Miracle-dz/UniFAR-FTUs huggingface dataset:
Nested Grassmannians for Dimensionality Reduction with Applications

In the recent past, nested structures in Riemannian manifolds has been studied in the context of dimensionality reduction as an alternative to the popular principal geodesic analysis (PGA) technique, for example, the principal nested spheres. In this paper, we propose a novel framework for constructing a nested sequence of homogeneous Riemannian manifolds. Common examples of homogeneous Riemannian manifolds include the n-sphere, the Stiefel manifold, the Grassmann manifold and many others. In particular, we focus on applying the proposed framework to the Grassmann manifold, giving rise to the nested Grassmannians (NG). An important application in which Grassmann manifolds are encountered is planar shape analysis. Specifically, each planar (2D) shape can be represented as a point in the complex projective space which is a complex Grassmann manifold. Some salient features of our framework are: (i) it explicitly exploits the geometry of the homogeneous Riemannian manifolds and (ii) the nested lower-dimensional submanifolds need not be geodesic. With the proposed NG structure, we develop algorithms for the supervised and unsupervised dimensionality reduction problems respectively. The proposed algorithms are compared with PGA via simulation studies and real data experiments and are shown to achieve a higher ratio of expressed variance compared to PGA.
Residual tensile force estimation method for earth anchor using elasto-magnetic sensing system

The earth anchor method is used to prevent landslides, and repair and reinforce cut or steep slopes due to its benefits of ease of construction and economic feasibility. However, the loss of anchor force has become a problem, which may cause failure and collapse of slopes when the anchor force drops below the design anchor force. While numerous studies have been conducted to solve this problem, measuring the residual tensile force of existing earth anchors remains a challenge, as prior studies required sensors to be installed inside structural members at the time of construction. Therefore, to address this limitation, an experiment was performed in this study to develop an elasto-magnetic (EM) sensor for measuring tensile force based on the EM effect, which could be installed on externally exposed anchor heads. The commercial software ANSYS Maxwell was used to analyze the optimal sensor design for the experiment. Additionally, a series of tests to measure the tensile force was conducted by fabricating the sensor based on the numerical analysis results. The area of B-H curves measured by developed EM sensor was increased according to the decrease of tensile force. Also, The tensile force estimation equation was derived and verified using measured data. According to the results, the proposed method can be one of the solution for measuring residual tensile force of earth anchor.
Loss to follow-up in a population-wide brief contact intervention to prevent suicide attempts - The VigilanS program, France

Background Brief Contact Interventions (BCIs) after a suicide attempt (SA) are an important element of prevention against SA and suicide. VigilanS generalizes to a whole French region a BCI combining resource cards, telephone calls and sending postcards, according to a predefined algorithm. However, a major obstacle to such real-life intervention is the loss of contact during follow-up. Here, we analyze the occurrence of loss of follow-up (LFU) and compare characteristics of patients LFU with follow-up completers. Methods The study concerned patients included in VigilanS over the period from 1st January 2015 to 31 December 2018, with an end of follow-up on 1st July 2019. We performed a series of descriptive analysis and logistic regressions. The outcome was the loss to follow-up, relative to the 6th month call marking the end of the follow-up; the predictive variables were the characteristics of the patient at entry and during follow-up. Age and sex were considered as adjustment variables. Results 11879 inclusions occurred during the study period, corresponding to 10666 different patients. The mean age was 40.6 ± 15 years. More than a third were non-first suicide attempters (46.6%) and the most frequent means of suicide was by voluntary drug intoxication (83.2%). 8335 patients were LFU. After simple and multiple regression, a significant relationship with loss to follow-up was identified among non-first suicide attempters, alcohol consumers, patients having no companion on arrival at the emergency room, patients who didn’t make or receive any calls. An increased stay in hospital after a SA was a protective factor against loss of follow-up. Conclusion A majority of patients were lost to follow-up by the expected surveillance time of 6 months. Characteristics of lost patients will help focusing efforts to improve retention in the VigilanS program and might give insights for BCI implemented elsewhere.
Integrated RNA gene expression analysis identified potential immune-related biomarkers and RNA regulatory pathways of acute myocardial infarction

Background Acute lesions are among the most important causes of death due to vascular lesions worldwide. However, there are no accurate genetic markers for Acute myocardial infarction (AMI). This project will use microarray integration analysis in bioinformatics analysis to find and validate relevant AMI gene markers. Methods Five microarray gene expression datasets were downloaded through the GEO database. We identified 50 significant DEGs by comparing and analyzing gene expression between 92 AMI and 57 standard samples. The BioGPS database screened differentially expressed genes specific to the immune system. DEGs were mainly involved in immune-related biological processes based on Enrichment analysis. Eight hub genes and three-gene cluster modules were subsequently screened using Cytoscape and validated using Box plot’s grouping comparison and ROC curves. Combined group comparison results and ROC curves analysis concluded that AQP9, IL1B, and IL1RN might be potential gene markers for the AMI process. We used the StarBase database to predict target miRNAs for eight essential genes. The expected results were used to screen and obtain target lncRNAs. Then Cytoscape was used to create CeRNA networks. By searching the literature in PubMed, we concluded that AQP9, IL1B, and IL1RN could be used as gene markers for AMI, while FSTL3-miR3303p-IL1B/IL1RN and ACSL4-miR5905p-IL1B could be used as RNA regulatory pathways affecting AMI disease progression. Conclusions Our study identified three genes that may be potential genetic markers for AMI’s early diagnosis and treatment. In addition, we suggest that FSTL3-miR-330-3p-IL1B/IL1RN and ACSL4-miR-590-5p-IL1B may be possible RNA regulatory pathways to control AMI disease progression.
SARS-CoV-2 seroprevalence among patients with severe mental illness: A cross-sectional study

Patients with severe mental illness (SMI) i.e. schizophrenia, schizoaffective disorder, and bipolar disorder are at increased risk of severe outcomes if infected with coronavirus disease 2019 (COVID-19). Whether patients with SMI are at increased risk of COVID-19 is, however, sparsely investigated. This important issue must be addressed as the current pandemic could have the potential to increase the existing gap in lifetime mortality between this group of patients and the background population. The objective of this study was to determine whether a diagnosis of schizophrenia, schizoaffective disorder, or bipolar disorder is associated with an increased risk of COVID-19. A cross-sectional study was performed between January 18th and February 25th, 2021. Of 7071 eligible patients with schizophrenia, schizoaffective disorder, or bipolar disorder, 1355 patients from seven psychiatric centres in the Capital Region of Denmark were screened for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. A total of 1258 unvaccinated patients were included in the analysis. The mean age was 40.5 years (SD 14.6), 54.3% were female. Fifty-nine of the 1258 participants had a positive SARS-CoV-2 antibody test, corresponding to a adjusted seroprevalence of 4.96% (95% CI 3.87–6.35). No significant difference in SARS-CoV-2-risk was found between female and male participants (RR = 1.32; 95% CI 0.79–2.20; p = .290). No significant differences in seroprevalences between schizophrenia and bipolar disease were found (RR = 1.12; 95% CI 0.67–1.87; p = .667). Seroprevalence among 6088 unvaccinated blood donors from the same region and period was 12.24% (95% CI 11.41–13.11). SARS-CoV-2 seroprevalence among included patients with SMI was significantly lower than among blood donors (RR = 0.41; 95% CI 0.31–0.52; p < .001). Differences in seroprevalences remained significant when adjusting for gender and age, except for those aged 60 years or above. The study is registered at ClinicalTrails.gov (NCT04775407). https://clinicaltrials.gov/ct2/show/NCT04775407? term=NCT04775407&draw=2&rank=1.
Cancer Categorization Using Genetic Algorithm to Identify Biomarker Genes

In the microarray gene expression data, there are a large number of genes that are expressed at varying levels of expression. Given that there are only a few critically significant genes, it is challenging to analyze and categorize datasets that span the whole gene space. In order to aid in the diagnosis of cancer disease and, as a consequence, the suggestion of individualized treatment, the discovery of biomarker genes is essential. Starting with a large pool of candidates, the parallelized minimal redundancy and maximum relevance ensemble (mRMRe) is used to choose the top m informative genes from a huge pool of candidates. A Genetic Algorithm (GA) is used to heuristically compute the ideal set of genes by applying the Mahalanobis Distance (MD) as a distance metric. Once the genes have been identified, they are input into the GA. It is used as a classifier to four microarray datasets using the approved approach (mRMRe-GA), with the Support Vector Machine (SVM) serving as the classification basis. Leave-One-Out-Cross-Validation (LOOCV) is a cross-validation technique for assessing the performance of a classifier. It is now being investigated if the proposed mRMRe-GA strategy can be compared to other approaches. It has been shown that the proposed mRMRe-GA approach enhances classification accuracy while employing less genetic material than previous methods. Microarray, Gene Expression Data, GA, Feature Selection, SVM, and Cancer Classification are some of the terms used in this paper.
Hepatic Fis1 regulates mitochondrial integrated stress response and improves metabolic homeostasis

Mitophagy and mitochondrial integrated stress response (ISR) are 2 primary protective mechanisms to maintain functional mitochondria. Whether these 2 processes are coordinately regulated remains unclear. Here we show that mitochondrial fission 1 protein (Fis1), which is required for completion of mitophagy, serves as a signaling hub linking mitophagy and ISR. In mouse hepatocytes, high fat diet (HFD) feeding induces unresolved oxidative stress, defective mitophagy and enhanced type I interferon (IFN-I) response implicated in promoting metabolic inflammation. Adenoviral-mediated acute hepatic Fis1 overexpression is sufficient to reduce oxidative damage and improve glucose homeostasis in HFD-fed mice. RNA-Seq analysis reveals that Fis1 triggers a retrograde mitochondria-to-nucleus communication upregulating ISR genes encoding anti-oxidant defense, redox homeostasis, and proteostasis pathways. Fis1-mediated ISR also suppresses expression of IFN-I–stimulated genes through activating transcription factor 5 (Atf5), which inhibits the transactivation activity of interferon regulatory factor 3 (Irf3) known to control IFN-I production. Metabolite analysis demonstrates that Fis1 activation leads to accumulation of fumarate, a TCA cycle intermediate capable of increasing Atf5 activity. Consequently, hepatic Atf5 overexpression or monomethyl fumarate (MMF) treatment improves glucose homeostasis in HFD-fed mice. Collectively, these results support the potential use of small molecules targeting the Fis1-Atf5 axis, such as MMF, to treat metabolic diseases.
The Application of FTIR Spectroscopy and Chemometrics for the Authentication Analysis of Horse Milk

Expensive milk such as horse's milk (HM) may be the target of adulteration by other milk such as goat's milk (GM) and cow's milk (CM). FTIR spectroscopy in combination with chemometrics of linear discriminant analysis (LDA) and multivariate calibrations of partial least square regression (PLSR) and principal component regression (PCR) was used for authentication of HM from GM and CM. Milk was directly subjected to attenuated total reflectance (ATR) spectral measurement at midinfrared regions (4000-650 cm−1). Results showed that LDA could make clear discrimination between HM and HM adulterated with CM and GM without any misclassification observed. PLSR using 2nd derivative spectra at 3200-2800 and 1300-1000 cm−1 provided the best model for the relationship between actual values of GM and FTIR predicted values than PCR. At this condition, R2 values for calibration and validation models obtained were 0.9995 and 0.9612 with RMSEC and RMSEP values of 0.0093 and 0.0794. PLSR using normal FTIR spectra at 3800-3000 and 1500-1000 cm−1 offered R2 for the relationship between actual values of CM and FTIR predicted values of >0.99 in calibration and validation models with low errors of RMSEC of 0.0164 and RMSEP of 0.0336 during authentication of HM from CM. Therefore, FTIR spectroscopy in combination with LDA and PLSR is an effective method for authentication of HM from GM and CM.
Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing

Abstract Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.
Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface

Abstract Unnatural base pairs (UBPs) which exhibit a selectivity against pairing with canonical nucleobases provide a powerful tool for the development of nucleic acid-based technologies. As an alternative strategy to the conventional UBP designs, which involve utility of different recognition modes at the Watson–Crick interface, we now report that the exclusive base pairing can be achieved through the spatial separation of recognition units. The design concept was demonstrated with the alkynylated purine (NPu, OPu) and pyridazine (NPz, OPz) nucleosides endowed with nucleobase-like 2-aminopyrimidine or 2-pyridone (‘pseudo-nucleobases’) on their major groove side. These alkynylated purines and pyridazines exhibited exclusive and stable pairing properties by the formation of complementary hydrogen bonds between the pseudo-nucleobases in the DNA major groove as revealed by comprehensive Tm measurements, 2D-NMR analyses, and MD simulations. Moreover, the alkynylated purine-pyridazine pairs enabled dramatic stabilization of the DNA duplex upon consecutive incorporation while maintaining a high sequence-specificity. The present study showcases the separation of the recognition interface as a promising strategy for developing new types of UBPs.
Translation model for anterior segment tomographic data to corneal spherical aberration derived from a Monte‐Carlo simulation based on raytracing

Intraocular lenses with a negative aspherical design for correction of corneal spherical aberration (SA) have gained popularity in recent decades. In most cases, a ‘one size fits all’ concept is followed, where all eyes receive lenses with the same SA correction. The purpose of this study is to develop a strategy based on raytracing using anterior segment tomography data to extract corneal SA and to provide simple multivariable linear models for prediction of corneal SA.
Self-reported Race/Ethnicity and Intraoperative Occult Hypoxemia: A Retrospective Cohort Study

Background: Pulse oximetry is ubiquitous in anesthesia and is generally a reliable noninvasive measure of arterial oxygen saturation. Concerns regarding the impact of skin pigmentation and race/ethnicity on the accuracy of pulse oximeter accuracy exist. The authors hypothesized a greater prevalence of occult hypoxemia (arterial oxygen saturation [Sao2] less than 88% despite oxygen saturation measured by pulse oximetry [Spo2] greater than 92%) in patients undergoing anesthesia who self-reported a race/ethnicity other than White. Methods: Demographic and physiologic data, including self-reported race/ethnicity, were extracted from a departmental data warehouse for patients receiving an anesthetic that included at least one arterial blood gas between January 2008 and December 2019. Calculated Sao2 values were paired with concurrent Spo2 values for each patient. Analysis to determine whether Black, Hispanic, Asian, or Other race/ethnicities were associated with occult hypoxemia relative to White race/ethnicity within the Spo2 range of 92 to 100% was completed. Results: In total, 151,070 paired Sao2–Spo2 readings (70,722 White; 16,011 Black; 21,223 Hispanic; 8,121 Asian; 34,993 Other) from 46,253 unique patients were analyzed. The prevalence of occult hypoxemia was significantly higher in Black (339 of 16,011 [2.1%]) and Hispanic (383 of 21,223 [1.8%]) versus White (791 of 70,722 [1.1%]) paired Sao2–Spo2 readings (P < 0.001 for both). In the multivariable analysis, Black (odds ratio, 1.44 [95% CI, 1.11 to 1.87]; P = 0.006) and Hispanic (odds ratio, 1.31 [95% CI, 1.03 to 1.68]; P = 0.031) race/ethnicity were associated with occult hypoxemia. Asian and Other race/ethnicity were not associated with occult hypoxemia. Conclusions: Self-reported Black and Hispanic race/ethnicity are associated with a greater prevalence of intraoperative occult hypoxemia in the Spo2 range of 92 to 100% when compared with self-reported White race/ethnicity. Among 46,523 patients with 151,070 paired arterial oxygen saturation (Sao2)–oxygen saturation measured by pulse oximetry (Spo2) intraoperative readings at a single center, the prevalence of occult hypoxemia (Sao2 less than 88% despite concurrent Spo2 greater than 92%) was significantly increased in patients self-reporting Black (2.1%) and Hispanic (1.8%) race/ethnicity compared with patients self-reporting White (1.1%) race/ethnicity. After adjusting for other clinical factors, Black or Hispanic race/ethnicity was independently associated with occult hypoxemia.
Understanding the association between reappraisal use and depressive symptoms during adolescence: the moderating influence of regulatory success

ABSTRACT Higher levels of reliance on cognitive reappraisal to manage daily emotional events are commonly associated with lower levels of depressive symptoms. However, reappraisal is a cognitively demanding regulation strategy, and its efficacy may depend on how successfully an individual is able to employ it. Individual differences in the association between reappraisal use and depressive symptoms may be particularly evident during adolescence, when the cognitive skills required to implement this complex strategy are still in development. The current study sought to determine whether the association between reappraisal use and subsequent depressive symptom development is contingent on perceived regulatory success when using reappraisal. At Wave 1, adolescents (n = 178, mean age = 13.92, 49.7% female) used an experience-sampling smartphone app to report on their reappraisal use and perceptions of regulatory success over the course of two weeks. Six, 12, and 18 months later, adolescents completed a self-report measure of their depressive symptoms. Results showed that a) reappraisal use was associated with both subsequent depressive symptoms and trajectories of depressive symptoms over time, b) these associations were moderated by perceptions of regulatory success. Higher levels of reappraisal use were associated with lower levels of depressive symptoms only for those who reported higher than average between-subject regulatory success when reappraisal was enacted.
Plasma β-Amyloid, Total-Tau, and Neurofilament Light Chain Levels and the Risk of Stroke

Background and Objectives To unravel whether Alzheimer disease–related pathology or neurodegeneration plays a role in stroke etiology, we determined the effect of plasma levels β-amyloid (Aβ), total-tau, and neurofilament light chain (NfL) on risk of stroke and its subtypes. Methods Between 2002 and 2005, we measured plasma Aβ40, Aβ42, total-tau, and NfL in 4,661 stroke-free participants from the population-based Rotterdam Study. We used Cox proportional-hazards models to determine the association between these markers with incident stroke for the entire cohort, per stroke subtype, and by median age, sex, APOE ε4 carriership, and education. Results After a mean follow-up of 10.8 ± 3.3 years, 379 participants had a first-ever stroke. Log2 total-tau at baseline showed a nonlinear association with risk of any stroke and ischemic stroke: compared to the first (lowest) quartile, the adjusted hazard ratio (HR) for the highest quartile total-tau was 1.68 (95% CI 1.18–2.40) for any stroke. Log2 NfL was associated with an increased risk of any stroke (HR per 1-SD increase 1.27, 95% CI 1.12–1.44), ischemic stroke, and hemorrhagic stroke (HR 1.56, 95% CI 1.14–2.12). Log2 Aβ40, Aβ42, and Aβ42/40 ratio levels were not associated with stroke risk. Discussion Participants with higher total-tau and NfL at baseline had a higher risk of stroke and several stroke subtypes. These findings support the role of markers of neurodegeneration in the etiology of stroke. Classification of Evidence This study provides Class II evidence that higher plasma levels of total-tau and NfL are associated with an increased risk of subsequent stroke.
Complete Genome Sequence of Clostridium cadaveris IFB3C5, Isolated from a Human Colonic Adenocarcinoma

We report the complete genome sequence of Clostridium cadaveris IFB3C5, a strain isolated from the resected tumor of a treatment naive colorectal cancer patient. This genome is comprised of a singular chromosome of approximately 3.63 Mbp in length, contains two plasmids, and has an overall mean GC content of 31.7%. ABSTRACT We report the complete genome sequence of Clostridium cadaveris IFB3C5, a strain isolated from the resected tumor of a treatment naive colorectal cancer patient. This genome is comprised of a singular chromosome of approximately 3.63 Mbp in length, contains two plasmids, and has an overall mean GC content of 31.7%.