP-like and LGS-like descriptors, in order to overcome the shortcomings of these approaches. We first designed two single-scale horizontal and vertical Petersen Graph-based Ternary Pattern descriptors (<inline-formula> <tex-math notation="LaTeX">$PGTP_{h}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$PGTP_{v}$ </tex-math></inline-formula>). The essence of <inline-formula> <tex-math notation="LaTeX">$PGTP_{h}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$PGTP_{v}$ </tex-math></inline-formula> is to encode each <inline-formula> <tex-math notation="LaTeX">$5\times 5$ </tex-math></inline-formula> image patch, extending the ideas of the LTP and LGS concepts, according to relationships between pixels sampled in a variety of spatial arrangements (i.e., up, down, left, and right) of Petersen graph-shaped oriented sampling structures. The histograms obtained from the single-scale descriptors <inline-formula> <tex-math notation="LaTeX">$PGTP_{h}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$PGTP_{v}$ </tex-math></inline-formula> are then combined, in order to build the effective multi-scale PGMO-MSTP model. Extensive experiments are conducted on sixteen challenging texture data sets, demonstrating that PGMO-MSTP can outperform state-of-the-art handcrafted texture descriptors and deep learning-based feature extraction approaches. Moreover, a statistical comparison based on the Wilcoxon signed rank test demonstrates that PGMO-MSTP performed the best over all tested data sets.
Mitigating medical student stress and anxiety: Should schools mandate participation in wellness intervention programs?

Abstract Purpose Medical students are at increased risk of poor mental health and need to regularly engage in preventive programs to maintain well-being. However, many do not and it remains an open question whether these programs should be mandatory. We implemented a RCT to examine the effectiveness of assigning medical students to a wellness intervention on adherence to engagement in the assigned intervention and on psychological and academic outcomes. Method Medical students participated in a 12-week randomized controlled intervention involving one-hour wellness sessions of either (1) yoga; (2) mindfulness; or (3) walking, held twice-weekly. Students completed standardized psychological assessments at baseline and following the intervention. Results Students randomized to the wellness intervention group engaged in more minutes of assigned activities than students randomized to the control. There was a significant difference in the change from pre- to post- intervention on measures of state anxiety and perceived stress, with better outcomes for the intervention group. Conclusions The assignment of twice-weekly wellness intervention sessions protects medical students from state anxiety and perceived stress with no negative impact on academic performance. Students adhered to the sessions and reported enjoying the sessions once trying them. Actual engagement is more important than wellness activity type.
Protocadherin 7–Associated Membranous Nephropathy

Significance Statement Membranous nephropathy (MN) results from antibodies targeting an antigen in the glomerular basement membrane (GBM). The target antigens identified so far include PLA2R, THSD7A, NELL1, SEMA3B, and EXT1/EXT2. Using laser microdissection and mass spectrometry analysis, the authors identified a novel protein, protocadherin 7 (PCDH7), that is present in the GBM of a subset of patients with MN who are negative for all of the known antigens associated with MN. PCDH7 shows granular GBM staining and colocalizes with Ig in the GBM. Furthermore, antibodies to PCDH7 were detected in both the serum and kidney biopsy tissue from individuals with PCDH7-associated MN but not from controls. These findings suggest that PCDH7-associated MN defines a distinct type of MN. Background Membranous nephropathy (MN) results from deposition of antigen-antibody complexes along the glomerular basement membrane (GBM). PLA2R, THSD7A, NELL1, and SEMA3B account for 80%–90% of target antigens in MN. Methods We performed laser microdissection and mass spectrometry (MS/MS) in kidney biopsies from 135 individuals with PLA2R-negative MN, and used immunohistochemistry/immunofluorescence and confocal microscopy to confirm the MS/MS finding, detect additional cases, and localize the novel protein. We also performed MS/MS and immunohistochemistry on 116 controls and used immunofluorescence microscopy to screen biopsy samples from two validation cohorts. Western blot and elution studies were performed to detect antibodies in serum and biopsy tissue. Results MS/MS studies detected a unique protein, protocadherin 7 (PCDH7), in glomeruli of ten (5.7%) PLA2R-negative MN cases, which also were negative for PLA2R, THSD7A, EXT1/EXT2, NELL1, and SEMA3B. Spectral counts ranged from six to 24 (average 13.2 [SD 6.6]). MS/MS did not detect PCDH7 in controls (which included 28 PLA2R-positive cases). In all ten PCDH7-positive cases, immunohistochemistry showed bright granular staining along the GBM, which was absent in the remaining cases of PLA2R-negative MN and control cases. Four of 69 (5.8%) cases in the validation cohorts (all of which were negative for PLA2R, THSD7A, EXT1, NELL1, and SEMA3B) were PCDH7-positive MN. Kidney biopsy showed minimal complement deposition in 12 of the 14 PCDH7-associated cases. Confocal microscopy showed colocalization of PCDH7 and IgG along the GBM. Western blot analysis using sera from six patients showed antibodies to nonreduced PCDH7. Elution of IgG from frozen tissue of PCDH7-associated MN showed reactivity against PCDH7. Conclusions MN associated with the protocadherin PCDH7 appears to be a distinct, previously unidentified type of MN.
Left Atrial Diameter and Atrial Ectopic Burden in Patients with Embolic Stroke of Undetermined Source: Risk Stratification of Atrial Fibrillation with Insertable Cardiac Monitor Analysis

Background and Purpose An insertable cardiac monitor (ICM) has been demonstrated to be a useful tool for detecting subclinical atrial fibrillation (AF) in patients with embolic stroke of undetermined source (ESUS). This study aimed to identify the clinical predictors of AF in ESUS patients with ICMs. Methods We retrospectively selected consecutive patients with an ICM implanted for AF detection following ESUS. The primary endpoint was defined as any AF episode lasting for longer than 5 min. The atrial ectopic burden (AEB) was calculated as the percentage of the number of conducted QRS from atrial ectopy on Holter monitoring. Results This study included 136 patients. AF lasting ≥5 min was detected in 20 patients (14.7%) during a median follow-up period of 6.6 months (interquartile range, 3.3–10.8 months). AF patients had a higher AEB (0.20% vs. 0.02%, p<0.001) and a larger left atrial diameter (LAD, 41.0 mm vs. 35.3 mm, p<0.001) than those without AF. The areas under the receiver operating characteristic curves were 0.795 and 0.816 for the LAD and log-transformed AEB, respectively, for the best cutoff values of 38.5 mm for LAD and 0.050% for AEB. AF lasting ≥5 min was detected in 34.6% (9/26) of patients with LAD ≥38.5 mm and AEB ≥0.050%, and in 0% (0/65) of those with LAD <38.5 mm and AEB <0.050%. Conclusions AF was detected in a significant proportion of ESUS patients during a 6.6-month follow-up. The LAD and AEB are good predictors of AF and might be useful for AF risk stratification in ESUS patients.
Calculation of therapeutic antibody viscosity with coarse-grained models, hydrodynamic calculations and machine learning-based parameters

ABSTRACT High viscosity presents a challenge for manufacturing and drug delivery of therapeutic antibodies. The viscosity is determined by protein–protein interactions among many antibodies. Molecular simulation is a promising method to study protein–protein interactions; however, all-atom models do not allow the simulation of multiple molecules, which is necessary to compute viscosity directly. Coarse-grained models, on the other hand can do this. In this work, a 12-bead coarse-grained model based on Swan and coworkers (J. Phys. Chem. B 2018, 122, 2867–2880) was applied to study antibody interactions. Two adjustable parameters related to the short-range interactions on the variable and constant regions were determined by fitting experimental data of 20 IgG1 monoclonal antibodies at 150 mg/mL. The root-mean-square deviation improved from 1 to 0.68, and the correlation coefficient improved from 0.63 to 0.87 compared to that of a previous model that assumed the short-range interactions were the same for all the beads. Our model is also able to calculate the viscosity over a wide range of concentrations without additional parameters. A tabulated viscosity based on our model is provided to facilitate antibody screening in early-stage design.
Magnesium and calcium overaccumulate in the leaves of a schengen3 mutant of Brassica rapa

Abstract Magnesium (Mg) and calcium (Ca) are essential mineral nutrients poorly supplied in many human food systems. In grazing livestock, Mg and Ca deficiencies are costly welfare issues. Here, we report a Brassica rapa loss-of-function schengen3 (sgn3) mutant, braA.sgn3. a-1, which accumulates twice as much Mg and a third more Ca in its leaves. We mapped braA.sgn3. a to a single recessive locus using a forward ionomic screen of chemically mutagenized lines with subsequent backcrossing and linked-read sequencing of second back-crossed, second filial generation (BC2F2) segregants. Confocal imaging revealed a disrupted root endodermal diffusion barrier, consistent with SGN3 encoding a receptor-like kinase required for normal formation of Casparian strips, as reported in thale cress (Arabidopsis thaliana). Analysis of the spatial distribution of elements showed elevated extracellular Mg concentrations in leaves of braA.sgn3. a-1, hypothesized to result from preferential export of excessive Mg from cells to ensure suitable cellular concentrations. This work confirms a conserved role of SGN3 in controlling nutrient homeostasis in B. rapa, and reveals mechanisms by which plants are able to deal with perturbed shoot element concentrations resulting from a “leaky” root endodermal barrier. Characterization of variation in leaf Mg and Ca accumulation across a mutagenized population of B. rapa shows promise for using such populations in breeding programs to increase edible concentrations of essential human and animal nutrients.
Event-Triggered Adaptive Neural Network Sensor Failure Compensation for Switched Interconnected Nonlinear Systems With Unknown Control Coefficients

In this article, a decentralized adaptive neural network (NN) event-triggered sensor failure compensation control issue is investigated for nonlinear switched large-scale systems. Due to the presence of unknown control coefficients, output interactions, sensor faults, and arbitrary switchings, previous works cannot solve the investigated issue. First, to estimate unmeasured states, a novel observer is designed. Then, NNs are utilized for identifying both interconnected terms and unstructured uncertainties. A novel fault compensation mechanism is proposed to circumvent the obstacle caused by sensor faults, and a Nussbaum-type function is introduced to tackle unknown control coefficients. A novel switching threshold strategy is developed to balance communication constraints and system performance. Based on the common Lyapunov function (CLF) method, an event-triggered decentralized control scheme is proposed to guarantee that all closed-loop signals are bounded even if sensors undergo failures. It is shown that the Zeno behavior is avoided. Finally, simulation results are presented to show the validity of the proposed strategy.
Evaluation of ropivacaine combined with dexmedetomidine versus ropivacaine alone for epidural anesthesia

Abstract Background: Ropivacaine is considered the most commonly used for epidural anesthesia. We compared the efficiency and safety of ropivacaine alone (R group) and ropivacaine combined with dexmedetomidine (RD group). Method: PubMed, the Cochrane Library, Google Scholar, Ovid Medline, the Web of Science, Scopus, Embase, and ScienceDirect were searched. We considered sensory and motor block, duration of anesthesia, time to rescue, hemodynamics, and adverse effects as the primary endpoints. Results: Eleven randomized controlled trials were included with 337 patients in the R group and 336 patients in the RD group. The RD group had a shorter time to onset of sensory (mean difference [MD]: 3.97 [1.90–6.04] minutes; P = .0002) and motor (MD: 2.43 [0.70–4.16] minutes; P = .006) block and a longer duration of anesthesia (MD: -164.17 [-294.43 to -33.91]; P = .01) than the R group. Comparison of the time to rescue between the groups showed no significant difference (MD: -119.01[-254.47–16.46] minutes; P = 0.09). The R group showed more stable hemodynamics than the RD group in heart rate and arterial pressure at 10 minutes. The R group had a lower incidence of bradycardia and a higher incidence of shivering than the RD group. Conclusion: RD may be a more suitable choice for epidural anesthesia with better anesthetic outcomes than R alone. However, the safety of the combination must be carefully assessed.
Structure of capped cadmium selenide clusters by EXAFS

Clusters of CdSe and CdS capped with −SeC 6 H 5 or −SC 6 H 5 terminations were produced by synthesis in micellar solution. These clusters were studied by Se K-edge EXAFS. Substitution of S for Se in the bulk and cap were done in order to separate the structural information about the cluster interiors from that pertaining to their surfaces. We find that the cluster interiors have bulklike Cd coordinations about the Se, with distances reduced from the bulk by a marginally detectable amount
VvHDZ28 positively regulate salicylic acid biosynthesis during seed abortion in Thompson Seedless

Summary Seedlessness in grapes is one of the features most appreciated by consumers. However, the mechanisms underlying seedlessness in grapes remain obscure. Here, we observe small globular embryos and globular embryos in Pinot Noir and Thompson Seedless from 20 to 30 days after flowering (DAF). From 40 to 50 DAF, we observe torpedo embryos and cotyledon embryos in Pinot Noir but aborted embryos and endosperm in Thompson Seedless. Thus, RNA‐Seq analyses of seeds at these stages from Thompson Seedless and Pinot Noir were performed. A total of 6442 differentially expressed genes were identified. Among these, genes involved in SA biosynthesis, VvEDS1 and VvSARD1, were more highly expressed in Thompson Seedless than in Pinot Noir. Moreover, the content of endogenous SA is at least five times higher in Thompson Seedless than in Pinot Noir. Increased trimethylation of H3K27 of VvEDS1 and VvSARD1 may be correlated with lower SA content in Pinot Noir. We also demonstrate that VvHDZ28 positively regulates the expression of VvEDS1. Moreover, over‐expression of VvHDZ28 results in seedless fruit and increased SA contents in Solanum lycopersicum. Our results reveal the potential role of SA and feedback regulation of VvHDZ28 in seedless grapes.
SARS‐CoV‐2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions

Abstract The SARS‐CoV‐2 virus has been rapidly spreading globally since December 2019, triggering a pandemic, soon after its emergence. While Iran was among the first countries confronted with rapid spread of virus in February 2020, no real‐time SARS‐CoV‐2 whole‐genome tracking in early phase of outbreak was performed in the country. To address this issue, we provided 50 whole‐genome sequences of viral isolates ascertained from different geographical locations in Iran during March–July 2020. The corresponding analysis on origins, transmission dynamics and genetic diversity of SARS‐CoV‐2 virus, represented at least two introductions of the virus into the country, constructing two major clusters defined as B.4 and B.1*. The first entry of the virus might have occurred around very late 2019/early 2020, as suggested by the time to the most recent common ancestor, followed by a rapid community transmission that led to dominancy of B.4 lineage in early epidemic till the end of June. Gradually, reduction in dominancy of B.4 occurred possibly as a result of other entries of the virus, followed by surge of B.1* lineages, as of mid‐May. Remarkably, variation tracking of the virus indicated the increase in frequency of D614G mutation, along with B.1* lineages, which showed continuity till October 2020. The increase in frequency of D614G mutation and B.1* lineages from mid‐May onwards predicts a rapid viral transmission that may push the country into a critical health situation followed by a considerable change in composition of viral lineages circulating in the country.